Multifunctional Cytochrome c: Learning New Tricks from an Old Dog

Review Cite This: Chem. Rev. 2017, 117, 13382-13460

pubs.acs.org/CR

Multifunctional Cytochrome c: Learning New Tricks from an Old Dog Damián Alvarez-Paggi,†,∥ Luciana Hannibal,‡,§ María A. Castro,† Santiago Oviedo-Rouco,† Veronica Demicheli,§ Veronica Tórtora,§ Florencia Tomasina,§ Rafael Radi,§ and Daniel H. Murgida*,† †

Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina ‡ Department of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany § Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo 11800, Uruguay ABSTRACT: Cytochrome c (cyt c) is a small soluble heme protein characterized by a relatively flexible structure, particularly in the ferric form, such that it is able to sample a broad conformational space. Depending on the specific conditions, interactions, and cellular localization, different conformations may be stabilized, which differ in structure, redox properties, binding affinities, and enzymatic activity. The primary function is electron shuttling in oxidative phosphorylation, and is exerted by the so-called native cyt c in the intermembrane mitochondrial space of healthy cells. Under pro-apoptotic conditions, however, cyt c gains cardiolipin peroxidase activity, translocates into the cytosol to engage in the intrinsic apoptotic pathway, and enters the nucleus where it impedes nucleosome assembly. Other reported functions include cytosolic redox sensing and involvement in the mitochondrial oxidative folding machinery. Moreover, posttranslational modifications such as nitration, phosphorylation, and sulfoxidation of specific amino acids induce alternative conformations with differential properties, at least in vitro. Similar structural and functional alterations are elicited by biologically significant electric fields and by naturally occurring mutations of human cyt c that, along with mutations at the level of the maturation system, are associated with specific diseases. Here, we summarize current knowledge and recent advances in understanding the different structural, dynamic, and thermodynamic factors that regulate the primary electron transfer function, as well as alternative functions and conformations of cyt c. Finally, we present recent technological applications of this moonlighting protein.

CONTENTS 1. Introduction 2. Architecture of Cytochrome c 2.1. Classification and Occurrence 2.2. Biogenesis 2.3. Structure and Dynamics 2.4. Folding/Unfolding Studies 2.5. Alternative Conformations 2.5.1. Alkaline Transition 2.5.2. “Alkaline Transitions” at Physiological pH 2.5.3. Acidic Transitions of Cyt c 2.5.4. Electrostatic and Hydrophobic Interactions of Cyt c with Model Systems 3. Cytochrome c as an Electron Shuttle 3.1. Complexes with Redox Partner Proteins 3.1.1. Cytochrome c Peroxidase 3.1.2. Cytochrome bc1 3.1.3. Cytochrome c Oxidase 3.1.4. Respiratory Chain Supercomplexes and Megacomplexes 3.2. Thermodynamic Redox Properties 3.2.1. Effect of Heme Type, Attachment Sequence, and Binding Distortions © 2017 American Chemical Society

3.2.2. First Sphere Ligands 3.2.3. Second Sphere Ligands 3.2.4. Surface Electrostatics: Ionic Strength, Surface Charge, Specific Ion Binding, and Beyond 3.3. ET Kinetic Parameters 3.3.1. Reorganization Energy of Cyt c 3.3.2. Electronic Couplings and Pathways 3.3.3. Role of Protein and Solvent Dynamics in ET Kinetics 3.4. Is the Electron Transport Function of Cyt c Regulated? 3.4.1. CuA Site 3.4.2. Negative Feedback Regulation of Cyt c Electron Transport 4. Alternative Functions of Cytochrome c 4.1. Occurrence and Detection 4.2. Apoptosis 4.2.1. Interactions of Cyt c with Lipids and the Case of Cardiolipin

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13399 13400 Received: May 11, 2017 Published: October 13, 2017

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DOI: 10.1021/acs.chemrev.7b00257 Chem. Rev. 2017, 117, 13382−13460

Chemical Reviews 4.2.2. Dual Role of Cardiolipin in Cyt c Function 4.2.3. Peroxidase Activity of Cardiolipin-Bound Cyt c 4.2.4. CL−Cyt c Interaction and the Mitochondrial Regulation of Apoptosis 4.2.5. Cyt c as a Target for Antiapoptotic Drugs 4.2.6. Cyt c Functions in DNA Regulation and Redox Signaling 4.3. Extracellular Cyt c 5. Cytochrome c under Stress 5.1. Post-translational Modifications in Cyt c 5.1.1. Nitration of Cyt c 5.1.2. Phosphorylation of Cyt c 5.1.3. Sulfoxidation of Cyt c 5.1.4. Methylation of Cyt c 5.1.5. Acetylation of Cyt c 5.2. Interactions of Cyt c with Other Biomolecules 5.3. Naturally Occurring Pathogenic Mutants of Cyt c 5.3.1. Cytochrome c Gly41Ser 5.3.2. Cytochrome c Tyr48His 5.3.3. Cytochrome c Ala51Val 5.3.4. Other Causes of Thrombocytopenia 5.3.5. Human Cyt c Mutations with Unknown Consequences 5.4. Cyt c as a Disease Biomarker 6. Technological Applications of Cytochrome c 6.1. Third Generation Electrochemical Biosensors 6.1.1. Hydrogen Peroxide Biosensors 6.1.2. Superoxide Biosensors 6.1.3. Nitrite Biosensors 6.1.4. Nitric Oxide Biosensors 6.1.5. Other Analytes 6.2. Multiprotein Electrochemical Sensors: Cyt c as Electron Shuttle 6.3. Optical Biosensors 6.3.1. Fluorescence Biosensors 6.3.2. Colorimetric Biosensors 6.3.3. Plasmonic Biosensors 6.4. Synthetic Receptors 6.4.1. Calix[n]arenes 6.4.2. Molecular Imprinting 6.5. Biosensors for Cyt c Detection 7. Summary and Outlook Author Information Corresponding Author ORCID Present Address Notes Biographies Acknowledgments Abbreviations References

Review

loproteins.1−3 Within the intermembrane space of mitochondria, cyt c shuttles electrons from respiratory complex III (cytochrome c reductase or cytochrome bc1) to the terminal oxygen reductase (complex IV or cytochrome c oxidase), thus critically contributing to sustain cellular life throughout an elaborate electron−proton energy transduction mechanism that ends up with the synthesis of ATP, the major energy currency molecule in living organisms.4 The simplicity, stability, and availability of this small redox protein have acted as a magnet for scientists from different fields, who have for several decades adopted cyt c variants and de novo designed heme proteins as robust models for understanding the physical basis of protein electron transfer (ET) at the atomistic level. This includes elaboration and validation of ET theories5,6 and detailed studies on how individual thermodynamic and kinetic ET parameters, such as redox potentials, reorganization energies, and donor− acceptor electronic couplings, are statically and/or dynamically influenced by first and second sphere ligands of the heme iron, solvent accessibility, redox-linked rearrangement of the Hbonding network, out-of-plane heme deformations, surface charges, local electric fields, specific and unspecific interactions, the overall protein fold, individual key residues, and heme− protein vibrational coupling, among other elements.2,7−15 Research performed during the last years has been particularly fruitful in unveiling many of these aspects, with special emphasis on the dynamical control of the ET parameters of cyt c and on the characterization of protein−protein complexes of cyt c with relevant redox partners such as cytochrome c peroxidase, oxidase, and reductase. Part of our current knowledge of cyt c as a redox biomolecule is derived from detailed electrochemical and spectroelectrochemical studies that take advantage of the efficient direct electrochemical activity of cyt c. This property is exploited not only for gaining deeper insight into the equilibrium and dynamics of the ET reaction and redox-linked conformational changes, but also for developing cyt c-based third generation electrochemical biosensors for a variety of analytes, such as hydrogen peroxide, superoxide, nitrite, nitric oxide, and homocysteine, among others. Further extension to developing cyt c-based optical biosensors has also been very active in recent years. From a structural perspective, new crystallographic and NMR structures of cytochromes c (cyts c) from different organisms became available recently, thus allowing for a more comprehensive and sound comparison of structure, stability, and flexibility among species.16−20 Great progress has also been made on the structural and functional characterization of the different maturation systems implicated in assembling the apoprotein and the heme group in different organisms.21,22 The subsequent folding (and unfolding) of cyt c is also a subject of intense experimental and theoretical work with groundbreaking recent results in both fronts, not only for understanding the structure and dynamics of the native cyt c fold, but also in terms of the mechanisms that lead to the stabilization of alternative conformations, including the formation of the so-called alkaline isomer,23−28 for which structural models have been recently solved.16,18 Although known for over 75 years, some crucial findings have renewed the interest in the alkaline isomer and other alternative conformations.29 It has been demonstrated that post-translational modifications, such as nitration of cyt c tyrosine residues under oxidative stress conditions, lead, even at neutral pH, to the stabilization of an alkaline-like conformation whose redox properties, binding affinity to relevant partners,

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1. INTRODUCTION Mitochondrial cytochrome c (cyt c), a ca. 13 kDa monehemic globular and soluble protein, is a prominent member of a large, diverse, and broadly distributed group of redox metal13383


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2. ARCHITECTURE OF CYTOCHROME c

and peroxidase activity differ significantly from the unmodified protein.30−32 Other modifications and alterations such as tyrosine phosphorylation, methionine sulfoxidation, lysine acetylation, heme nitrosylation, or the action of local electric fields also lead to alternative conformations with altered properties that may be of biological significance.12,33−35 Moreover, recent investigations have revealed naturally occurring cyt c mutations in humans that alter redox and structural properties, and may be associated with certain diseases.36,37 On the other hand, if confirmed, the recent proposal that mitochondria may operate at temperatures significantly higher than those currently accepted (up to 50 °C) will impose a need for revision of our structural and dynamic understanding of cyt c related to both the canonical and the alternative functions.38,39 It is now well established that cyt c behaves as a moonlighting protein whose structure and function are determined by external stimuli and localization inside the cell. The canonical function of electron transport is exerted inside the intermembrane mitochondrial space by the “native” conformation of cyt c, but other functions and localizations have been identified for which a detailed structural characterization of cyt c remains elusive despite extensive ongoing efforts and some significant progress. In response to certain stimuli such as DNA damage, metabolic stress, or accumulation of unfolded proteins, cells may activate ordered cell suicide sequences (apoptotic pathways). In the so-called intrinsic apoptotic pathway, mitochondrial cyt c is released into the cytosol where it engages the apoptotic protease-activating factor-1 (Apaf-1) and forms the apoptosome.40−42 Notably, there is increasing evidence that cyt c is actively involved in its own liberation through permeabilization of the mitochondrial membrane. The proposed mechanism involves cyt c binding to the membrane component cardiolipin (CL), which induces a transition to an alternative conformation that presents high peroxidase activity toward CL itself.34,40,43 Interestingly, some of the post-translational modifications of cyt c observed under oxidative stress conditions interfere with the binding to CL and to Apaf-1, thus suggesting a complex interplay of pro- and antiapoptotic functions of cyt c.32,33 Furthermore, very recent studies have revealed that cyt c translocates into the nucleus in response to DNA damage where it prevents nucleosome assembly, thus blocking cell survival.44 The mechanism of translocation and the relevant conformations of cyt c in each step remain unknown. What clearly appears to emerge is the fact that the conserved structural flexibility of this protein is central to its tunable functionality, which in turn poses the hypothesis that alternative conformations of cyt c may actually be involved in redox signaling and in other biologically relevant functions that await to be discovered. In the following sections, we summarize and unify the current knowledge, with special emphasis in the advances of the past decade, regarding (i) cyt c classification, biogenesis, structure, and dynamics, (ii) factors that regulate the electron shuttling function, (iii) perturbations and modifications that result in intracellular relocalization and/or in alternative conformations that enable new biological functions, (iv) the natural occurrence and biomedical relevance of cyt c and interactions with other proteins, and (v) the employment of cyt c for the design of electrochemical and optical biosensors.

2.1. Classification and Occurrence

Cytochromes are a group of over 75.000 proteins,5 whose encoding genes are broadly distributed across eukaryotes, bacteria, and archaea.1 While most of them are involved in ET reactions, the vast structural and functional diversity hinders a unique simple classification scheme. The common feature to all cytochromes is the presence of one or more units of ironprotoporphyrin IX derivatives, usually referred to as heme groups, which give rise to the characteristic intense red color that inspired the term cytochrome (cellular color) nearly 90 years ago. Usually these proteins are classified into six types, a, b, c, d, f, and o, which differ in either the chemical substituents of the heme tetrapyrrole, its linkage to the proteins, or both (Figure 1).

Figure 1. Structures of different heme groups. Reprinted with permission from ref 2. Copyright 2014 American Chemical Society.

These differences, in turn, result in characteristic shifts of the electronic absorption bands, particularly of the so-called α band whose maximum is tuned over ca. 80 nm.2,45 Note that hemes b and c are identical except that in the second case the vinyl groups at positions 2 and 4 form thioether bonds with sulfhydryl groups of two cysteine residues. Actually, most monohemic cyt c domains display a single Cys-Xaa-Xaa-CysHis (CXXCH) motif for covalent attachment of the heme through the cysteines and axial coordination of the iron through the histidine side chain. A few cases of cyts c with unconventional binding motifs, such as AXXCH, FXXCH, CXXCK, CXXXCH, CXXXXCH, and CX15CH, have also been identified.46 Two different nomenclatures are commonly used to designate subgroups of cyts c on the basis of subscripts. In one case, the subscript identifies functional classes (e.g., cyt c1), and in the other this number is the maximum of the absorption α band of the ferrous protein (e.g., cyt c550).1,47 Another classification proposed by Ambler divides cyts c into four classes or types.48 Class 1 cyts c are the most abundant; typically these are small (8−12 kDa) soluble proteins characterized by a distinctive fold, a single low-spin heme with His/Met axial coordination, and a conserved N-terminal CXXCH porphyrin binding sequence. Class 2 cyts c are monoheme proteins with 13384


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Figure 2. Mechanisms of cyt c biogenesis by mitochondrial holocytochrome c synthase (HCCS). Reprinted with permission from ref 21. Copyright 2015 Elsevier Ltd.

employ a single component cyt c heme lyase (HCCS), also known as system III, which is a soluble protein peripherally associated with the outer leaflet of the inner mitochondrial membrane. Plants use system I in mitochondria, but also systems II and IV on the p- and n-sides of the thylakoid membrane, respectively. Systems I−III are the most prevalent and catalyze the formation of the two thioether bonds characteristic of most cyts c, while systems IV, as well as systems V and VI, for other organisms, mature single-cysteine attached cyts c. Despite the great structural and functional diversity, all of these biogenesis systems produce the same thioether stereospecificity with the vinyl groups at positions 2 and 4 bound to the N- and C-terminal cysteines of the CXXCH (or equivalent) motif. Furthermore, in all cases, it is required that the iron and the cysteine residues are in the reduced form for the reaction to occur. In the bacterial periplasm, the CXXCH motif is the substrate of the thiol-oxidizing pathway; the produced disulfide is reduced by thiol−disulfide oxidoreductases CcmH and ResA/CccS in systems I and II, respectively.59−62 The redox state regulation in system III is less clear; so far the only redox system III component that has been identified solely in the intermembrane space (IMS) from yeast mitochondria is the flavoprotein Cyc2p, and was proposed to reduce either the cysteines or the iron. Thus, while the distribution of the different systems does not follow the evolutionary tree of life, this suggests that the functioning of the HCCS enzyme may depend on evolutionary optimization of the mitochondrial redox environment.21,59 The HCCS-mediated assembly of H-cyt c in human mitochondria has been recently described in detail on the basis of a four-step model (Figure 2).21,52,63 In the first step, the membrane-bound HCCS binds a ferrous porphyrin moiety through axial ligation of the heme iron by a histidine residue.52 Mutational analysis suggests that the heme binding site is located in domain II of human recombinant HCCS and involves the conserved residues H154, E159, W162, and W168.52,64 Interestingly, the E159 K mutation of HCCS has been identified as one of the modifications present in patients with the human pathology known as microphthalmia with linear skin defects.65 Step 2 comprises the transport of apocytochrome c from the cytoplasm into the IMS, and its binding to HCCS. The translocation of cyt c is mediated by transporter outer membrane proteins, but HCCS itself is also involved in the process.22,51,66,67 Once translocated, the apoprotein coordinates the free axial position of Fe2+ in the preexisting HCCS/heme

four-helix bundle structure; class 3 are multiheme and class 4 are high molecular weight tetraheme units. According to sequence, phylogeny, and function, class 1 cyts c have been divided into 16 subclasses that include mitochondrial and bacterial proteins.4 All members of the type 1 family present a fold that includes a minimum of three α helices arranged around the heme group, and further less conserved structural elements. Some class 1 cyts c can be found fused to a second monoheme cyt c domain49 or to membrane proteins such as some bacterial heme-copper terminal oxygen reductases.50 In this Review, we focus on the prototypic class 1 cyt c present in eukaryotic mitochondria, with emphasis on mammal representatives such as horse heart and human proteins (hh-cyt c and H-cyt c, respectively), as well as on some yeast and bacterial cyt c variants that represent useful model systems. 2.2. Biogenesis

All members of the cyt c superfamily are assembled in the same biological location where they exert their primary function, which, with only few exceptions, is the p-side, that is, the protochemically positive side of energy transduction membranes. The apoprotein and the heme, however, are synthesized at the n-side, that is, the protochemically negative side, of the cytoplasmic membrane of prokaryotic cells. Eukaryotes synthesize apo-cyt c in the cytoplasm, and the newly made protein undergoes heme insertion by hemo lyases in the intermembrane space of the mitochondrion.51,52 A similar dualcompartment mechanism exists for the maturation of cyt c in the stroma of chloroplasts.21,53,54 Regardless of species-specific mechanistic steps, the building blocks apo-cyt c and heme associate with or transport across a membrane. The highly conserved biosynthetic pathway of hemes has been described in detail elsewhere.55 It starts with the synthesis of 5-aminolevulinic acid that is used as a precursor for the synthesis of pyrroles. The four pyrroles are then assembled to form a tetrapyrrole ring, and side chains are subsequently modified according to the heme type; the iron ion is inserted in the last step. The mechanisms of intracellular heme trafficking are not general, and many aspects still remain largely elusive, although a number of potential transporters have been identified.56−58 Moreover, the molecular machinery evolved for the assembly of these two components to form c-type cytochromes is quite diverse and can be very complex depending on the organism or organelle. So far, six different cyt c maturation systems have been identified or predicted. Most bacteria utilize the multicomponent systems I and II embedded in the cytoplasmic membrane. Animals, yeast, and some protozoa, in contrast, 13385


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complex employing H19 (H18 in hh-cyt c).52,64,68 The resulting bis-His complex stabilizes the reduced form of the heme, which has been shown to be crucial for the subsequent thioether formation reaction,46,59,60 and positions the cysteines of the CXXCH motif (C15 and C18 in H-cyt c; C14 and C17 in hhcyt c) close to the vinyl substituents of the porphyrin, that is, in the required position for spontaneous stereospecific attachment (step 3).21,52,64 The last step includes dissociation of the HCCS residue H154 from the iron, which is probably driven by distortions of the heme upon thioeter bond formation, thus inducing the release of holocytochrome c.63 Finally, the released protein spontaneously folds into the native structure, which includes distal binding of Fe2+ by a methionine residue (M81 or M80 for human or equine proteins, respectively).23

respectively, while H18 and M80 are the proximal and distal axial ligands of the heme iron. Only in a few cases is the heme attached via a single thioether bond.94,95 The heme group is slightly saddled, with the vinyl-substituted rings A and B exhibiting the strongest deviations from the average tetrapyrrole plane.98,99 Multiple alignment of all known eukaryotic cyt c sequences shows amino acid identities from 28% to 99%.69 For instance, yeast and mammals share about 45% amino acid identity, while within mammals the identity is above 90% among species.100 Humans and other primates have a single cyt c gene that expresses in all tissues and is essentially monomorphic,100,101 but other mammals, such as mouse, present one somatic and one testis isoform.102 While recent versions of cyt c, that is, in humans and new world monkeys, are markedly resistant to mutational change, it is believed that the primary sequences of anthropoid primates changed rapidly during early evolution stages mirroring mutations in the cytochrome c oxidase (CcO) binding site, thereby optimizing interprotein ET efficiency to cope with the increasing demands of cellular respiration.100,103,104 However, in addition to substitutions in the ET binding site, many of the evolutionary mutations in primates are found in the Ω loop 40−57,20 which is not directly involved in the electron transport function but, instead, has been found to be critical for exploring alternative conformations.105,106 It is interesting to note that, although the tertiary structure of eukaryotic cyts c appears to be largely preserved throughout the evolutionary scale, only residue C17 is identical in all known sequences, and about 10% of the residues are highly conserved, including G6, F10, C14, H18, P30, W59, Y67, P71, K72, P76, T78, M80, L94, and Y97 (hh-cyt c numbering).69 Also of note, a minimum of two buried water molecules have been consistently observed in high-resolution crystal structures of mitochondrial cyts c, which are part of extended hydrogenbonding networks that have been implicated in modulation of protein dynamics, ET, and alternative functions of cyt c. One of these structural waters mediates a charge interaction between the carboxyl group of ring D propionate substituent and the guanidinium group of R38. The other is hydrogen-bonded to the side chains of Y67, N52, and T58, and its position has been shown to be sensitive to the redox state, at least for the cyts c from horse, tuna, yeast, and rice, being closer to the heme iron in the ferric form by ca. 0.9 Å, depending on the organism.73,74,78,85,86 X-ray crystallography reveals no other significant redox-linked structural changes, although these results may be affected by the action of crystal packing forces73,74,78,85,86 and X-ray induced photoreduction.107−109 A large number of solution studies employing different NMR methodologies confirm that the structures of ferric and ferrous cyts c are highly similar and only exhibit relatively minor redoxlinked conformational changes. In general, the main differences refer to the reorganization of the hydrogen-bonding network involving one of the heme propionates, buried water molecules, and side chains of several residues mainly on the distal side, such as G41, N52, W59, and A81, although the details are somehow contradictory.83,84,88−93,110−115 For yeast and horse cyts c, these NMR studies consistently suggested higher protein flexibility in the oxidized form, which has been postulated as a key feature for regulating binding and dissociation in interprotein ET,84,110,114,115 consistent with the redox statedependent interaction between cyt c and CcO.116 Interestingly, recent nuclear resonance vibrational spectroscopy studies on

2.3. Structure and Dynamics

Mitochondrial cyts c are a subgroup of the class I globular and water-soluble proteins with average size 104 ± 10 amino acid residues that contain a single covalently attached heme group. Complete primary sequences are established for about 285 cyts c from different eukaryotes,69 while crystal and/or solution 3D structures of ferrous and ferric cyts c have been solved for a few species, including bonito,70 tuna,71 rice,72 baker’s yeast (Saccharomyces cerevisiae),73−84 horse,85−93 cattle,17 the parasitic excavate Crithidia fasciculate,94 the parasite Leishmania major,95 spider monkey,20 and human.19,20,37,96 Overall the different structures are largely superimposable and present Cα root-mean-square deviations typically below 0.7 Å,17,20,73,85,95,97 as shown in Figure 3 for the isoform 1 of Saccharomyces cerevisiae (iso-1-cyt c) and H-cyt c.

Figure 3. Structural superimposition of H-cyt c (blue) and iso-1-cyt c (cyan) (Protein Data Bank codes 3ZCF and 1YCC, respectively).

The typical cyt c fold consists of five α-helices of different length interconnected by extended Ω loops, in addition to a couple of very short two-stranded antiparallel β-sheets structures. The heme group is almost completely buried into a hydrophobic pocket with only the edge of pyrrol B partially solvent exposed and the two propionate substituents from rings C and D completely shielded from the bulk solvent and stabilized by interactions with polar side chains. Four highly conserved residues are responsible for the tight binding and primary electronic properties of the heme: C14, C17, and H18 belonging to the CXXCH motif and M80 (hh-cyt c numbering). The two cysteines form covalent thioether bonds with the vinyl substituents of pyrrole rings A and B, 13386


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ferric cyt c552 from Hydrogenobacter thermophilus reveal strong dynamic coupling between low frequency modes of the heme and vibrations of the CXXCH motif, which in turn is near to the interaction interface with redox partner proteins.9,117 Moreover, NMR and EPR studies on this protein variant11 and resonance Raman and femtosecond vibrational coherence spectroscopy studies on cyt c551 from Pseudomonas aeruginosa10 demonstrate a dramatic effect of the heme ruffling distortion on spin densities and ET rates. On the basis of these results, it was proposed that this dynamic coupling lowers the energy barrier for interprotein ET either due to minimization of the Marcus reorganization energy or through thermal energy transduction from the protein surface to the heme that is released upon formation of the interprotein complex.9,10,117 In sharp contrast with yeast and horse cyts c, 2D 15N NMR relaxation experiments on H-cyt c show that the generalized order parameter S2 is higher in the oxidized form for most residues (Figure 4), thus indicating a more restricted flexibility

redox-dependent backbone differences in several regions (Figure 4). This includes residues 12−16, 22−28, and 79− 82, which partake in the interactions with CcO.116 The most significant changes are found in loop 22−28, but also for residues 45−47 and 52−55, in agreement with previous observations for hh-cyt c.85 Interestingly, relaxation dispersion experiments on H-cyt c identified local conformational exchange on the microsecond−millisecond time scale for the region around H33 but not for the front face that constitutes the interaction site for CcO.19 Despite the conserved tertiary structure, mitochondrial cyts c from different species may differ in either local or global stability, or both. For instance, the protein from yeast exhibits 1.5 kcal mol−1 lower unfolding free energy (ΔGu°) than the equine counterpart, as determined from GdnHCl denaturation experiments,119,120 which is not surprising considering that these two proteins differ in more than 40 residues. On the other hand, human and spider monkey cyts c, which differ in five residues, exhibit virtually identical values (ΔΔGu° = 0.2 kcal mol−1), while equine and bovine versions that differ in only three positions of the primary sequence exhibit ΔΔGu° = 1.11 kcal mol−1.20 These apparent contradictions highlight the difficulties in assessing the contribution of individual residues to the stability, dynamics, and function of proteins in general. Nevertheless, as expected, the stability of cyts c is significantly affected upon replacement of invariant or highly conserved residues.69,121−124 The mutational analysis of the conserved amino acids and their structural and functional relevance have been recently reviewed by Zaidi and co-workers.69 Among these key residues, the heme axial ligands H18 and M80, along with the two Cys residues 14 and 17 that form thioether linkages to the heme, critically define the folding of the holoprotein and the electronic properties of the heme, including redox potential and kinetic ET parameters.21,46,125−132 Moreover, M80 has been proposed to stabilize the monomeric protein as compared to the dimeric form in domain swapping processes that lead to cyt c oligomers.133,134 In contrast to the labile M80−Fe bond, H18 remains coordinated to the ferric heme even under relatively strong denaturing conditions.29,32,35,135−138 L94 and Y97 from the Cterminal helix interact with two residues from the N-terminal helix, G6 and F10, respectively. Thus, although these four conserved residues are not implicated in ET, their interactions are crucial for structure and stability, including preservation of the hydrophobicity of the heme pocket. Moreover, F10 has been implicated in the recognition of the HCCS enzyme, thus pointing out the importance of these residues in assembly and folding of the protein to the native state.52,68,139−141 W59 is Hbonded to one of the heme propionates, which along with the hydrophobic character of its side chain is thought to strongly modulate the electrostatic environment of the heme.142,143 Y67 participates in an extensive redox-sensitive H-bonding network that includes a water molecule and the side chains of N52, T78, and the axial ligand M80.73−75,78,85 These interactions are regarded as important determinants of the redox potential and ET reorganization energy of cyt c.74,75,144−146 Moreover, Y67 is considered crucial in tertiary structure stabilization as it participates in H-bonds that interconnect loops 40−57 and 71−85, which are involved in pH-dependent and other conformational changes relevant to the apoptotic function.96,144,147−149 F82 is a conserved surface residue located in the region of interaction with partner redox proteins but also in close proximity to the heme and, therefore, has been

Figure 4. Top: Difference of generalized order parameters between the oxidized and reduced forms of H-cyt c (ΔS2 = S2ox − S2red) obtained from 2D 15N NMR experiments. Reprinted with permission from ref 118. Copyright 2010 Elsevier Inc. Bottom: RMSD per residue for the backbone atoms between the 20 final energy-minimized solution structures obtained by NMR for reduced and oxidized H-cyt c. Reprinted with permission from ref 19. Copyright 2015 Elsevier Inc.

of the human ferric protein, particularly for fluctuations in the nanosecond−picosecond time scale.118 This suppression of backbone flexibility was found to be pronounced for loops 75− 79 and 81−87, which are rich in Lys residues that participate of the interactions with CcO, but relatively large effects were also observed in other regions, including residues in the heme pocket such as C14 and Q16 (hh-cyt c numbering).118 Very recently, Imai and co-workers reported a detailed NMR study of the solution structure H-cyt c in both redox states.19 The reported structures (PDB ID codes 2n9i and 2n9j) reveal 13387


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that are populated during downhill folding.23 The overall picture emerging from the HX studies is schematically represented in Figure 5. Downhill kinetic folding of cyt c

implicated in modulating the redox potential and in establishing efficient interprotein ET pathways.116,150,151 The highly conserved prolines 30, 71, and 76 are thought to play important structural roles. P30 is important in stabilizing the distal H18 ligand; P71 helps to position the proximal ligand M80 and contributes to shield the heme group from the bulk solvent.152−154 T78, also a conserved residue, participates in a H-bonding network that is important for determining the heme environment.155 Finally, the remaining highly conserved residue K72 is part of the patch of positively charged residues in cyts c from higher organisms that surround the partially exposed heme and participate in electrostatic interactions with the partner redox proteins,156 as well as with natural and artificial membranes157,158 and with Apaf-I.159,160 Interestingly, in yeast iso-1-cyt c, the K72 residue is naturally trimethylated, which along with the presence of free C102 constitutes a distinct feature.18 As compared to mammalian cyts c in general, the yeast protein exhibits more clearly defined clusters of uncompensated positively and negatively charged surface residues in the front and back sides, respectively, which determine a significantly larger dipole moment.161 These regions were found to be considerably more fluctuating in yeast cyt c, which has been considered a key determinant of the lower conformational stability and higher peroxidatic activity of the yeast protein.97

Figure 5. Schematic representation of the foldon-dependent defined pathway model for the folding/unfolding of cyt c. Partially unfolded (U) forms correspond to the high free energy space above the native protein (N). Adapted with permission from ref 23. Copyright 2016 National Academy of Sciences.

proceeds through intermediate structures in a reproducible stepwise pathway that mirrors unfolding results, thus indicating reversible equilibrium between consecutive intermediates. The protein can be divided into at least five small cooperative units or foldons that fold in a stepwise all-or-none manner. When one of these units folds, it assists the subsequent folding of neighboring foldons by stabilizing interactions. The different foldons are named according to the color code represented in Figure 5. The blue foldon encompass seven residues of the Nterminal helix 1−14 and eight in the C-terminal helix 88−104, whose concerted folding leads to the first partially unfolded intermediate (irygB) starting from the totally unfolded protein (U = irygb). The next intermediate (iryGB) is formed upon folding of the green unit, which includes five residues from the 61−69 helix and one from the nearby omega loop 20−35. Subsequent steps are the folding of (i) the yellow foldon (irYGB) comprised of a short two-stranded β sheet (57−60 and 37−40), (ii) the red omega loop 71−85 (iRYGB), and (iii) the infrared (also called gray or nested yellow) omega loop 40− 57 (N = IRYGB). To obtain a detailed in silico description of the folding of cyt c and to clarify the role of the heme group in this process, different models and computational strategies have been applied. Cárdenas and Elber191 employed an all-atom model to perform nanoseconds long molecular dynamics simulations, obtaining a pattern of trajectories that reproduces many of the experimental observations. In sharp contrast, the Wolynes group utilized a completely funneled simplified model based on simulations of the associative memory Hamiltonian.25,192 Unlike all-atom molecular dynamics simulations, this methodology allows extensive sampling and, therefore, facilitates the precise computation of free energy profiles. The results show that collapse and folding are highly correlated in the completely minimally frustrated model. Moreover, the simulations predict a similar trend of sequential ordering of folding units found in HX experiments.25,192 Moreover, this approach can describe alternative folding pathways at low and high pH as a result of chemical frustration, predicting well the structures and relative stabilities of intermediates species.25,29,193 These types of simulations, when taken together with experiments, also

2.4. Folding/Unfolding Studies

The mechanisms of protein folding in general and of cyt c in particular have been a subject of intense research and debate over several decades. Two apparently antagonist positions have dominated the discussions: (i) a classical view in which proteins fold following a distinct pathway through a number of intermediate states and (ii) a statistical view that considers multiple routes and intermediate conformations arranged in a funnel-shaped energy landscape.26,27,162−169 A clear distinction between these two models optimally requires the time-resolved detection and structural elucidation of the short-lived intermediate conformations. To this end, the unfolding and refolding of cyt c has been studied employing a variety of experimental strategies and spectroscopic methods, including NMR, UV−vis, fluorescence, IR, and CD.122,170−182 Each approach has specific advantages and limitations regarding time resolution, structural information, and ensemble-averaged information, among others. Comprehensive hydrogen exchange (HX) studies of hh-cyt c by Englander and co-workers have provided the most detailed picture. The HX methods rely on the fact that main-chain amide hydrogens of most amino acids (except proline) are involved in extensive hydrogen-bonding networks that participate in defining protein structural elements. When exposed to the aqueous solvent, these hydrogen atoms can be exchanged, and, thus, unfolding and folding processes can be directly monitored in a site-resolved manner through HX measurements employing NMR and/or MS techniques.26,27,183 Early studies employed NMR to explore equilibrium and kinetic HX upon reversible unfolding of WT cyt c and selected mutants in the presence of increasing, yet small, amounts of denaturants.184−190 These experiments allowed the identification of a sequence of partially unfolded intermediates that are defined by the energetically uphill unfolding of one or more folding units. Very recently, Hu et al. employed a HX pulse labeling method followed by quenching, protein digestion, and HPLC−MS analysis to determine the structure and time progression of the short-lived intermediates 13388


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(RIXS) study of a bis-imidazole porphyrin model and cyt c in both redox states, the authors conclude that the Fe3+−S(M80) bond strength is 7.1 kcal/mol, versus 5.0 kcal/mol for Fe2+− S(M80). Recent work by the same group shows that more than 50% of the bond stabilization arises from contributions of the protein scaffold, probably involving the network of H-bond interactions described in section 2.3.203 These remarkable results, if further confirmed, would compel a reinterpretation of previous work assessing the stability of the axial ligands, their role in attaining alternative protein conformations, and the regulation of the thermodynamic redox parameters (see section 3.2). By far, most studies over the last 75 years have focused on the structure, physicochemical characterization, and functional properties of the alkaline conformer IV. This includes the design of a number of point mutants to identify those residues that can be implicated as sixth ligand, particularly among the nearby lysines 72, 73, and 79 as the most likely candidates.105,204,205 The results show that for the equine protein the distal axial position in the alkaline conformer is mainly occupied by K79, although a minor fraction of K73 coordination has been detected as well,193 while K72 does not participate as sixth ligand.199,205 For the yeast protein the distal axial ligand can be either K73 or K79.198,206,207 The K72 residue in iso-1-cyt c is post translationally trimethylated at ε-N, and, therefore, it is unable to bind the heme iron.208 TrimethylK72 is a relatively rigid residue209 that has been implicated in the modulation of the ligand exchange dynamics involved in the alkaline transition.210 Actually, reducing the steric size of this residue favors the replacement of M80,18 and, in contrast to hhcyt c, the lack of trimethylation in iso-1-cyt c turns K72 into the thermodynamically preferred sixth ligand in state IV.205,211,212 In general, site directed mutagenesis studies reveal that pKa values and other thermodynamic parameters of the alkaline transition for the wild-type protein are intermediate between those determined for the formation of the K73- and K79coordinated forms,198,207,212,213 thus indicating that state IV is actually a mix of more than one conformer.193,198 Replacement of the M80 ligand by a lysine residue is a priori expected to result in a negative enthalpy change based on the greater affinity of the lysine nitrogen for the heme iron.214 Experimental determinations for cyts c from different species, however, yield either positive or negative enthalpy changes,213 which has been ascribed to a certain diversity in structural and solvation properties that, in turn, determines the relative abundances of the possible alkaline conformers. Entropy changes for the alkaline transition also display a large variability among species but enthalpy and entropy variabilities largely compensate, thereby resulting in pKa values for the different species that spread over a narrow range.213 Attempts to determine the 3D structure of state IV for wildtype cyt c have been unsuccessful, probably due to the presence of more than one conformer. Assfalg et al.215 designed a K72A/ K79A/C102T triple mutant of iso-1-cyt c that at pH 11 stabilizes a single alkaline conformer with K73 distal coordination, as revealed by paramagnetic NMR spectroscopy. More recently, Amacher et al.16 found that the T78C/K79G double mutant of iso-1-cyt c crystallizes at close to neutral pH in a conformation that resembles the alkaline state regarding the fact that K73 occupies the sixth ligand position, according to the resolved X-ray crystallographic structure (Figure 6). Both model proteins exhibit a compact and globular structure similar to the native state of the wild-type iso-1-cyt c, but with

provide a detailed description of electrostatic effects versus hydrophobic forces in denatured protein ensembles.24 Thus, despite the long-standing controversies, the experimental foldon-dependent pathway and the theoretical energy landscape model seem to predict compatible results. Interestingly, Brunori and co-workers pointed out some evidence that suggests a consensus folding mechanism operative in very different members of the large cyt c family.194 2.5. Alternative Conformations

The so-called native structure of cyt c, derived from crystallographic or NMR studies in neutral solutions described above, is regarded as the competent species for electron transport in the respiratory chain. A more realistic picture, however, should include subtle alterations of the structure and dynamics imposed by the environmental conditions that characterize the intermembrane space, including crowding effects, local electric fields, and pH values (particularly at the membrane interface) as well as specific and unspecific protein− protein and protein−lipid interactions. Such effects may be crucial in fine-tuning protein ET parameters (see section 3), but under certain conditions can go far beyond and induce alternative cyt c conformations with new functionalities that may be biologically and/or technologically relevant. 2.5.1. Alkaline Transition. The investigation of alternative conformations of cyt c was pioneered by Theorell and Åkenson, who already in 1941 demonstrated that ferric hh-cyt c undergoes several pH-dependent changes.195 One of these transitions was identified as an equilibrium between two different low-spin species of cyt c characterized by an apparent pKa of 9.35 and, therefore, is usually referred to as an alkaline transition.195 Latter studies showed that the distinct feature of this transition is the loss of the native distal ligand M80 (state III) and, thereby, of the 695 nm band in the electronic absoption spectrum, and replacement by a lysine residue (state IV).196,197 Alkaline transitions occur in ferric cyts c from other organisms as well, although pKa values and some properties of state IV may be different. On the other hand, ferrous cyt c presents pH-dependent changes only at extreme pH values, and none of these can be attributed to a ligand exchange analogous to the alkaline transition of the ferric form.195 Further increment of pH leads to subsequent conformational changes. For iso-1-cyt c, a second transition from state IV to a new lowspin conformer called state V has been reported to occur with an apparent pKa around 10.5−11.198,199 Spectroscopic studies on the WT protein and selected mutants suggest that state V actually represents an equilibrium between two species that share the same H2O/His axial coordination pattern but differ in structural details of the heme pocket.199 Interestingly, double mutants that lack lysine residues 73 and 79 do not form state IV and, instead, undergo a direct III → V transition.198 Even higher pH values, typically above 12, result in the formation of a U-conformer, which retains V-like axial coordination pattern but undergoes partial loss of tertiary structure, particularly at the level of the 60’s helix.199,200 The fact that these transitions are only observed for ferric cyt c has been ascribed to a reduced strength of the Fe3+−S(M80) bond,201 and to the lower conformational flexibility of the ferrous protein (at least for the hh- and iso-1-cyt c variants) that hinders the required structural rearrangement.83 However, this well-established notion has recently been challenged on the basis of theoretical and experimental work by Solomon and collaborators.202 On the basis of a comparative resonance inelastic X-ray scattering 13389


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spectroscopy, and photon counting histogram with single molecule sensitivity, provided clear evidence that the detailed mechanism is significantly more complex.217−219 Stopped flow studies reveal biphasic kinetics, with each phase consisting of an acid−base pre-equilibrium and a rate-limiting structural change.105,220,221 The rate constant of the first phase increases with pH; hence it was proposed to include the opening of a structural gate followed by fast deprotonation equilibrium of a usually buried residue.105 The second phase, which is consistent with the mechanism proposed by Davis and co-workers, includes the titration of a second residue followed by slow ligand exchange. The identity of the ionizable residue that triggers the second kinetic phase remains a matter of debate. Possible candidates are the lysine residues that surround the partially exposed heme edge as the pKH value determined for the triggering group is very similar to the pKa of the lysine side chain in solution.216 Independent of the nature of the triggering group, deprotonation of either K73 or K79 is required as a prerequisite for iron coordination, and, therefore, the similarity between pKH and the pKa of lysines suggests that these two processes may be strongly intertwined.29 To clarify whether the same lysine residues that coordinate the distal position in state IV may also serve as triggering groups, several mutants of iso-1-cyt c were produced and studied. The variants K73H and K73H/K79A were found to undergo a transition to the bis-His ligated heme state at neutral pH, and, furthermore, the K73H mutant exhibits a second transition to Lys/His-ligated heme at higher pH.222,223 The low pH transition is affected by three ionizable groups, including H73 and two other not identified residues that modulate the rate constants.217,218 The single mutant K79H, in contrast, exhibits only two ionizable groups, thus suggesting that the alkaline ligand K79 is a likely ionizable triggering group. Note, however, that most of these mutants do not lead to a Lys/His-ligated state IV, and, therefore, these conclusions should be taken with caution. Moreover, the mechanism of alkaline transition for cyt c from unicellular organisms may differ significantly from that of vertebrates. In addition to the lysine residues, other possible triggering groups have been proposed such as a heme propionate carboxyl, the proximal histidine ligand, and a buried water molecule, among others.197,224,225 Infrared spectroscopic studies show that the apparent equilibrium pKa of one of the heme propionates is very similar to the pKa of the alkaline transition, and, moreover, the trifluoroacetyl-lysine derivative of hh-cyt c exhibits similar upshifts of both apparent pKa values.224 EPR spectra, on the other hand, point out the axial ligand H18 as the most likely triggering group.197 Deprotonation of this residue is expected to result in a remarkable trans effect that would significantly weaken the Fe3+−S(M80) bond. Moreover, the highly conserved buried water molecule Wat166 is part of an extended hydrogen-bonding network that includes Y67, N52, and T78 and, therefore, has been proposed a key player in mediating the mobility of different protein regions, including those involved in the alkaline transition.225 Hydrogen exchange NMR experiments on hh-cyt c show that the regions involved in the dynamics of the alkaline transition are the so-called infrared and red Ω-loop foldons that are also involved in the first two steps of the unfolding pathway (see Figure 5), while the remaining three foldons seem not to participate.105,193 The red loop 71−85 shields the distal face of the heme from the solvent and contains not only the native axial ligand M80 but also the putative alkaline ligands K73 and

Figure 6. Structures of iso-1-cyt c variants with different distal ligands: K73 (PDB ID: 4Q5P), hydroxide (PDB ID: 4MU8), or M80 (PDB ID: 2YCC). Carbons are colored as follows: K73-ligated T78C/K79G = cyan, M80-ligated C102T = yellow, hydroxide-ligated WT* = green. Noncarbon atoms are colored by element: N = blue, O = red, S = yellow, Fe = orange. (a) Alignment of the three structures by mainchain atoms. (b−d) Heme coordination geometry for K73-ligated T78C/K79G (b), M80-ligated C102T (c), and hydroxide-ligated WT* (d). WT* is a pseudo wild-type variant of iso-1-cyt c with mutations K72A and C102S. These stabilizing mutations are also included in the other two variants. Adapted with permission from ref 16. Copyright 2015 American Chemical Society.

K73 axial coordination and the M80 residue exposed to the solvent. The most important deviations relative to the native structure are observed at the level of the loop 70−85, which is not unexpected considering that both K73 and M80 are located in this region. In the T78C/K79G variant, the 70−85Ω-loop refolds into a compact β-hairpin structure, while the K72A/ K79A/C102T mutant shows a less compact structure in this region, with a lower amount of intraloop and intraprotein hydrogen bonds. Another interesting structural feature observed in these state IV models is an ca. 25% expansion of the heme pocket in T78C/K79G and some conformational rearrangement that may suggest the opening of a channel to the heme group of K72A/K79A/C102T, although in both cases it remains unclear whether these changes imply increased solvent accessibility to the heme.16,215 Interestingly, the largest structural differences between the native protein and the state IV models are localized in the regions that exhibit increased conformational dynamics in ferric iso-1-cyt c as compared to the ferrous form,215 which may explain why the alkaline transition is only observed in the oxidized state. In their pioneering work, Davis and co-workers proposed a minimal two-step mechanism for the alkaline transition of hhcyt c that includes a fast ionization step followed by slow ligand exchange:216 KH

kf

cyt c ‐Hstate III XooY cyt cstate III ⇄ cyt cstate IV kb

In terms of this mechanism, the apparent pKa of the transition can be expressed as indicated in eq 1: ⎛k ⎞ pK a = pKH − log⎜ f ⎟ ⎝ kb ⎠

(1)

Later kinetic studies employing a variety of experimental techniques, such as stopped flow, time-resolved Raman 13390


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ments reveal increased peroxidase activity relative to the native state III.31,237,238 As shown by Canters and co-workers,239 the Lys/His-coordinated cyt c is unlikely to exhibit peroxidase activity, and most likely the enhanced catalytic activity is ascribable to the presence of a minor amount of an intermediate five-coordinated high-spin species.31,32 Therefore, state IV-like conformations of cyt c are not suitable electron shuttles in the respiratory chain but might play a role in the pro-apoptotic permeabilization of the mitochondrial membrane. However, this requires the conformational transition to take place at physiologically relevant pH values, which is not the case for wild-type cyts c. For that reason, the alkaline transition has limited biological significance per se, although it has been long considered a useful system for fundamental biophysical research and a model for other conformational changes. This view has changed in recent years with the discovery that certain post-translational modifications of mammalian cyt c and some naturally occurring point mutations trigger a similar conformational change at pH values significantly closer to neutral.30,31,33,240,241 The finding that for these protein variants state IV reaches high concentrations at physiological pH revitalized the hypothesis of the proapoptotic function of the alkaline conformation in vivo. One of these modifications is the naturally occurring Y74 nitration, which results in deprotonation of the phenolic ring at neutral pH31 concomitant with Met → Lys axial ligand exchange.30 The mechanism of this early alkaline transition is not yet completely understood. It has been proposed that nitration of Y74 sterically destabilizes the flexible Ω-loop, thus triggering a rearrangement of the extended hydrogen-bonding network that includes interruption of the Y67−M80 contact, thus finally leading to M80 detachment.30 In this model, deprotonation of nitro-Y74 is excluded as the triggering event. More recent experimental and computational studies suggest that the change of electrostatic field caused by the deprotonation of nitro-Y74 stabilizes the Lys/His form relative to the intermediate pentacoordinated species, thereby increasing the activation barrier for the inverse Lys → Met ligand exchange. This kinetic effect results in a downshift of the apparent pKa of the transition.31 Phosphorylation of at least tyrosines 48 and 97 is another reported post-translational modification that is thought to regulate canonical versus alternative functions of cyt c.242,243 This variant, however, remains poorly characterized mainly due to difficulties in obtaining sufficient amounts of the phosphorylated protein. To overcome this obstacle, point mutants in which tyrosine residues of H-cyt c are replaced by glutamate have been used as phosphomimetic model systems.33 The Y97E variant shows lower stability than the unmodified protein, but no other significant differences in the physicochemical parameters. For the Y48E mutant, in contrast, the authors report pKa = 7.0 for the alkaline transition, a drastic downshift of the redox potential and formation of a nonfunctional apoptosome.33 The early alkaline transition in Y48E has been ascribed to the loss of the Tyr-OH group at this position, which disrupts the hydrogen-bonding network that includes the heme propionate. The extra negative charge carried by the glutamate residue may also alter the local electric field and, thereby, the size and exposure of the heme crevice.33 In a different approach, phosphorylation of Y48 has been mimicked by generating a variant that contains the synthetic amino acid p-carboxymethyl-L-phenylalanine (pCMF) at position 48 (Y48pCMF mutant).244 This variant exhibits an

K79, and, therefore, major distortions of this segment are not unexpected, as confirmed by in silico226 and ex silico16,215 structural models. Consistent with this observation, the structural alteration of the red loop has been shown to have a strong impact on the alkaline transition of cyts c from different vertebrates and unicellular organisms.226−230 For instance, mutation of F82 downshifts the midpoint of the alkaline transition to nearly neutral pH,227 while an increased steric size of residue 81 slows the opening of the heme crevice.228 Molecular modeling studies show that the red Ωloop in the human protein is located further away from the heme as compared to the yeast and equine versions, which has been invoked as the basis for the upshifted alkaline transition observed for H-cyt c. 229 On the other hand, recent thermodynamic and kinetic studies on several iso-1-cyt c variants have shown that lower stability of this loop does not necessarily correlate with a faster alkaline transition.230 Interestingly, for hh-cyt c, the unfolding rate of the red loop obtained from kinetic HX-NMR experiments matches the limiting rate of the misligation slow phase determined by stopped flow. Moreover, the unfolding rate of the infrared loop 40−57 matches the limiting rate (internal deprotonation) of the fast phase observed in stopped flow experiments. Thus, the infrared foldon can be regarded as a structural gate that, upon pH-induced distortion, enables the access of solvent molecules to the heme crevice.105 Notably, most mutations along the rapid evolution of primate cyts c are found in the 40−57 Ωloop, and these mutations affect the hydrogen-bonding network that extends up to the red loop. Therefore, mutations at the level of the infrared foldon affect the stability of the heme crevice and produce the concomitant shift of the alkaline transition.20 Similar effects were verified upon mutational analysis of the 40−57 loop in the yeast protein.231,232 Moreover, a noncovalent artificial construct based on the excision of the 39−56 fragment in hh-cyt c exhibits lower stability and downshifted alkaline transition pKa as compared to the wild-type protein, thus highlighting the importance of this loop.233 Spectroscopic studies show the existence of intermediate structures between states III and IV.199,234 At low ionic strength, hh-cyt c populates an intermediate state called III* that retains the M80 axial ligand and resembles one of the intermediates of the thermal unfolding process.234,235 At high ionic strength, a different intermediate called state 3.5 is instead populated.199 While still a low-spin species, the spectral evidence suggests that residues M80, K72, K73, and K79 are probably not involved in the coordination sphere of the heme iron in state 3.5.199 Most likely these intermediate states represent partially stabilized structures along the unfolding process of the red Ω-loop, thus leading to an equilibrium between species with weakly coordinated M80 and a misligated heme.236 Notably, M80X point mutants of iso-1-cyt c, which can be considered structural models for the intermediate states of the alkaline transition process, show no evidence of high-spin species.225 The spectroscopic evidence, instead, suggests that the sixth ligand can be H2O, OH−, or a lysine residue, depending on the nature of the X residue and the solution pH.225 2.5.2. “Alkaline Transitions” at Physiological pH. The alkaline transition of cyt c implies a drastic drop of the reduction potential by ca. 300 mV. On the other hand, it has been consistently reported that under conditions that favor state IV like axial coordination pattern, experimental measure13391


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(i) cyt c crosses the mitochondrial membrane during apoptosis,266 (ii) a monoclonal antibody that binds mouse cyt c in apoptotic and necrotic cells is unable to bind the free protein in solution but recognizes cyt c/phospholipid complexes,267 (iii) cyt c is able to catalyze lipid peroxidation,268 and (iv) in electrostatically stabilized (low ionic strength) fully oxidized and fully reduced cyt c/CcO complexes, the active site of cyt c undergoes conformational changes spectroscopically similar to those observed upon interaction with artificial models.269−272 Thus, the hypothesis that protein−lipid and protein−protein interactions may induce conformational changes relevant to the electron transport and apoptotic functions of cyt c motivated a large number of biophysical studies in the following decades employing simplified and spectroscopically silent model systems. This includes detergents (SDS, CYMAL, ω-UDM), vesicles from a variety of lipids (such as DOPG, DPPS, DPPC, DOPC, DPPE, DPPG, DPPA, DSPA, DOPA, DLPA, DOPS, and DSPG), fatty acids, and denaturants such as urea and GuHCl.136−138,273−292 Many of these studies focused on the characterization of heme axial coordination and spin state of the non-native cyt c species stabilized under the various conditions, employing a variety of spectroscopic approaches, mainly UV−vis absorption, resonance Raman, EPR, and NMR.137,138,274,277,288 The different studies consistently show that at physiological pH the electrostatic interaction of cationic cyt c with negatively charged surfaces (micelles and vesicles) perturbs the most labile distal side of the heme pocket leading to dissociation of the M80 ligand in all of the detected non-native cyt c states. The distal axial position may remain vacant leading to a five-coordinated high-spin species (5cHS; with H18 proximal coordination), or be occupied by either H26 or H33 leading to a six-coordinate low-spin form (6cLS; with H23,33/H18). Eventually, and depending on the specific conditions, small amounts of a sixcoordinate high-spin form with H2O/H18 axial coordination can also be found. The species are often referred to as B2 conformations, that is, B2-5cHS, B2-6cLS, and B2-6cHS, respectively. The contribution of the B2 forms relative to the native M80/H18 conformation (also called B1-6cLS) increases at lower cyt c/lipid vesicles12,274,288 or cyt c/SDS micelles ratios,277 that is, at higher surface charge densities (Figure 7), which also implies locally higher interfacial electric fields. Spectroscopically identical non-native B2 species have been detected by surface-enhanced resonance Raman (SERR) spectroelectrochemistry of cyt c adsorbed on metal electrodes coated with specifically adsorbed sulfate anions or with selfassembled monolayers (SAMs) of ω-substituted alkanethiols that include either carboxylate or phosphate tail groups. SERR experiments show that both B2 species have redox potentials that are downshifted by around 400 mV with respect to the native protein.13,14,293,294 The surface concentration of the B2 alternative conformations relative to the B1 form shows a clear correlation with the local electric field calculated at the SAM/ protein interface, which varies with the chain length of the SAM, the charge of the tail group, the potential of zero charge of the coated metal, and the pH and ionic strength of the electrolyte (Figure 7). Under otherwise identical conditions, the different tail groups fall all into the same B2 concentration versus electric field dependency, thus strongly suggesting that the B1 → B2 conformational transition may be the result of unspecific electrostatic forces.12,13 Quantum mechanical calculations show that the stability of the M80−Fe bond is not significantly affected upon application of physically meaningful

early alkaline transition with pKa = 6.70, which has been ascribed to increased dynamics of 40−57 loop, as revealed by NMR studies.245 The naturally occurring G41S mutant of H-cyt c has also been reported to present an early alkaline transition, pKa = 7.8, as well as enhanced pro-apoptotic activity.240,246,247 Replacement of G41 affects the heme propionate environment through alteration of the hydrogen-bonding network, thereby increasing the mobility of the Ω-loop 40−57.37,240,247 As mentioned above, the heme propionate side chain could serve as a trigger of the alkaline transition, and loop 40−57 is implicated in major structural readjustment during the process, thus suggesting that the alkaline conformer is kinetically and thermodynamically more accessible in the G41S mutant.247 Other mutations away from the heme coordination loop, such as T49 V and Y67R/ M80A, also favor a Lys/His axial coordination pattern at neutral pH probably due to disruption of the H-bonding and packing of the heme coordination loop, respectively.248 Thus, IV-like alternative conformations of cyt c, particularly those that can form at physiological pH, are likely to be involved in induction and regulation of the apoptotic process. 2.5.3. Acidic Transitions of Cyt c. Conformational changes of cyt c have also been reported at the acidic end of the pH scale.137,195,249−251 At pH values around 2, the nativelike protein undergoes a loss of tertiary structure, although with partial retention of secondary elements, to yield a fully uncompact (U) conformer250,252,253 that lacks the native M80 ligand.240 The axial coordination pattern of the acidic form is dominated by six-coordinated high-spin (6cHS) species, mainly bis-aquo, although five-coordinated high-spin (5cHS) species and non-native six-coordinated low-spin (6cLS) forms have also been reported depending on specific conditions such as pH, ionic strength, and temperature.137 Further addition of acids or salts to the U-conformer results in the formation of the so-called A-state that has been associated with the molten globule form and includes a mixture of high- and low-spin species.249,254−256 This highly structured A-state retains a native-like subdomain that includes the hydrophobic core formed by the heme group together with the N- and C-terminal helices, as well as fluctuating loop regions.172,173,249,254,255,257−260 The collapse of the U-state into the A-state has been assigned to specific binding of anions and to unspecific ionic strength effects, which in turn control the equilibrium between a dimeric and less compact A1-state and a more compact globule-like A2-state.249,251,256,256,261,262 The stability of the A-state appears to be closely related to the flexibility of the native protein. For instance, Y67 is Hbonded to the native axial ligand M80 and is implicated in the stabilization of the Ω-loop 40−57, and thus it is not unexpected that perturbation of this residue turns cyt c more susceptible to acid unfolding.147 Interestingly, the H26Y/C102T double mutant of iso-1-cyt c presents a molten globule structure at neutral pH, probably due to the destabilizing effect of disrupting the H26−E44 hydrogen bond.255 2.5.4. Electrostatic and Hydrophobic Interactions of Cyt c with Model Systems. It has been early recognized that electrostatic interactions of cyt c with a variety of negatively charged model systems, including phospholipid vesicles, micelles, polyanions, and others, induce conformational changes that imply the disruption of the labile M80−Fe bond, mainly in the ferric form, thus leading to different nonnative conformations.263−265 These studies gained renewed interest after some crucial findings during the 1980s and 1990s: 13392


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distal ligand M80. On the basis of spectroscopic, structural, and ET kinetics arguments, this hydrophobic patch has been assigned as the binding site for monomeric SDS molecules and for the adsorption of cyt c to electrodes coated with hydrophobic alkanethiol SAMs, which in both cases lead to the formation of B2 species (mainly B2-6cLS and B2-5cHS) that are spectroscopically similar to those formed in electrostatic complexes.137,301 Moreover, it has been shown that the nature of the interactions of cyt c with anionic lipid vesicles critically depends on the protein/lipid concentration ratio. At low protein concentrations, the binding of cyt c to the vesicles is regarded as peripheral and is attributed to electrostatic interactions of the lysine-rich domain with negatively charged head groups of the lipids, leading to a high conversion to the B2-6cLS form and lower amounts of the B2-5cHS and B26cHS species.137,209,274 At higher protein coverage of the vesicle surface, the electrostatic interactions are assumed to be significantly weakened, thereby favoring hydrophobic contacts that involve the protein segment I81−I85. In this regime, about 50% of the adsorbed protein retains the native axial coordination, about 40% corresponds to the same B2-6cLS spectroscopic component identified in peripheral binding, and the rest is a mixture of HS species.12,274 In this case, the loss of helical structure has been estimated as less than 3%. Thus, at least for this type of model system, perturbation of the front face of cyt c by either electrostatic or hydrophobic contacts leads to the dissociation of the M80−Fe bond and to the stabilization of a bis-His B2-6cLS form that is spectroscopically identical in both types of interactions. Taken together, the different studies suggest that the binding of cyt c to lipid bilayers implies a minimum of three steps: (i) electrostatically driven peripheral adsorption that involves complementary charges and hydrogen bonds between the surface amino acid side residues and phospholipid head groups, (ii) structural perturbation of the adsorbed protein and concomitant reorganization of the lipid bilayer, and (iii) hydrophobic protein−lipid interactions. The last step has been rationalized either in terms of partial penetration of nonpolar amino acid residues into the hydrophobic core of the membrane or the opposite, that is, incorporation of lipid acyl chains into the hydrophobic core of cyt c. The first model assumes that electrostatic interactions destabilize the heme crevice, thus facilitating the displacement of the I81−I85 hydrophobic peptide segment and its insertion into the membrane.274 This hypothesis is supported by EPR experiments with spin labeled lipids,302 hydrogen exchange NMR determinations,292 atomic force microscopy,290 and current−voltage286 measurements on solid-supported lipid bilayers, and by resonance energy transfer experiments with fluorescent markers placed at different depths into the bilayer.283,303 The second model of hydrophobic interactions is the so-called extended lipid anchorage, and was specifically proposed for the interactions of cyt c with cardiolipin (CL).157,275,281,289,304 The complex interactions between cyt c and CL are still a matter of thorough investigation32,157,209,289,305−309 and, due to its relevance in apoptosis, will be discussed separately in section 4 at length. We will only mention here that in the extended lipid anchorage model, the hydrophobic interaction is ascribed to the insertion of one or two acyl chains of the CL molecule into a hydrophobic channel of cyt c. This model of interaction was originally inspired by the observation that the binding of cyt c to CL-containing membranes yields a peroxidase complex that specifically catalyzes CL oxidation.43,268 Further evidence was

Figure 7. Relative contributions of the B2 states for ferric hh-cyt c bound to DOPG vesicles as a function of the protein/lipid ratio (top) and for hh-cyt c bound to coated electrodes as a function of the electric field strength (bottom). The light blue circles represent electrodes coated with ω-carboxyl-alkanethiols (HS-(CH2)n-COOH, with n = 15, 10, 5, 2, 1; light blue). Dark blue symbols correspond to specifically adsorbed sulfate anions and SAM of HS-(CH2)11-PO3H. Adapted with permission from ref 12. Copyright 2011 FEBS.

homogeneous electric fields.295 Molecular dynamics simulations, on the other hand, show that under the action of moderate electric fields cyt c exhibits a distorted and more flexible structure. These structural fluctuations are restricted to specific protein segments comprised of loops, short helices, short sheets, and turns, such as the flexible segments 21−29, 40−59, and 69−87. The effect is ascribed to the alignment and polarization of these structural elements with the electric field. Moreover, the calculations show that the application of electric fields favors the B1 → B2 transition both energetically and entropically, and also lowers the activation barrier of the process.296 Note that the crucial residues involved in the artificial SAM/cyt c electrostatic complexes are the same involved in more realistic protein−protein complexes158,297 (see section 3.1). Even milder electric fields only produce subtle distortions that may be relevant for fine-tuning the ET function (see section 3.3.1).146 Interestingly, circular dichroism (CD), Fourier transform infrared absorption (FTIR), and surface-enhanced infrared absorption (SEIRA) techniques show that for the B2 alternative conformations formed under these relatively mild interactions with model lipid vesicles, micelles, and SAMs, the protein secondary structure remains largely unaffected while tertiary structures become more open.136,137,274,276,298−300 On the other hand, electronically enhanced chiral sum frequency generation vibrational spectroscopy reveals that amino acid residues around the heme that may involve either M80 or H18 adopt a β-sheet structure upon binding to negatively charged phospholipids.280 Previously, we have discussed peripheral binding of cyt c to anionic model membranes, which is attributed to electrostatic interactions that involve the lysine-rich domain around the exposed heme edge: lysines 13, 27, 72, 73, 79, 86, and 87 (hhcyt c numbering). Noteworthy, a small hydrophobic patch that includes residues I81, F82, A83, G84, and I85 exists at the center of this semicircular domain, and connects directly to 13393


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obtained from biophysical studies mainly based on fluorescence techniques,157,275,281,289,303−306,309 but the atomically resolved structure of the complex is still missing. Very recently, McClelland and co-workers were able to obtain high-resolution X-ray structures from cocrystals of the K72A mutant of iso-1cyt c with three different nonionic detergents.273 As exemplified in Figure 8, the obtained domain-swapped dimer structures

Figure 9. Schematic energy landscapes showing the conformational energy as a function of a “conformational coordinate” connecting the bound conformation of the complex for (a) simple docking (left), (b) gated (or conformationally coupled) docking that involves two major conformational substates, and (c) dynamic docking that involves multiple conformations of the complex. Reprinted with permission from ref 311. Copyright 2002 American Chemical Society.

Figure 8. Domain-swapped dimer structure of WT* iso-1-cyt c in complex with the detergent CYMAL-5 (PDB code: 5KKE). There is one molecule in the unit cell (cyan). A symmetry-related molecule (mauve) is used to form the dimeric biological assembly. Adapted with permission from ref 273. Copyright 2016 American Chemical Society.

exhibit the hydrophobic tail of the detergents accommodated into a channel close to the heme, which in turn has lost the distal M80 ligand that is replaced by a water molecule. The B26cHS-like axial coordination of the heme suggests that this complex presents peroxidase activity and, furthermore, the structure deviates only modestly from the monomeric native cyt c. Although simplified, this structure is probably a good model for the hydrophobic interactions of cyt c with phospholipids, fatty acids, and detergents in general. Although most studies focus on the structural and spectroscopic features of cyt c in the complexes with lipids, one can anticipate that the structure of the model membranes may also be affected by the interaction to different extents, depending on experimental conditions such as lipid composition and lipid/protein ratio.281 The different perturbations that have been reported include weakening and disruption of the bilayers,284,285 phase segregation and formation of micron-sized domains in multicomponent lipid membranes,282,287 protein aggregation associated with dragging of lipid molecules from the membrane,279 and cyt c-mediated fusion of vesicles.289 From the protein side, note that in all of the alternative cyt c conformations induced by relatively mild perturbations, the proximal ligand H18 is preserved, and its replacement requires harsh conditions such as addition of high concentrations of denaturants and/or extreme pH and temperature.137,138,278

surfaces in a single, well-defined orientation is required to perform their function.312 When two major conformations are involved, GD takes place, as protein complex needs to reorient from a more energetically favored conformation toward the ET reactive one. The DD scenario allows redox proteins to form multiple productive complexes.313 Efficient tunneling across the interface can take place by means of a high electronic coupling HDA, which decays exponentially with the distance between donor and acceptor.6,314 The different members of the large cyt c superfamily form a wide variety of complexes.2 Mammalian cyts c, in particular, bind to the mitochondrial membrane, to the apoptosome, and to integral membrane proteins related to the electron transport function, among other partners. In the case of respiratory complexes, cyt c does not simply collide with the redox partner randomly until a favorable encounter orientation is achieved that elicits the ET reaction. The emerging picture is much more complex and dynamic. It involves multiple steps, which include (but are not limited to) transient complex formation, complex stabilization, reorientation, structural modifications that may alter the thermodynamic and kinetic ET parameters, the ET reaction per se, and complex disruption. The molecular basis of these steps lies in the surrounding conditions (ionic strength, pH) and the strength, nature, and dynamics of the contacts that are established between the redox partners. Altogether, they shape the energy landscape. 3.1.1. Cytochrome c Peroxidase. Among the redox complexes presented in this section, the adduct involving cytochrome c peroxidase (CcP) has been the most thoroughly studied. Indeed, a crystal structure is available, and the key residues of cyt c that participate in complex formation have been identified.315 The last remaining controversies were whether CcP interacts with one or two cyt c molecules simultaneously and the description of the intermediaries in the redox reaction, although they appear to have been settled recently.316

3. CYTOCHROME c AS AN ELECTRON SHUTTLE 3.1. Complexes with Redox Partner Proteins

Protein complex formation can be understood in terms of an energy landscape along a conformational coordinate.310 Depending on the features of the energy landscape and which conformations are ET active, Hoffman and co-workers put forward a classification for interprotein complexes consisting of “simple docking” (SD), “gated docking” (GD), and “dynamic docking” (DD) (Figure 9),311 which will be used throughout this section. The SD scenario can be found in many protein complexes, in which accurate alignment of the binding 13394


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from cyt c to the W191+• radical. After the first intermolecular redox process, intraprotein ET involving Fe(IV)O regenerates W191+• that is again reduced by a second cyt c molecule that binds at the same site after release of oxidized cyt c. Although the crystallographic structure constitutes the dominant orientation in solution, it is not unique. The first evidence of a large ensemble of electrostatically favorable encounter complexes came from the pioneering work of Northrup and co-workers.326 Employing coarse-grain Brownian dynamics simulations, they were able to identify multiple complex structures that could be clustered into three different CcP regions: one centered around D34, including the crystallographic high affinity binding site, one centered around D148, and a third site involving D217 that connects the other two sites. Paramagnetic relaxation enhancement (PRE) NMR experiments showed that proteins spend 70% of the lifetime of the complex in the dominant orientation of the high affinity site represented in the crystallographic structure, while the other 30% is spent exploring multiple orientations in the dynamic encounter state, characterized mainly by rotational motion of cyt c near the crystallographic site.321,327 The majority of the orientations of the complex ensemble yields distances between redox centers that are incompatible with effective ET reaction, rendering these orientations as redox inactive. Volkov suggests that, although redox inactive, these conformations allow for a reduced dimensionality search toward the functionally active bound form, accelerating the formation of the productive complex as compared to three-dimensional diffusion, according to the model proposed by Adam and Delbruck.322,328 The second model, proposed by Hoffman and collaborators, 323 involves the existence of multiple complex orientations that can lead to the ET reaction. Initial evidence of the second low affinity binding site was put forward on the basis of a 2:1 cyt c−CcP complex formation at low ionic strengths. Furthermore, flash photolysis experiments suggest that direct heme-to-heme ET occurs through the low-affinity site, resulting in a redox process that is faster than that through the crystallographic site. The structure of the low-affinity complex has remained elusive until recently, as Volkov and coworkers have been able to resolve it by blocking the highaffinity CcP site through cross-linking to cyt c via a disulfide bond.324 This allowed for performing PRE NMR experiments in the absence of binding effects from the crystallographic site. The low-affinity complex consists, in fact, of a dominant protein−protein orientation and an ensemble of minor binding geometries and presents an affinity 10 000 times lower than that of the crystallographic site. The dominant orientation encompasses a region bordering D148 and D217 on CcP, while residues K5, T12, and K86 from cyt c are involved in complex formation. The dominant binding form results ET inactive, with heme−heme and heme−W191 distances of 22 and 21 Å, respectively. Meanwhile, the conformational ensemble that constitutes the minor species consists of multiple ET competent orientations and encompasses two spatial regions: one bordering CcP residues D148 and D217 (that does not overlap with the site of the dominant orientation) and extending to the surface patch containing D33 and E35, and the other defined by the CcP residues E167, D261, and E267. The heme−heme distances inferred for the minor species are 7.5), and that the differences between both protons occur by formation of an intramolecular hydrogen bond between the second phosphate group and the 2′ hydroxyl group of the central glycerol.595 However, there is mounting evidence that CL in dispersions as well as in liposomes of varying compositions present, in fact, almost indistinguishable pK constants of ∼2.5; thus at neutral pH CL carries two negative charges.596−599 Despite the apparent symmetry of the CL molecule, it has two chiral centers that can lead to several diasteromers, with R/ R being the one found in nature.593,600 In higher eukaryotes, CL is composed exclusively of fatty acids with 18 C atoms,601−604 distributed as summarized in Table 1, with unsaturated acids the most abundant (∼80%).605

Table 2. Main Proteins Found Bound to CL in Mitochondriaa mitochondrial compartment inner membrane

inter membrane space

fatty acid

Adapted with permission from ref 601. Copyright 2000 Elsevier Science Ltd.

The interaction of CL with proteins involves noncovalent interactions, which can lead in some cases (as it will be further discussed in the case of cyt c) to a functional activation. Even though these interactions are relatively nonselective, there is a preference of many proteins to interact with CL over other phospholipids, probably due to its structure and some shared characteristic among hydrophobic domains of proteins.601 4.2.2. Dual Role of Cardiolipin in Cyt c Function. 4.2.2.1. Structural Determinants of Cyt c−CL Interaction. In mitochondria, cyt c is reported to exist in two states: (i) the form that participates in electron transport and that is easily separated from the membrane upon increasing ionic, and (ii) a second form that comprises about 15% of the total cyt c content, which is strongly attached to CL.629 The second population is not involved in the respiratory chain and is assumed mainly responsible for the enhanced peroxidase activity of cyt c.546,630 These subpopulations have been referred to as sites 1 and 2631 and will be discussed in the following lines. The interaction of cyt c with CL has been reported to occur between different sites of the protein, sites A and C: site A, which includes K72 and K73, that facilitates electrostatic interactions that rely on the positive charge of the residues, as recently postulated,632 and site C (N52) opposed to site A, that has been proposed to interact with high affinity with protonated acidic phospholipids by both hydrogen bonds and hydrophobic interactions.304,633,634 However, in light of the latest evidence regarding the protonation state of CL (see section 4.2.1.1), the molecular mechanism underlying the interaction through site C should be reassessed. Adding to the controversy, it has been

content (mol %) 20.2 25.6 23.5 30.7

± ± ± ±

ref 616 617 618 619 620 620 621 622 623 624 625−628

a

Table 1. Fatty Acid Composition of CL in Rat Mitochondria Reported by Ellis et al.605 saturated monounsaturated polyunsaturated n − 3 polyunsaturated n − 6

protein ADP−ATP carrier phosphate carrier pyruvate carrier carnitine carrier complex I complex III complex IV ATP synthase cyt P450 SCC cardiolipin synthase cyt c

3.2 1.5 1.6 3.0

This observation is of crucial importance because oxidation of this phospholipid is one of the principal outcomes regarding its interaction with cyt c, as will be discussed in the next sections. 4.2.1.2. Localization of Cardiolipin in Mitochondria. Cardiolipin is found mainly in the inner mithocondrial membrane,606,607 where it accouts for 25% of all phospholipids.608 Within the inner mitochondrial membrane, CL is located in over 95% in the matrix side of said membrane in 13415


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region contains multiple Lys residues and is similar to those identified for binding to complexes III and IV, thus indicating that cyt c recognizes lipids and partner proteins in a similar way, which appears to be mainly electrostatic. Interestingly, the Cand L-sites were not identified as interaction sites of cyt c with this model membranes, further stressing that CL−cyt c interactions remain far from being fully understood. 4.2.2.2. Native and Non-native Conformations of Cyt c− CL. As has been previously shown, cyt c exists in at least two functionally relevant conformations, a native state and a nonnative state that has an enhanced peroxidase activity.630 Pletneva and collaborators characterized the heterogeneous ensemble of CL-bound cyt c employing time-resolved FRET measurements of dansyl-labeled variants at different positions, which allowed for estimation of the degree of protein unfolding.309 They found that a compact, non-native form is in equilibrium with a substantially unfolded conformation with a submillisecond rate of conformational exchange.639 The authors suggest that the binding mechanism does not involve deep protein insertion into the membrane, instead consisting of peripheral binding, leading to the extended conformation that was proposed to dominate the peroxidase activity of the CLbound ensemble. 309 Notably, the equilibrium between conformations is perturbed by addition of ATP, as the population of the largely unfolded cyt c conformers is reduced, weakening the cyt c−CL binding interactions while also boosting the peroxidase activity of bound protein.640 Recently, two new binding sites were described, named sites 1 and 2, which represent a new binding model that does not represent sites A, C, and L but more precisely two binding states. In the work by Pandicia et al., by examining the surface interactions of cyt c with liposomes preloaded with CL, it was revealed that two distinct binding sites on the protein exist that cause different extents of unfolding.631 The results showed the coexistence of two distinct conformations of cyt c, one that resembles the native structure, site 1, and a second, partially unfolded non-native conformation, site 2. Site 1 is a high affinity region that is postulated to support the native state of cyt c, allowing its function as an electron carrier in the respiratory chain. This site is not affected by ionic strength, unlike site 2, which can reverse the conformational changes toward a native state in the presence of high salt concentrations. Binding site 2 represents a conformation of cyt c bound to CL that is not capable of performing ET in the respiratory chain, likely because of the disruption of the Fe−M80 bond. This site might possibly be conformed by an equilibrium of partially unfolded proteins bound via electrostatic interactions and less unfolded proteins supported by H-bonds with Lys side chains or hydrophobic contacts.631 4.2.2.3. Heme Ligation States in Cyt c upon Binding with Cardiolipin. For cyt c to fulfill the thermodynamic requirements to act as an electron carrier in the mitochondrial respiratory chain, the heme iron should retain the native hexacoordination pattern with H18 and M80 occupying the proximal and distal axial positions, respectively (see section 3). Displacement of the distal M80 ligand site enables interactions of the metal center with small molecules, such as hydrogen peroxide, thereby conferring cyt c different reactivity.197 As described in section 2, a multiplicity of environmental conditions and perturbations leads to displacement or replacement of M80, particularly for ferric cyt c, including the interaction with anionic lipids in general and with CL in particular.137,274 Thus, establishing the heme axial ligation

recently proposed that interaction through this site would not, in fact, take place.306 The interaction of cyt c with phospholipids through site A does not generate critical changes in the protein secondary structure, and the interaction can be reversed by the addition of ATP. In contrast, interaction with site C generates changes that include modification in the Soret band absorption, suggesting a conformational change involving the heme moiety that cannot be reversed by ATP.291 Structurally, site C includes a hydrophobic cleft that intrudes from the surface into the heme crevice of cyt c that allows the second acyl side chain of CL to be stabilized by a hydrogen bond with N52, which leads to the disruption of the H-bond between the residues H26 and P44.635 Interaction of CL with site C changes the conformation of cyt c into an alternative one that has disrupted the Fe−M80 coordination, therefore enhancing peroxidase activity.635,636 However, it has been proposed that the conformational changes of cyt c originate, at least partially, due to the interaction with liposomes that exhibit a positive curvature and low macromolecular crowding as compared to the mitochondrial membrane, and not due to the specific interaction with CL.306 Thus, the identity of the interaction sites and conformational changes of cyt c upon CL complex formation remain an open question of fundamental interest. Figure 28 represents the sites A, C, and L, along with the tyrosines in cyt c, whose importance in the interaction with CL will be further discussed in the next section.

Figure 28. Cartoon showing the sites of CL interaction in cyt c (blue) and tyrosine residues (green). PDB code: 1HRC.

Besides sites A and C, a site L was later described, involving an area of positively charged amino acids, specifically K22, K25, H26, K27, and H33.289,637 This site, which has a preference for acidic phospholipids, is markedly sensitive to pH.289 Because ET is coupled with proton pumping in the intermembrane space, cyt c is subjected to changes in pH that lead to the conclusion that interactions at this site could be influenced heavily by the functioning of the mitochondrial respiratory chain. Last, a third, independent new site has recently been reported, named site N (or “novel” site) including residues F36, G37, T58, W59, and K60.306 Recently, Kobayashi et al.638 characterized the interaction of cyt c with CL-containing bicelles by NMR spectroscopy. The results show that the interaction occurs through a wide region that includes the A-site, the CXXCH motif, and the N- and Cterminal helices, which interact cooperatively. This interaction 13416


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4.2.2.4. Redox Potential Changes in Cyt c. To perform its function as an electron carrier between complexes III and IV, cyt c must maintain the redox potential within a narrow range around 250−285 mV (vs SHE).649 Upon binding to CLcontaining membranes, the heme iron axial ligand M80 is replaced by an alternative axial ligand such as His, Lys, or H2O, thereby undergoing changes of the redox potential.294,446,643,650,651 This change has been reported to be either a small decrease651 or a significant (∼350−400 mV) downshift that is accompanied by an inhibition of cyt c reduction of respiratory complex III (both purified and within mitochondria) leading to an interruption of mitochondrial electron transport (Figure 29).650 The loss of the ET function is

pattern upon interaction with CL is of crucial interest as this determines the fate of cyt c as electron shuttle or peroxidase enzyme. While there is a general consensus that the interaction of ferric cyt c with CL disrupts the Fe−M80 bond, the extent of the perturbation is not always clear,305,306,309,641,642 and the final axial coordination pattern in the cyt c/CL complex has been controversial (see Table 3).32,35,274,306,643−646 Resonance Table 3. Different Axial Coordination Patterns Proposed for Cyt c upon Interaction with Lipid Vesicles model system

method

low-spin species

high-spin species H2O/His, FeHis H2O/His, FeHis OH−/His Fe-His (minoritary)

ref 274,644

DOPG vesicles CL liposomes

RR

ethanolic CL CL liposomes

MCD RR/UV−vis

His/His, Lys/His His/His, Lys/His Lys/His His/His

SDS/SDS micelles ethanolic CL

NMR

His/His

646

RR/UV−vis/ EPR NMR

His/His

645

Met/His

306

reverse micelles

RR

609 643 32

Raman studies of cyt c in complexes with model phospholipid vesicles revealed alternative hexa- and penta-coordinated species with ligation patterns such as His/His, H2O/His and Fe-His,274 or Lys/His and Fe-His species.644 Magnetic circular dichroism (MCD) studies using cardiolipin suggest that the coordination of the ferric protein at neutral pH is Lys/His and OH−/His.643 Recent RR and UV−vis spectroscopic studies showed that the interaction of WT cyt c with CL-containing vesicles leads to His/His as main species in equilibrium with residual amounts of high-spin species, probably Fe-His.32 Moreover, this study showed that other alternative conformations such as Lys/His or OH−/His obtained by nitration and sulfoxidation of cyt c, respectively, also converge to His/His as main species upon interaction with CL.32 These studies are in agreement with the results obtained by NMR using cyt c exposed to SDS vesicles.646 Moreover, recent RR, UV−vis, and EPR studies of cyt c variants, including mutations in key residues involved in cyt c/CL interactions (H26, H33, K72, K73, and K79), further confirmed the His/His assignment for the coordination pattern of the non-native low-spin state protein in the complex.645,647 These controversies can be partially ascribed to the different model membranes, experimental conditions, and advantages and limitations of the employed spectroscopic methods. Note, for example, that the oxidation state of CL is important for its interaction with cyt c, but the oxidation of zwitterionic lipids that conform the membrane structure also promotes changes in the secondary and tertiary structure of cyt c and influence the affinity of the protein for lipid bilayers.648 Notably, in sharp contrast with nearly all other studies, a recent NMR investigation of cyt c encapsulated in CL containing reverse micelles reveals that the protein is not significantly disturbed by the binding of CL, certainly not to the extent required for ligand exchange.306 These divergent results further highlight the great impact of apparently minor experimental differences on the conclusions that can be drawn on cyt c/CL interactions.

Figure 29. Interaction of cyt c with cardiolipin results in a down shift of redox potential that interrupts electron transport from CIII to CIV and leads to the gain of peroxidase activity. Adapted with permission from ref 650. Copyright 2007 American Chemical Society.

accompanied by a gain of the peroxidase activity due to the increase of a penta-coordinated population of cyt c, or at least a population presenting a weakened Fe/M80 bond that confers higher accessibility to the heme Fe of substrates such as hydrogen peroxide or phospholipids.43,296,546,652,653 In line with these findings, interaction of hh-cyt c with SDS or sodium bis(2-ethylhexyl) sulfosuccinate/hexane reverse micelles changed the configuration of the heme center to a low-spin state characterized by a lower redox potential (ca. +200 mV) as compared to the wild-type native protein (+220 mV).654 It was suggested that this alternative state is compatible with a more open heme crevice, and that this conformer could be generated in vivo by interaction of cyt c with CL in the inner mitochondrial membrane.288,654 4.2.3. Peroxidase Activity of Cardiolipin-Bound Cyt c. Cyt c, in its native state, is a poor peroxidase239 that reacts with hydrogen peroxide with a Km ≈ 70 mM,268 a value higher than those reported for other heme proteins in the mitochondrial membrane such as CcO (Km for hydrogen peroxide ∼1.2 mM). 655 In the presence of CL and other anionic phospholipids, cyt c increases its peroxidase activity in a range that varies from 7-fold to 2 orders of magnitude, thus gaining the capacity to oxidize several molecules including CL itself, leading to a series of events that unleash the apoptotic machinery,546 as will be discussed in the next sections. Besides the increase in peroxidase activity, it has also been shown that conformational states of cyt c that favor peroxidase activity correlate with CL oxidation and apoptosis. Miyamoto et al. demonstrated the generation of singlet oxygen by a cyt c−CL complex in a membrane model containing CL.656 The study revealed that singlet oxygen generation required binding of cyt 13417


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a positive feedback in ROS production.677 In addition, Ca2+ can bind to CL in the inner mitochondrial membrane, leading to decreased lipid mobility, formation of CL-enriched domains, and protein aggregation.677 These events culminate in a stress response known as the “inner membrane permeability transition” that involves the opening of the permeability transition pore (PTP),678,679 which consists of several proteins including the voltage-dependent anion channel (VDAC), the adenine nucleotide translocase (ANT), and cyclophilin D.680,681 The PTP opening is coupled with mitochondrial swelling and permeabilization that ultimately leads to the release of cyt c and other mitochondrial proteins.674 On the other hand, cyt c release can occur via a Ca2+independent mechanism, mainly by permeabilization of the outer membrane by the pro-apoptotic Bcl-2 family of proteins, such as Bax and Bak.549,682 The importance of this mechanism over others is demostrated by the finding that mice deficient in both Bax and Bak are resistant to most apoptotic stimuli.676 The interaction with CL itself and the changes in the conformation generated by this interaction could be factors that can also contribute to the translocation of cyt c by changes in the membrane.683−685 In the work by Bergstrom and collaborators using giant phospholipid vesicles, leaking of cyt c was monitored by fluorescence microscopy. The results showed that cyt c interacted strongly with CL embedded in membrane vesicles, and this was accompanied by bursts of cyt c leakage through the lipid structure.684 Imaging analysis showed that cyt c translocated through newly formed pores that remained open to all molecules of a certain size, events that could be prevented by the addition of ATP.684 These results, especially regarding pore size, were further confirmed.686 Very recently, optical-trapping confocal Raman microscopy experiments provided compelling evidence of concomitant disruption of the M80−Fe bond of cyt c upon interaction with lipid vesicles of PC/CL, and the permeabilization of such vesicles was demonstrated by monitoring the leakage of the Raman tracer 3-nitrobenzenesulfonate.642 Once cyt c is liberated it interacts with Apaf-1 and caspase 9,266,553,687 to form the “apoptosome”, which then activates procaspases 3688 and 7,689 via inactivation of the “inhibitor of apoptosis proteins” by Smac/Diablo,690 thus unleashing the steps of apoptosis.660,691,692 Altogether, changes in cyt c conformation are essential for membrane permeation and leak of mitochondrial components that can, therefore, trigger the signaling cascade that leads to apoptosis. Attempts have been made to elucidate the exit mechanism of cyt c from the mitochondrion;545 however, the real-time analysis of this transport event has proven challenging and awaits further investigation. 4.2.5. Cyt c as a Target for Antiapoptotic Drugs. As discussed in previous sections, pore formation in the outer mitochondrial membrane to enable cyt c exit is critical for the initiation of apoptosis. The peroxidase activity of cyt c gained upon complex formation with CL in the presence of ROS enhances mitochondrial pore formation.546 Inhibitors of the peroxidase activity of cyt c targeted to the mitochondria were shown to significantly reduce apoptosis.693,694 The first structure-based designed compound was a triphenylphosphonium-6-imidazole stearic acid conjugate (TPP-6-ISA), which was shown to effectively inhibit the peroxidase activity of cyt c and to reduce apoptosis in mouse embryonic cells exposed to irradiation.693 A follow-up study identified a subset of four

c to CL, and occurred at pH values higher than 6, suggesting a requirement for deprotonated CL and positively charged cyt c.656 Notably, cyt c reacts faster with lipid-derived hydroperoxides than with H2O2.657 Cyt c reacts with cholesterol- and linoleic acid hydroperoxides via a homolytic mechanism that generates lipid and protein radicals and promotes inactivation of cyt c (bleaching) and formation of dimers, trimers, and tetramers.657 Therefore, it is possible that pathological conditions that favor the formation of lipid hydroperoxides may contribute to mitochondrial stress via a process that is enhanced by cyt c. 4.2.4. CL−Cyt c Interaction and the Mitochondrial Regulation of Apoptosis. 4.2.4.1. Initiation of Apoptosis. The participation of the mitochondria in apoptosis is a very well-documented process, and both cyt c and CL play a primordial role. Two steps are crucial for the triggering of this event: the first is the release of proteins from the mitochrondrial intermembrane space such as cyt c,658,659 and the second is the alteration of multiple parameters leading to dysfunction.660 The time course of cyt c release has been described in terms of five consecutive events: (i) migration of CL from the inner to the outer leafleat of the inner mitochondrial membrane, facilitated by phosphorylation of the enzyme scramblase;661−663 (ii) formation of a high affinity complex between cyt c and CL with enhanced peroxidase activity;43,274,292,630,652,664,665 (iii) selective peroxidation of CL mediated by cyt c546,666−668 and reactive oxygen species;669−671 (iv) dissociation of cyt c from oxidized CL due to a decreased affinity of the oxidized lipid;658 and (v) participation of said oxidized CL in the permeabilization of the mitochondrial membrane.546 Regarding steps (iii)−(v), in 2005 Kagan and colaborators determined that CL would be the only phospholipid suffering an early oxidation during the onset of apoptosis, this oxidation being catalyzed by the specific peroxidase activity of cyt c toward CL, and essential for the liberation of pro-apoptotic factors from mitochondria to cytosol.546 Conformation of cyt c itself is another factor involved in its liberation and the onset of apoptosis. Studies using the M80A cyt c mutant, which has an inherently enhanced peroxidase activity, showed that, even though this cyt c variant readily translocates to the cytoplasm, it did not remain in that subcellular space but continued to migrate toward the nucleus, avoiding, therefore, the onset of apoptosis.545 Interestingly, for knock-in animals that generated the K72A mutant cyt c, that is, a variant with altered lipid binding site A, it was observed that the modified protein was able to transfer electrons in the respiratory chain, but it did not activate Apaf-1.579 In later stages of apoptosis, the cytosolic cyt c can catalyze the peroxidation of another anionic phospholipid, phosphatidylserine (PS), present in the plasma membrane and playing a part in the externalization of said lipid that signals the phagocytosis onset via macrophage activation.672 4.2.4.2. Mechanisms of Cyt c Release. As stated before, cyt c release is a process that depends on the formation of superoxide radical and hydrogen peroxide,669 and the liberation of cyt c ultimately depends on the formation of a pore in the mitochondrial outer membrane. There are two routes that lead to the formation of the pore via an increase of ROS, a Ca2+dependent673,674 and a Ca2+-independent mechanisms.675,676 In the Ca2+-dependent pathway, oxidative stress results in an increase of this ion, which by itself can affect the binding of CL to several respiratory complexes, including cyt c, which leads to 13418


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additional drugs acquired from the ZINC library,695,696 L254614, 9009967, 002-126-168, and 016-629-555, which were as competent or better than TPP-6-ISA for the inhibition of peroxidase activity of cyt c.697 These compounds reduced the peroxidase activity of cyt c 3 to 25% of control with IC50 in the range 0.15−0.71, and are thus promising drug candidates for further investigation.697 Aside from this, drugs that could selectively inhibit the peroxidase activity of cyt c may help to distinguish underlying mechanisms between its canonical and alternative functions.697 4.2.6. Cyt c Functions in DNA Regulation and Redox Signaling. 4.2.6.1. DNA Regulation. Apart from the role of cyt c in the intrinsic apoptotic pathway, immunofluorescence and subcellular fractionation studies showed that under conditions of apoptosis as well as in nonapoptotic cells,545 cyt c localizes to the nuclei of cells.698 It was documented that buildup of cyt c in the nucleus was mirrored by export of nuclear acetylated histone H2A, but not of unmodified H2A into the cytosol, with the concomitant induction of chromatin condensation.698 This study provided the first line of evidence for the involvement of cyt c in nuclear events of apoptosis. An in vivo study where adult male Wistar rats where chemically induced to develop seizures showed translocation of cyt c as well as of lysosomal proteins cathepsins B and D into the nucleus of cells before the onset of signs of irreversible neuronal death.699 It was proposed that this event of nuclear translocation of death-promoting proteins constituted part of the mechanism of seizure-induced nuclear pyknosis and fragmentation of DNA.699 Global proteomic studies aimed at elucidating the interactome and signalosome of apoptosis identified the oncoprotein SET/ template activating factor (TAF)-Ibeta (SET/TAF-Ibeta), a protein that belongs to the nucleosome assembly protein family of histone chaperones, as a target for cyt c, after its release from mitochondria in apoptotic human cells.529,561 A follow-up study showed structural and functional evidence that DNA damage is accompanied by the subsequent association of histone chaperone SET/TAF-Ibeta with cyt c.44 The results from the study showed that cyt c translocated into the nucleus and acted as a competitor of SET/TAF-Ibeta binding to core histones, thereby inhibiting its inherent nucleosome assembly activity.44 An electrophoretic mobility assay confirmed the disruptive effect of increasing doses of cyt c on SET/TAF-Ibeta-histone complex formation (Figure 30). 4.2.6.2. Redox Signaling. Cyt c operates in cellular compartments with varying redox conditions. For instance, alterations in nitric oxide homeostasis that stimulate Tyr nitration lead to gain in peroxidase activity, whereas conditions that would favor heme nitrosylation (Fe-NO)700 would inhibit turnover of H2O2.701 Given the inherent resistance of cyt c to axial ligand exchange, it has been proposed that conformational changes that weaken the coordination environment of the heme at the fifth or sixth position are a prerequisite for •NO binding to the heme. One such conformational effector is CL, which has been shown to increase the reactivity of cyt c toward • NO, thus making it a plausible candidate for the pro-apoptotic effects of Fe−NO cyt c.702

Figure 30. Inhibitory effect of cyt c on the binding of SET/TAF-Iβ to histones in an electrophoretic mobility assay. Reduced mobility of SET/TAF-Iβ associated with histones is depicted in lane 4. The addition of increasing concentrations of cyt c (lanes 5−14) led to inhibition of the chaperone−histone complex. Lane 15 shows the mobility pattern of preformed cyt c-SET/TAF-Iβ complex. Cyt c and SET/TAF-Iβ migrate in different directions due to their opposite charges. Adapted with permission from ref 44. Copyright 2015 National Academy of Sciences.

c in serum revealed that serum itself interfered with the detection of cyt c.711 The interfering factor was isolated and identified as leucine-rich alpha-2-glycoprotein-1 (LRG1),711 a protein that appears to be involved in neutrophil degranulation.712 Follow-up investigation of this interaction showed that LRG-1 has sequence similarity with Apaf-1, and that these two proteins compete for cyt c binding in vitro.713 At the functional level, it was found that, unlike Apaf-1, LRG-1 functions as a survival signal. Lymphocytes grown in culture medium devoid of LRG-1 were more sensitive to the cytotoxic effect of exogenous cyt c.713 An independent study confirmed the direct interaction of cyt c with LRG-1 by native PAGE and surface plasmon resonance, as well as the protective role of LRG-1 against cytotoxicity caused by autologous extracellular cyt c.714 The extracellular presence of cyt c could hold diagnostic value, as will be discussed in upcoming sections.

5. CYTOCHROME c UNDER STRESS Conditions of cellular stress characterized by the concomitant production of oxidants or abnormal phosphorylation and methylation homeostasis can lead to the occurrence of posttranslational modifications that result in gain or loss of function. This has been documented for cyt c, and includes nitration of Tyr residues, phosphorylation of Tyr and Thr residues, methylation and acetylation of Lys residues, and sulfoxidation of Met residues. 5.1. Post-translational Modifications in Cyt c

5.1.1. Nitration of Cyt c. A summary of post-translational modifications and natural single amino acid variants of cyt c that have been reported to date is presented in Table 4. Among these, the most deeply studied is the nitration of the various Tyr residues present in cyt c, under conditions relevant to pathologies associated with oxidative stress.715,716 hh-Cyt c possesses four Tyr residues of which Y74 and Y97 are exposed to the solvent, Y67 is buried within the protein skeleton, and Y48 exhibits enough solvent accessibility to undergo phosphorylation33 (Figure 31). Methods for the production and isolation of mono and dinitrated variants of cyt c have been developed using low fluxes of peroxynitrite and tetranitromethane.715−717 Nitration of Tyr residues occurs in vivo,718−720 and endogenous nitrated cyt c has been identified in cultured cells and in ex vivo and in vivo disease models characterized by nitroxidative

4.3. Extracellular Cyt c

While the vast majority of the literature has covered the roles of cyt c inside the cell, the protein also partakes in extracellular functions. First evidence of this emerged from the identification of cyt c in serum, which suggested aberrant apoptosis in various pathological conditions.703−710 An ELISA assay to measure cyt 13419


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Table 4. Structural Modifications That Alter Cyt c Functiona modification

organism

Ala81His Lys79His acetylation of Lys

yeast yeast mouse

trimethyl Lys72Ala

yeast

Gly41Ser

human

Tyr48His

human

Tyr48His Gly41Ser Gly41Thr Gly41Ala nitration of Tyr46

yeast human mouse

nitration of Tyr48

human

nitration of Tyr74

human

nitration of Tyr74

horse

phosphomimetic Tyr48Glu

human

phosphomimetic Tyr97Glu individual nitration of Tyr46, Tyr48, Tyr67, Tyr74, and Tyr97

human human

sulfoxidation of Met80

horse

a

human

effect

ref

alkaline conformer less stable than native conformer alkaline conformer more stable than native conformer decrease of positive charge increased hydrophobicity lengthening of the side chain, steric effects disrupted Fe−Met80 axial bond higher peroxidase activity increased apoptosis increased spin density on pyrrole ring C and a faster electron selfexchange rate higher peroxidase activity stabilization of protein radicals increased apoptosis decreased respiration lower heme midpoint potential (ca. 80 mV) higher peroxidase activity as compared to native cyt c no changes in peroxidase activity as compared to cyt c bound to cardiolipin rearrangement of H-bond network high-spin heme facile alkaline transition defective apoptosome protein degradation rearrangement of H-bond network high-spin heme facile alkaline transition defective apoptosome degradation increased peroxidase activity disrupted interaction with caspase-9; inhibition of apoptosis lower pKa for alkaline transition lower midpoint potential deprotonation of Tyr74 high peroxidase activity lower heme midpoint potential (ca. 80 mV) lower pKa alkaline transition disrupted Apaf-1-mediated caspase activation disrupted interaction with cardiolipin less stable than native protein lower midpoint potential nitration effects are additive lower affinity for Apaf-1 disrupted caspase activation high-spin heme high peroxidase activity

228 228 739,740

18 37,240,246,532

36 741 241

729,742

729,742

728 31

33

33 725,726

35

Adapted with permission from ref 106. Copyright 2016 American Chemical Society.

stress.719,721,722 From a mechanistic standpoint, exposure of cyt c to nitrating conditions such as treatment with peroxynitrite yields preferential nitration of Y74 or Y97, both of which are exposed to the solvent.719 In contrast, nitration of Tyr residues mediated by H2O2-dependent chemistry is proposed to favor mononitration of Y67, a residue located adjacent to the heme of cyt c.713 This pathway would involve coordination of H2O2 to the heme to form a “compound I-like” species that oxidizes Y67 to yield Tyr• (radical). Reaction of Tyr• with •NO forms 3nitroso-Tyr, which in the presence of H2O2 oxidizes to form 3nitro-Tyr. Conditions where NO2− can be oxidized to •NO2 would also lead to the formation of 3-nitro-Tyr.552 Biochemically, the major effect is that nitration of cyt c disrupts its ability

to activate caspase-9, thereby hampering apoptosis.659,723 At the molecular level, incorporation of a nitro group to Tyr residues reduces the pKa of the phenolic −OH group by approximately 3 units, and increases steric bulk and molecular weight by 45 Da (Figure 31a and b). For example, nitration of Y74 weakens the axial Fe−M80 bond, enabling more facile transition to alkaline conformers of cyt c.30 This change in the electronic properties of the heme led to a reduction of the midpoint potential, which compromises the ET function of cyt c in the mitochondrial respiratory chain,716,724,725 but the exact functional consequences are difficult to assess. At the functional level, it was shown that kidney mitoplasts devoid of cyt c were less proficient than their control counterparts in catalyzing 13420


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Figure 31. Chemistry and conformational impact of Tyr nitration in cyt c. (a) Deprotonation of the alcohol group of Tyr has a pKa of 10.5. Oxidation to form tyrosyl radical and reaction with •NO2 to form 3-nitrotyrosine reduces the pKa of the phenolic group, thereby habilitating deprotonation under physiological conditions (pKa = 7.1). (b) Structure of natural human cyt c variant G41S (PDB entry 3NWV) nitrated at residue Tyr74 (NO2 is depicted as spheres). A mesh surface diagram shows increased steric bulk upon incorporation of the nitro group. (c) Color-coded arrangement of flexible Ω loops (residues 12−28, blue; residues 29−40, orange; residues 41−57, red; and residues 70−85, yellow) of human cyt c variant G41S. (d) Position of Tyr residues within a semitransparent surface representation of human cyt c. Tyr46 and Tyr48 of loop 41−57 are depicted as red sticks, and Tyr 74 located in loop 70−85 is shown as yellows sticks. Residue Tyr67 is part of a helical structure and is herein displayed as cyan sticks. Reprinted with permission from ref 106. Copyright 2016 American Chemical Society.

H2O2-induced mitochondrial lipid peroxidation.726 Remarkably, lipid peroxidation was directly proportional to the concentration of cyt c, and remained near control levels even when cyt c concentration was reduced to 34% of control values.726 This suggests that near full depletion of cyt c would be required to elicit severe functional consequences. Incorporation of one or two nitro groups to cyt c reduces its midpoint potential as compared to the native protein.727 However, biophysical studies indicate that perturbations of the heme environment due to Tyr nitration and local electric fields involve different mechanisms.727 Controversy exists regarding the H-bonding interactions of 3-nitro-Tyr residues in cyt c and the properties of the Fe−M80 bond. The individual nitration of Y74 (exposed to the solvent) has been shown to favor an early alkaline transition, with a pKa value of 7.1.30 Thus, cyt c nitrated in position Y74 is able to adopt the alkaline conformation at physiological pH with the characteristic substitution of the native axial ligand M80 by a Lys residue to form a stable low-spin hexacoordinated complex.30 It was hypothesized that nitration of Y74 influences heme geometry by steric perturbation of the highly flexible Ω loop 70−85, which is transmitted to the heme center via the neighboring Y67.30 Notably, replacement of Y67 with Phe increased the pKa of the alkaline transition to 11, antagonizing the effect of nitration at Y74. This has been interpreted in the

context of a H-bond interaction between Y67 and the sulfur atom of M80 that would mediate this long-range effect via a spatially contiguous network of amino acid residues Y74-E66Y67-M80-Fe.30 This nitrated variant of cyt c exhibits a drastically downshift redox potential at neutral pH, as well as increased peroxidase activity.31 Resonance Raman titrations show that deprotonation of the nitrated Y74 residue and replacement of the heme axial ligand (Met → Lys) occurs with nearly identical apparent pKa values,31 but MD simulations show only subtle structural alterations of the Y74 nitrated protein (for both protonated and deprotonated Y74), with respect to unmodified cyt c. Steered MD simulations, on the other hand, reveal a significant stabilization of the Lys/His alkaline conformer when Y74 is nitrated and deprotonated, as compared to the non-nitrated protein.31 Structurally, Y67 is the only Tyr residue restrained within a helical structure, positioned close to the heme (Figure 31c and d). Replacement of Y67 by Arg in H-cyt c led to axial Fe−M80 bond rupture, weak distal ligation by Arg, and an 8-fold gain in peroxidase activity.96 These properties resemble the characteristics of the Y67R variant of yeast iso-1-cyt c.148 Further examination between human and yeast cyt c showed that replacement of Y67 by His in human cyt c had no impact on peroxidase activity or Fe-Met80 ligation,96 whereas the yeast counterpart exhibited a marked gain in peroxidase activity.148 13421


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phenotype except for its lower stability as compared to the native protein. Cyt c variant Y48E exhibited a lower pKa for the alkaline transition, a reduced midpoint redox potential, and an antagonic effect toward Apaf-1-mediated caspase activation.33 These findings led to the proposal that cyt c phosphorylated at position Y48 may act as an antiapoptotic switch in vivo.33 Chemically, phosphorylation occurs at Tyr residues other than the preferred substrates for nitration, which render phosphorylation and nitration viable as concerted structural and functional events. A mimic of phosphorylated cyt c incorporating the noncanonical amino acid p-carboxymethyl-L-phenylalanine (pCMF) at position 48 (Y48pCMF) was shown to destabilize the axial Fe−M80 bond and to lower the pKa for the alkaline transition of the protein.244 Recent NMR studies on this mimetic variant reveal conformational differences and enhanced dynamics around the artificial pCMF residue, which could explain the enhanced peroxidase activity as compared to the WT protein.245 Interestingly, the Y48pCMF mutant was shown to impair channeling between respiratory complexes III and IV. Ex vivo, phosphorylation of cyt c has been documented as a signaling step in frozen thawed buffalo spermatozoa.730 In vivo, cyt c from brains of pigs treated with insulin showed phosphorylation of Y97.731 In the same study, this posttranslational modification was not detectable in brains of pigs isolated after ischemia-reperfusion.731 Treatment of rats with insulin in the absence of ischemia-reperfusion showed substantial phosphorylation of Y97, which suggests that this modification is associated with insulin signaling.731 Isolation of cyt c from bovine kidney demonstrated tissuespecific phosphorylation of the amino acid residue T28.732 This modification leads to partial inhibition of respiration, but has no effect on the activation of apoptosis.732 Allegedly, phosphomimetic mutants T28D and S47D of H-cyt c do not exhibit significant variations of either pKa or E° values, but present enhanced peroxidase activity with respect to the WT protein.733 5.1.3. Sulfoxidation of Cyt c. Two concentration thresholds define physiological levels of H2O2: one that enables redox signaling (H2O2 1−10 nM) and has been termed oxidative eustress, versus another state where supraphysiological concentrations of the oxidant (H2O2 > 100 nM) lead to damage of biomolecules and is defined as oxidative distress.734 Cyt c reacts with H2O2 leading to sulfoxidation of axial M80 and, eventually, to bleaching of the heme group, depending on the relative concentrations.32,35 Notably, the phosphatemediated interaction of cyt c with the main components of the mitochondrial membrane, that is, the zwitterionic lipids phosphatidylcholine and phosphatidylethanolamine, leads to specific sulfoxidation of M80 with submillimolar doses of H2O2, with a concomitant gain of peroxidase activity.32 Sulfoxidated cyt c exhibits a 4-fold greater affinity for CL as compared to the unmodified protein, which could potentially amplify the proapoptotic sequence of reactions triggered by cyt c−CL interactions.32 While detection of this variant of cyt c ex vivo and in vivo may prove challenging, these valuable in vitro studies predict that this post-translational modification could hold biological relevance under conditions of oxidative distress. 5.1.4. Methylation of Cyt c. Trimethylation of K72 occurs in cytochromes from fungi to plants but has not been documented in higher animals. Sequence analysis of the amino acid stretch 67−77 across species suggested that Y74 located in the vicinity of K72 is a determinant for trimethylation of K72.735 For example, replacement of Y74 for Lys abolishes trimethylation of K72, although the Y74F

This demonstrates that minute structural differences in the Hbond network of these cyt c variants may deeply impact their peroxidase activity.148 A structural analysis of yeast iso-1 cyt c indicated that the geometry of Y67 is such that it could itself serve as a weak axial ligand replacing Met80 upon alkaline transition.215 Strikingly, molecular dynamics calculations performed on mammalian cyt c suggested the presence of a hydrogen bond between Y67 and T78,728 the latter residue belonging in the same folding unit, but no evidence of the previously postulated H-bond between residue Y67 and axial ligand M80.215 A study combining wet-bench and computational data showed that the use of a search algorithm that includes optimized parameters to describe H-bonds with an S atom as acceptor confirms the existence of a weak Y67−M80 H-bond that tunes ET and involves conformational motions of the flexible Ω loops 20−30 and 70−87.146 Furthermore, Ω loop 70−85 was shown to contribute substantially to the axial ligand substitution reaction that takes place during the alkaline transition.193 While formation and rupture of H-bonding interactions via residue Y67 may be a highly dynamic event, it is broadly accepted that far-reaching effects control heme electronics and, therefore, the peroxidase activity of cyt c. Resonance Raman studies investigating individual and successive substitutions of Tyr by Phe residues demonstrated additive effects in redox potential, but no direct correlation with previously reported values of peroxidase activity715,728 or with the relative contribution of each non-native conformer in these mutagenic variants.727 It is important to know that this apparent lack of correlation may not accurately reflect the authentic behavior of each variant, as the technique itself does not measure the conformational changes that accompany each coordination state within the alkaline ensemble. In sum, modification of Y74 and Y67 is fatal to the activity of cyt c both in cellular respiration and apoptosis, by facilitating the alkaline transition and the formation of alternative conformers dysfunctional for these important cellular roles. This was best illustrated by the finding that a conformer of cyt c where M80 was replaced with Ala had elevated peroxidase activity and underwent spontaneous translocation from mitochondria to the cytoplasm and nucleous even in the absence of apoptotic signals.545 The efflux of the M80A cyt c conformer from mitochondria was dependent on peroxidase activity, but the specific oxidation targets remain to be identified.545 The same study characterized high-spin, non-nitrated variants of cyt c, which had high peroxidase activity and were immunoreactive toward mAb 1D3.545 Because nitrated wild-type cyt c also undergoes translocation to extra-mitochondrial compartments, the M80A variant is considered a model of a naturally occurring alternative conformation of cyt c. In addition to translocation across compartments, the eliciting of alternative variants of cyt c has also been shown to affect protein turnover. Individual nitration of residues Y46 and Y48 of human cyt c led to specific protein degradation upon transition to a high-spin state.729 In conclusion, it is possible that nitration of individual Tyr residues leads to various alternative conformations of cyt c, and this property could confer functional diversity and specificity in vivo. 5.1.2. Phosphorylation of Cyt c. Cyt c is a substrate for phosphorylation, particularly at Tyr residues at positions 48 and 97.33 Site-directed mutagenesis and biophysical characterization of phosphomimetic cyt c mutants Y48E and Y97E indicate that these phosphorylation sites may be operative under physiological conditions. Mutant cyt c Y97E has an unremarkable 13422


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variant is trimethylated to the same level as the WT protein.735 Similar substitutions in other regions of the protein had no effect on K72 methylation. Thus, K72 and a nearby aromatic residue are proposed to be critical for trimethylation of iso-1cyt c. Further, trimethylation of K72 of yeast cyt c requires a dedicated methyltransferase denominated Ctm1p.736 Ctmlp is located in the cytosol, which is consistent with the view that the natural substrate is apo-cyt c and not mitochondrial holo-cyt c.736 Studies where yeast cyt c was expressed in E. coli suggested that in the absence of trimethylation, K72 could serve as an exchangeable axial ligand to the iron center of the heme.205 Yeast iso-1-cyt c does not partake in intrinsic apoptosis requiring the activation of caspases. In vitro studies showed that this is not necessarily associated with trimethylation of K72, as nonmethylated yeast iso-1-cytc still did not activate caspases.737 Crystallographic analysis of a K72 to Ala mutant of iso-1-cyt c showed a disrupted Fe−M80 bond with replacement of this axial coordination position by a water molecule.18 This variant of iso-1-cyt c possesses increased peroxidase activity that appears to arise from a wider opening of the heme crevice as compared to the corresponding wild-type protein and as compared to the cyt c of higher animals.18 Interestingly, expression of rat cyt c in S. cerevisiae led to 66% yield in trimethylation of K72,738 and 40% overall expression as compared to native iso-1-cyt c from yeast. These results do not concur with sequence predictions on the importance of aromatic residue conservation in the vicinity of K72, and suggest alternative mechanisms dictating methylation of K72 in yeast, perhaps related to the existence of dedicated methyltransferases, such as Ctm1p.736 The heterologous expression of rat cyt c in yeast, with near normal conservation of function, suggests that the 40% in amino acid conservation between the species is not critical for the import and functional maturation of cyt c in the mitochondrion. 5.1.5. Acetylation of Cyt c. Early studies investigating the effect of chemical acetylation of ca. 60% of the Lys residues of equine cyt c revealed impairments in the reduction of cyt c by mitochondrial and microsomal partners and in its oxidation by mitochondrial cytochrome c oxidase.739 Interestingly, acetylated cyt c had comparable rates of reduction by superoxide as compared to the native protein.532 Acetylated cyt c occurs endogenously, as demonstrated in a proteomic study utilizing extracts of HeLa cells and murine mitochondria.740 While this post-translational modification is certain to decrease the positive charge of cyt c, increase hydrophobicity, and incorporate steric hindrance by lengthening of the side chain of the substrate Lys residue, the functional consequences are currently unknown.

summarizes the cyt c interacting partners identified in this study.561 ́ Table 5. Interaction Partners of Cyt c Reported by MartinezFabregas et al.561 and González-Arzola et al.745 protein name

protein abbreviation

casein kinase II subunit β chaperonin containing TCP1 subunit 2 coronin-like protein eukaryotic translation initiation factor 2 α fructose 1,6-bisphosphate aldolase A ribosomal protein S7 tubulin β chain tumor rejection antigen 1 14-3-3 epsilon heterogeneus nuclear ribonucleoprotein C1/C2 histone-binding protein RBBP7 minichromosome maintenance complex 6 minichromosome maintenance complex 7 SET nuclear oncogene acidic nuclear phosphoprotein 32B heterogeneus nuclear ribonucleoprotein L nucleolin nucleosome assembly protein 1-like 4 Ser/Thr kinase receptor associated protein ATP synthase subunit β heat shock 70 kDa protein histone chaperone

CSNKIIβ CCT2 CORO1A elF2α ALDOA RPS7 TUBB Hsp90B1 YWHAE hnRNP C1/C2 RBBP7 MCM6 MCM7 SET ANP32B hnRNP L NCL NAP1L4 STRAP ATP5β HSPA5 NRP1

While this study permitted the identification and validation of novel interacting partners under controlled experimental conditions relevant to apoptosis, it is possible that cyt c employs additional physical interactions to attain its multiple cellular functions. The unified human interactome (UniHI, accessed March 2017)744 retrieves a total of 255 interacting partners for human somatic cyt c. Some of these interactions have been validated experimentally, while others are based on prediction of protein−protein interactions. More recently, it was found that cyt c competes with histones for the binding site of the histone chaperone NRP1 in Arabidopsis thaliana.745 Transfer RNA (tRNA) has also been found to interact with the released cyt c to prevent the formation of the apoptosome complex, thus preventing cell apoptosis.746−749 In recent years, a new family of hexacoordinated globins that express in the nervous system of humans and other mammals has been identified (neuroglobin; Ngb).750,751 While the actual physiological function of Ngb remains a matter of debate, it has been experimentally and computationally shown that Ngb is able to reduce cyt c.752,753 Interestingly, it has been hypothesized that Ngb may regulate the pro-apoptotic activity of ferric cyt c released from the mitochondria by reducing it to ferrous cyt c, which is no longer pro-apoptotic.754,755

5.2. Interactions of Cyt c with Other Biomolecules

Given the exposure of cyt c to various cellular compartments and components, elucidating its interactome is a matter of substantial interest. In addition to the well-established interacting partners such as Apaf-1 and antiapoptotic protein Bcl-XL,743 a targeted proteomic study using affinity chromatography with immobilized cyt c elucidated novel interacting partners relevant to apoptosis and presumably new functions of cyt c.561 The study identified interactions of cyt c with prosurvival and antiapoptotic proteins that take place after cyt c release into the cytoplasm.561 Jurkat cells were grown under control conditions (RPMI 1640 medium) or in the presence of the apoptosis-inducing drug camptothecin (10 μM). Table 5

5.3. Naturally Occurring Pathogenic Mutants of Cyt c

Given the essentiality of cyt c, very few viable natural variants of this protein have been documented in humans. As discussed earlier, Li et al. demonstrated the embryological lethality of knockout mice for somatic cyt c.577 Mice lacking both copies of the cyt c allele (cyt c−/−) were not viable beyond midgestation, and the embryos have a reduced size.577 Three pathogenic mutations in cyt c have been reported to date, and the affected individuals present autosomal dominant thrombocytopenia 4 13423


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undergo increased release into the cytoplasm upon apoptotic stimuli as compared to wild-type cyt c.241 This is in good agreement with the fact that patients with thrombocytopenia do not present signs of elevated apoptosis. Noteworthy, while G41 is a highly conserved residue in all eukaryotic cyt c, the effect of H-cyt c G41S in binding Apaf-1 appears to be species-specific. Substitution of G41 in mouse or in Xenopus led to a marked decrease in caspase activation in embryo extracts, an effect not observed in the human counterpart.759 5.3.2. Cytochrome c Tyr48His. The description of a second mutation in the human cyt c gene was provided by Rocco and co-workers, with mutation Y48H in an Italian family.36 Four members of the family were affected by thrombocytopenia, and the patient of the case study was a 3year-old boy ascertained though a routine blood test.36 Similar to patients carrying the G41S mutation, the affected members of this family had thrombocytopenia with decreased platelet count of otherwise normal size and morphology, but without prolonged bleeding episodes.36 To probe the effect of this mutation, the authors constructed experimental models in yeast and in immortalized mouse lung fibroblasts. Variant Y48H exhibited a reduction in oxygen consumption of about 30−40% as compared to that observed in cells expressing the wild-type protein, and an increase of apoptotic activity,36 that is, similar to the G41S mutation. The yeast iso-1-cyt c Y48H mutant showed a slight change in redox potential as compared to the wild-type protein (210 mV vs 290 mV of wild-type cyt c).741 It was hypothesized that patients harboring both mutations (cyt c G41S and Y48H) would have a premature pro-platelet release within the bone marrow resulting in ineffective platelet production.36,532 This hypothesis is supported by the presence of platelet-like structures in the bone marrow of patients with thrombocytopenia.760 These platelet-like structures are released into the marrow space by a mechanism independent of pro-platelet formation, and they lack the microtubule coil characteristic in circulating platelets.760 This phenotype was first attributed to the enhanced apoptotic activity of cyt c mutants,36,760 but this hypothesis has been discarded due to lack of proof for the existence of apoptotic megakaryocytes in the bone marrow.760 The mechanism of platelet release without pro-platelet formation is currently unknown. In vitro, megakaryocytes of patients with thrombocytopenia are able to produce proplatelets normally, releasing platelets with the normal microtubule coil.760 5.3.3. Cytochrome c Ala51Val. Recently, Ong and coworkers performed whole exome sequencing of 37 patients with thrombocytopenia and of 18 related family members. This study identified three subjects who are likely to have thrombocytopenia caused by another mutation in the cyt c gene: A51V.760 Currently, there is no information on the structure and function of this cyt c mutant, and thus functional insight awaits further investigation. 5.3.4. Other Causes of Thrombocytopenia. Not all cases of genetic thrombocytopenia are caused by mutations in the cyt c protein. In 2009, the same group that described the Y48H mutation described another family in Italy with thrombocytopenia, but this family does not present any mutations in the cyt c gene.761 In 2016 a whole genome sequencing study performed on 55 patients with thrombocytopenia identified mutations in several proteins including transcription factors, proteins involved in cytoskeletal rearrangement, and others

(OMIM 612004). Thrombocytopenia refers to a heterogeneous group of inherited diseases characterized by low platelet counts (less than 150 000 platelets/μL in blood). The three described cyt c mutations are located in the Ω-loop that includes residues 40−57, G41S, Y48H, and A51V, and are described below. 5.3.1. Cytochrome c Gly41Ser. The first mutation identified in the gene of cyt c was the G41S mutation, described for a family from New Zealand, presenting autosomal dominant thrombocytopenia.532 The mutated residue, G41, is highly conserved and is invariant among 113 eukaryotic species.756 G41 belongs in the 15 most conserved cyt c residues by comparison of the primary sequences of cyt c from about 300 species.69 All 29 members of the family under study showed a decrease in platelet count, with a mean of 109 000/ μL as compared to 260 000/μL in healthy subjects. Platelets from individuals carrying the G41S mutation have normal volume and morphology, with normal count of other peripheral blood cells, in contrast with other inherited thrombocytopenias characterized by larger platelets as compared to unaffected individuals.757 The cyt c G41S mutant has been studied in vitro. Recombinant cyt c G41S exhibits an oxygen consumption rate similar to that of wild-type cyt c, in good agreement with the fact that the affected members of this family do not present any symptoms of a mitochondrial respiration dysfunction.36 Other authors who constructed a model of yeast with the analogous cyt c mutation (G46S) observed a reduction in oxygen consumption of about 40% as compared to that observed in cells expressing the wild-type protein.36 When they used immortalized mouse lung fibroblasts as a model carrying all copies of cyt c with the mutation G41S, they also observed a decrease of 40% in oxygen consumption. 36 Although recombinant G41S H-cyt c has an increased peroxidase activity,532 the affected patients do not exhibit phenotypic indication of abnormal apoptosis.532 The most remarkable finding is that cyt c G41S mutant was unable to assemble the apoptosome in vitro, as up until that date, it was thought that the interactions of cyt c with Apaf-1 were only mediated by charged surface residues.579,758 NMR experiments and DFT calculations reveled that the G41S mutant of H-cyt c presents altered spin density, particularly at the level of the partially solvent-exposed pyrrole ring C, as well as faster electron self-exchange.37 On the basis of these findings, it was proposed that the G41S mutation may enhance Apaf-1 binding and activation, or it can promote the reoxidation of cyt c, apoptosome assembly, and activation.37 Another research group reported that in cyt c G41S there is an increase in the dynamics of the 40−57 Ω-loop that promotes the dissociation of the M80 ligand, increasing the peroxidatic activity of cyt c.247 However, mutants of G41 in mouse cyt c exhibit increased peroxidase activity without changes in the M80−Fe bond strength, indicating that there must be another mechanism for increased peroxidase activity.241 It was hypothesized that the G41S mutant increases the accessibility of H2O2 to the heme, enhancing its peroxidase activity, probably due to the movement of the 40−57 Ω loop, and the consequent change in H-bond network around the heme moiety.241 Recombinant G41S mutant stabilizes the multiple radical formed in cyt c−phospholipid complexes under H2O2 treatment, and this enhances the pro-apoptotic activity of the mutant.246 Despite the increase in peroxidase activity, the G41S mutant did not show increased affinity to CL and does not 13424


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proteins of unknown function.762 Approximately 30 different genes lead to thrombocytopenia. About one-half of these proteins are involved in transcription regulation, cytoskeletal organization, apoptosis, thrombopoietin signaling, granule trafficking, receptor signaling, megakaryocyte differentiation, platelet production, and platelet removal, and others remain to be characterized.763−766 It would be of interest to determine whether these genes or their expressed proteins interact with the pathways of cyt c, particularly in patients with similar clinical phenotype. 5.3.5. Human Cyt c Mutations with Unknown Consequences. Results from a massive sequencing study of the exomes of 60 706 unrelated individuals were made available through the ExAc database.767 This study identified 19 missense mutations in the human somatic cyt c (Table 6).

have diagnostic value. One such scenario is that of antiretroviral therapy.768 Work by Langs-Barlow and colleagues identified elevated cyt c in plasma in HIV-infected patients receiving antiretroviral therapy as compared to healthy controls. It was found that after correction for CD4 count, viral load, and duration of the HIV infection, patients on antiretroviral therapy were 7.86 times more likely to have values of plasma cyt c higher than 0.216 ng/mL.768 Another study showed elevated serum cyt c in patients with hepatitis C.772 This study revealed that patients with greater scores of histological activity index (which reflect TNF-alpha activity, and therefore inflammation) exhibited increased serum levels of cyt c (range 57−426 ng/ mL) as well as of caspases 8 and 3.769 Further, elevation of cyt c correlated with apoptosis activity markers caspase 8 and 3.769 Two studies have shown that elevation (defined by one study as cyt c levels higher than 25 ng/mL703) of plasma cyt c occurs during chemotherapy and serves as a useful marker of spontaneous cell death in various types of cancer.703,704 As can be gathered from available studies, establishing the range of cyt c values in the healthy population requires further investigation.

Table 6. Mutations Found in the Cyt c Amino Acid Sequence with Their Corresponding Allelic Frequencies and Regions of Origin, Extracted from the Analysis of 60 706 Unrelated Individualsa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

cyt c mutant

allele frequency (×10−6)

origin of population

Gly1Asp Ile11Phe Met12Ile Thr28Ala His33Tyr Arg38Trp Ser47Ala Ser47Phe Ala50Thr Ala50Val Ala51Thr Asn52Ser Ile57Val Asn70Ser Ile75Val Ile81Asn Val83Ile Asp93Asn Thr102Ala

8.546 8.356 75.09 8.268 8.263 8.265 24.80 49.61 8.267 8.267 8.268 24.80 16.54 8.279 16.58 8.317 8.327 8.393 17.05

South Asian African Latino European European European South Asian South Asian Latino European European European European European African European European European European

6. TECHNOLOGICAL APPLICATIONS OF CYTOCHROME c The redox and coordination plasticity of the heme moiety of cyt c have motivated its use as a biosensor for small ligands of biological relevance including hydrogen peroxide, superoxide, nitric oxide, and nitrite. 6.1. Third Generation Electrochemical Biosensors

A biosensor can be defined as a device consisting of a biological recognition element in contact with a transducer, which converts the biological recognition reaction or biocatalytic process into a measurable electronic signal. Third generation biosensors are based on direct electron transfer (DET) where the absence of mediators results in many advantages. DET devices usually show superior selectivity not only as they operate in a potential window closer to the redox potential of the enzyme, being therefore less prone to interfering reactions, but also because of the simplicity of the reaction system. Another attractive feature of these systems is the possibility of modulating the properties of the analytical device by means of protein modification with genetic or chemical engineering techniques as well as novel interfacial technologies. The development of these biosensors has been somewhat limited due to the difficulty of achieving direct electrical communication between redox proteins and electrode supports. Therefore, extensive studies have been carried out toward finding novel surface functionalization, new electrode materials, and new proteins that have direct electron transfer properties. Significant efforts have been dedicated to developing methods for immobilizing cyt c in such an orientation that maximizes electrode−heme electronic coupling and, therefore, allows for DET.158,770 Given that the partially exposed heme edge of cyt c is enclosed by a ring-shaped arrangement of positively charged lysine residues, this patch constitutes the preferential binding domain for electrostatic adsorption on negatively charged surfaces, thus leaving the heme edge oriented toward this surface.13 In the case of metal electrodes, the surface is usually coated with self-assembled monolayers (SAMs) of ω-functionalized alkanethiols carrying charged head groups such as carboxylate, phosphonate, or sulfonate for subsequent cyt c adsorption.8,13 Alternatively, cyt c can be adsorbed on mixed

a

Data were taken from the Exome Aggregation Consortium (ExAC).767

While no information is available on whether these mutations are related to pathologies in the patients analyzed, the list of amino acid substitutions and allelic frequencies is summarized in Table 6. On the basis of what is known about the most highly conserved residues in the primary sequence of cyt c, asparagine 52 is among the 15 most conserved amino acids, and it is involved in the formation of a hydrogen bond between cyt c and CL.633 Thus, this natural mutation could have clinical relevance based on the mechanistic importance of cyt c−CL interactions. 5.4. Cyt c as a Disease Biomarker

While cyt c participates in essential cellular functions and resides in at least three cellular compartments (mitochondrion, cytoplasm, and nucleus), its usefulness as a biomarker of disease has been poorly explored. However, the presence of elevated cyt c in serum (i.e., extracellular cyt c) has been documented in various pathologies, including arthritis, myocardial infarction, and liver disease.703−710 Pathologies or treatments that would promote apoptosis are conditions where elevation of cyt c could 13425


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molecular scale. Chitosan-stabilized gold NPs were immobilized on the surface of cysteine-coated Au electrodes to construct cyt c-modified electrodes by a self-assembly method.785 The modified electrodes displayed increasing amperometric responses to H2O2 with good linear ranges from 0.85 to 13 mM, and the detection limit (DL) was estimated at about 9.8 μM. Following this strategy, different NP morphologies and assembly strategies have been proposed to increase the linear range and achieve better detection limits in the micromolar and submicromolar range. Oxide semiconductor NPs have also received considerable attention as they are suitable substrates for biomolecule immobilization due to their good biocompatibility and easy preparation. Nanostructured biointerfaces based on TiO2 nanoneedles,793,794 TiO2 nanotubes,795 ZnO nanosheets,796 and CoOx,797 NiO,798,799 and WO3 nanoparticles800 have been reported for sensing applications. Luo et al. have employed the high conductive TiO2 nanoneedles as a support matrix for immobilizing cyt c.793 This nanocomposite film presented a dynamic linear range for detection of H2O2 from 0.8 μM to 24 mM at the applied potential of 0.0 V (vs Ag|AgCl). Furthermore, anodic interferences like ascorbic acid, uric acid, and 3,4-dihydroxyphenylacetic acid and cathodic interference such as molecular oxygen were effectively avoided. Carbon materials also possess suitable properties for the design of electrodes used in electroanalytical chemistry because of their relatively wide potential windows in aqueous media, low cost, and relative chemical inertness in most electrolyte solutions. Since the work from Zhao et al.,801−810 various groups have shown that H2O2 biosensors based on multiwalled carbon nanotubes (MWCNT) exhibit good sensitivity, selectivity, and reproducibility. MWNTs were combined with gold NPs by Xiang et al.,808 and a composite film based on (Au NPs)/room-temperature ionic liquid (RTIL)/MWCNTsmodified glassy carbon electrode (GCE) was prepared by a layer-by-layer self-assembly technique. Cyt c was successfully immobilized on the RTIL-nanohybrid film-modified GCE by electrostatic adsorption and exhibited excellent electrocatalytic activity toward the reduction of H2O2. Dinesh et al.801 described a sensor with exceptional selectivity toward H2O2 and a very low DL of 27.7 pM. This amperometric biosensor was based on immobilized cyt c over a graphene oxide (GO)MWCNT composite on a nano Au-modified GCE. Graphene811−814 and graphite815,816 are also often employed for electrochemical applications due to their low residual current, readily renewable surface, and wide potential window. Carbon fibers have also attracted attention due to the fact that they have more edge sites on the outer wall than CNTs, which can facilitate the ET of electroactive analytes.817 Mesoporous materials have attracted significant attention in electrochemical biosensing, as they exhibit large surface areas and large pore volumes that can encapsulate or immobilize a large amount of enzymes.818−824 Moreover, they often offer a versatile functionalization. Zhu et al.825 showed that SBA-15 (Santa Barbara Amorphous) can provide a favorable microenvironment for immobilizing cyt c. It presented optimal DET, which resulted in a high sensitivity for H2O2 and an estimated DL of 21 nM. Recently, Zhou et al. used a small molecular hydrogel as a surrounding matrix to stabilize cyt c.825 The dynamic detection linear range for H2O2 was estimated to be from 0.3 μM to 0.8 mM with a DL of 50 nM, and it was successfully applied in the determination of H2O2 released from live cells.

SAMs carrying varying proportions of charged and uncharged functional groups299−301,451 or be covalently attached to carboxyl- or amino-terminated SAMs employing cross-linking reagents.504 Phosphate and ATP-mediated adsorption to positively charged SAMs is also possible and provides efficient DET.453,771 An interesting immobilization alternative that results in very high electronic coupling is the direct wiring of the heme iron to the metal electrode employing pyridinyl- or imidazoyl-terminated SAMs that are able to replace M80 as axial ligand.448,499,512,772 Other strategies include direct chemisorption of iso-1-cyt c on Au surfaces through the surface-exposed C102 residue,773 cross-linking of C102 to SHterminated SAMs,774 and cross-linking modification of Lys surface residues with mercaptopropionic acid for subsequent self-assembly of the chemically modified protein on Au.775 Layer-by-layer deposition of cyt c and polyelectrolytes on electrode has also been successfully tested.776,777 Protocols for immobilization of cyt c on other electroactive material such as graphene oxide derivatives,778 porous silicon materials,779,780 and boron-doped diamond electrodes781,782 were developed as well. In the past decade, cyt c has been widely used for developing biosensors employing multiple types of electrode supports to optimize DET. The use of cyt c has several advantages: the heme prosthetic group is covalently bound to the protein, it is known to have some intrinsic peroxidase activity, it is active over a wide pH range, it can be modified to enhance its thermal stability, and it is inexpensive. Cost and stability are two of the main factors that should be addressed to accomplish biocatalysis on a large scale. In the following sections, an overview of the different applications of cyt c in third generation biosensors will be provided with special attention on novel surface functionalization and new electrode materials. 6.1.1. Hydrogen Peroxide Biosensors. Hydrogen peroxide is a member of the reactive oxygen species (ROS) group that serves as a key regulator for a number of oxidative stress related states and is also a product of several enzymatic reactions that can be used as diagnostic tools for the detection of the onset of various biological conditions. Hence, it is considered to be a relevant analyte because of its importance in clinical diagnosis, as well as industrial and environmental applications.734,783,784 H2O2 can be electrochemically oxidized or reduced directly at ordinary solid electrodes; however, due to slow electrode kinetics and high overpotential, the sensing performance is greatly reduced and the analytical applications are rather limited. Moreover, the existence of other electroactive species in real samples such as ascorbate, urate, or nitrates results in severe interferences. To overcome these issues and due to its redox capability, cyt c is widely used in enzyme-based H2O2 biosensors. However, as ET between cyt c and solid electrodes is usually slow, it is necessary to search for a way to develop cyt c-modified electrodes that enhance DET, while still maintaining a wellbehaved electrochemistry and good stability. To achieve this, several types of hybrid materials based on cyt c and nanomaterials, such as transition metal nanoparticles, metal oxides, and carbon nanotubes, have been employed to perform electrocatalytic H2O2 detection. Immobilization of proteins or enzymes on nanoparticles (NPs)785−792 has become a popular surface derivatization procedure as NPs are largely versatile, easy to prepare, and they offer the possibility of establishing a high level of order on a 13426


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Figure 32. Reaction mechanisms for oxidation of nitrite by cyt c. Reprinted with permission from ref 850. Copyright 2008 Elsevier Ltd.

lated-MWCNT-RTIL nanocomposite,847 and on SAM functionalized Au NPs.848 More recently, a 3D macroporous mesh of nanoporous gold functionalized with cyt c was used to measure the release rate of drug-induced O2•− from skeletal muscle tissue.849 High sensitivity and a low DL of 70 pM were achieved providing a platform for the development of highly sensitive molecular electrochemical biosensors. 6.1.3. Nitrite Biosensors. The potential toxicity of the nitrite anion, which can easily interact with amines to form toxic and carcinogenic nitrosoamines, has resulted in the development of a large number of analytical methods for its determination. However, as many require centralized and sophisticated analytical systems, much attention has been paid to the development of high performance nitrite biosensors. These biosensors were mostly based on the complex protein catalysis of the reductive reaction of nitrite until the work by Geng et al.,850 who reported the first biosensor based on the biocatalytic oxidative reaction of nitrite by cyt c. This study opened a new prospect for the determination of nitrite, and, at the same time, a new field for the application of cyt c. They designed a SiO2 gel/cyt c/SiO2 gel sandwich-like structure that was constructed on a conductive boron-doped diamond (BDD) film substrate. The most attractive feature of this system is that cyt c in the sandwich structured electrode could be further oxidized into highly reactive cyt c π-cation by two-step electrochemical oxidation, which could oxidize NO2− into NO3− in solution at an operating potential of 0.7 V vs SCE (Figure 32). The oxidation current was proportional to the concentration of nitrite in the range from 1 μM to 1 mM, and the DL was 0.5 μM. It should be noted that this detection limit was lower than those obtained with other electrochemical methods. Since then, several other strategies have been employed such as immobilizing cyt c onto MWNT-poly(amidoamine)-Chit nanocomposite-modified GCEs,851,852 on poly(3-methylthiophene)/MWCNT/GCE,802 on Nafion-modified Cu−Mg−Al layered double hydroxide,853 on polyaniline chains grafted onto nanodiamond,854 and on multicomponent nanocomposite films.855 Some were successfully applied in food analysis.851,853 Recently, cyt c immobilized on MWCNTs decorated with titanium nitride NPs856 showed a large range of linear response from 1 to 2000 μM and a low DL of 1.4 nM. The proposed electrode showed good reproducibility and long-term stability and was validated by the successful detection of nitrite in tap and seawater samples. 6.1.4. Nitric Oxide Biosensors. Nitric oxide (•NO) is a highly diffusible and reactive molecule that has been implicated in the pathogenesis of many diseases and plays a major role in several physiological processes. Therefore, its quantification in biological tissues is highly relevant, which resulted in the development of a large variety of sensing systems. Among these, electrochemical sensors are most advantageous due to simplicity, speed, and sensitivity, being able to perform in vivo

Other studies have demonstrated that cyt c immobilized on conductive polymers,826 on a poly(ferrocenylsilane)-DNA (PFS-DNA) composite film-modified gold electrode,827 and on a 3D porous nickel foam828 also show good electrocatalytic activity. Other strategies include chemically modified cyt c with short-chain thiol derivatives adsorbed on bare gold electrodes775 and PEG-modified cyt c, which has shown an increased stability of the constructed electrodes.829 6.1.2. Superoxide Biosensors. Like H2O2, superoxide anion, O2•−, is also a ROS that is involved in various physiological and pathological conditions. For instance, generation of O•− 2 is known to increase with skeletal muscle contractile activity and fatigue. It is therefore important to selectively detect and accurately quantify the release of O•− 2 within both physiological and pathological levels. As cyt c is not specific for O•− 2 , efforts are centered on improving selectivity. Moreover, due to cyt c’s inherent property as a peroxidase, catalase is usually added to the reaction media to avoid interferences in real samples. Most developments are based on the constructs proposed by McNeil et al.830 and by Ge and Lisdat,831,832 which consisted of cyt c-modified gold electrodes. These sensors have been used for real-time measurements of the extracellular oxidative burst in renal cells after the addition of calcium oxalate crystals,831−834 to detect ROS produced by human neutrophils,835 to analyze the antioxidant capacity of orange juices and other natural samples,836,837 and for in vitro monitoring of O•− 2 production by cultured glioblastoma cells.838 Ganesana et al.839 proposed a modification to these constructs, where a combination of thiols was used to covalently immobilize cyt c onto gold wire electrodes, modified with gold nanoparticles, which resulted in an enhanced sensitivity. This biosensor allowed continuous monitoring of superoxide radicals in the extracellular matrix of brain slices from mice with high temporal resolution, high sensitivity, and high selectivity. Using the Ge and Lisdat approach, some authors tried to and H2O2.831,832,835,840,841 simultaneously detect both O•− 2 Following the concept of “lab-on-a-chip”, Krylov et al.840 developed a fluidic chip that combined the generation of O•− 2 and H2O2 with a two-electrode biosensor chip detector. In this way, the antioxidant capacity of different potential scavengers of the respective reactive species was quantified in a flow-injection mode. The same group has applied this fluidic chip to the determination of the antioxidative capacity of complex lipophilic mixtures, such as cosmetic creams.841 To achieve higher sensitivities, Wegerich et al.842,843 have proposed several mutations for introducing positively charged lysines in H-cyt c with the aim of increasing the reaction rate with superoxide radicals. Other strategies to increase the sensitivity and selectivity of these biosensors include multilayered structures of cyt c and poly(aniline sulfonic acid),844,845 immobilization of cyt c on a transparent indium tin oxide film with a well-defined mesoporosity (mpITO),846 on carboxy13427


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generation of an internal electron shuttling molecule.844 However, reaction partners of cyt c such as sulfite oxidase867−869 or laccase870,871 allow the construction of electrode assemblies without the need of any diffusing redox mediator. This strategy has been employed in the development of electrochemical glucose biosensors taking advantage of the associated high sensitivity, low cost, simplicity, and rapid response. These biosensors are based on glucose oxidase (GOD) as recognition element and usually are constructed including nanomaterials with a large surface-to-volume ratio and good conductivity to improve the performance of the device.790,872−875 For example, Song et al. coentrapped cyt c and GOD in chitosan-gold NPs873 and PDDA-graphene nanosheets−gold NPs composites,874 while Xiang et al. used a gold NPs/polyaniline nanosperes composite790 that presented a wide linear range 0.01−3.2 mM for the detection of glucose. The detection limit could be decreased to the nanomolar scale by coupling pyrroloquiniline quinone-dependent glucose dehydrogenase to cyt c/DNA multilayered systems.875 Another example is the multicopper oxidase bilirubin oxidase (BOD) where cyt c can act as electron donor instead of the natural substrate bilirubin and can thus mediate the catalytic oxygen reduction of BOD.876−878 In this biprotein electrode, electrons are transferred from the gold electrode to the cyt c monolayer and then via the cyt c molecules in the different layers to BOD where finally the four-electron reduction of oxygen takes place. Similar strategies have been employed for the detection of lactose,879 D-lactate,880 H2O2,881 HCHO,882 DNA,883 and microRNA.884 The latter work shows an electrochemical biosensor based on catalyzed hairpin assembly target recycling and cascade electrocatalysis (cyt c and alcohol oxidase) where the signal amplification allowed for the highly sensitive detection of microRNA. This newly designed biosensor provided a sensitive detection of microRNA-155 from 0.8 fM to 1 nM with a low detection limit of 0.35 fM. Further use of cyt c as mediator includes its use for biofuel cell design due to its ability to act as a reversible redox mediator.885 Cyt c was also used to perform a hybrid wiring of the Rhodobacter sphaeroides reaction center for biophotoelectrochemical solar cells.886 Here, a docking mechanism was used to bind the wild-type Rhodobacter sphaeroides RC from the primary donor side onto an Au electrode using immobilized cyt c.

measurements. Although most electrochemical sensors exploit the direct redox reaction of •NO on metal or carbon surfaces, several protein complexes have been used in biosensors as catalysts. Although Liu et al.857,858 studied the electrocatalytic activity of cyt c toward •NO, Alvin Koh et al.859 used for the first time the electrocatalytic properties of cyt c to directly monitor the fluctuation levels of •NO in vivo. In this work, cyt c was immobilized onto a functionalized conducting polymer (polyTTCA) layer for the in vivo measurement of •NO release stimulated by cocaine. The linear range reported was of 2.4− 55.0 μM, and the DL was determined to be 13 nM. The microbiosensor was applied into a rat brain to test cocaineinduced •NO fluctuation. Among other constructs for •NO determination,823,860,861 it is interesting to point out the work by Wu et al.862 that reports a simple (and currently popular) procedure for preparing graphene in aqueous solution for the first time. The as-prepared chitosan-dispersed graphene was immobilized on the surface of glassy carbon electrode to form a graphene-modified electrode and was successfully used to construct a •NO biosensing platform. 6.1.5. Other Analytes. Cyt c biosensors have also been developed for the detection of other relevant analytes. Oxygen was catalytically reduced at a cyt c/porous carbon nanofiber (PCNF)/RTIL chitosane film-modified electrode.823 A cyt cboron doped diamond electrode was used to detect selected arsenic and cyanide compounds with very low detection limits. 863 A novel strategy, using Zr(IV) ion as an immobilization matrix to interface cyt c on gold surface via thiol SAMs, was used for the detection of ascorbic acid.864 A cyt c-modified nanocomposite electrochemical biosensor was developed for the electrochemical determination of rebaudioside A in different food samples865 where the electrode surface was fabricated with graphene oxide assimilated with gold nanoparticles decorated on MWCNT. Recently, a new miniaturized electrochemical assay forhomocysteine (HcySH) was developed.866 The determination of HcySH is highly beneficial in human physiology and pathophysiology for diagnosis and prognosis of cardiovascular diseases. Madasamy et al.866 developed an electrochemical assay for HcySH in which cyt c immobilized on AuNP-modified screen-printed carbon electrode was employed as a biosensing element. The sensor was validated through the measurement of HcySH in blood plasma samples, and the selectivity was ensured by eliminating the impact of the common interfering biological substrates using a Nafion membrane.

6.3. Optical Biosensors

6.3.1. Fluorescence Biosensors. Quantum dots (QDs) have unique photophysical properties, such as high luminescence intensity and efficiency, stability against photobleaching, and size-controlled luminescence properties, thus offering significant advantages for biosensing. However, the biosensing applicability of QDs has been limited, as they usually need further modification before use and are composed of heavy metals that may lead to toxicity and environmental pollution.887 Graphene quantum dots (GQDs) are single or few-layer graphenes with a size of only a few nanometers. They show stable photoluminescence, high fluorescent activity, low toxicity, and excellent solubility and biocompatibility, and therefore they are promising tools in the field of bioimaging and electrochemical biosensing.888 On the basis of cyt cinduced self-assembled GQDs, Li et al.889 demonstrated a novel fluorescent biosensor for trypsin with remarkable fluorescence

6.2. Multiprotein Electrochemical Sensors: Cyt c as Electron Shuttle

The construction of protein multilayer films on electrodes using synthetic polyelectrolytes, DNA, and NPs has gained much attention in the biosensors field, as it is one of the ways to drastically increase the surface concentration of the biological recognition element. As electronic communication within such assemblies is usually hindered by long ET distances, electron shuttling molecules are used to transfer the information on redox conversion from the protein molecule to the electrode. Other approach is to embed other enzymes in these layers to obtain a bi- or triprotein artificial signal chain. Cyt c can act here as a redox protein that can drive electrons between the electrode and the enzyme without any external mediator. The first assemblies of cyt c with xanthine oxidase still relied on the 13428


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immediately. The absorbance at 652 nm was proportional to the concentration of trypsin in the range from 0.2 to 80 nM with a detection limit of 0.18 nM. The procedure has been successfully applied to the determination of trypsin in human urines and for inhibitor screening, demonstrating its potential application in clinic diagnosis and drug development. 6.3.3. Plasmonic Biosensors. A label-free, ultrasensitive method for the optical detection of polychlorinated biphenyl (PCB) was described by Hong et al.899 The detection mechanism for PCB is based on PCB-induced conformational changes of immobilized cyt c on an Au thin film altering the local dielectric function of the supported cyt c, which can be detectable by surface plasmon resonance (SPR) spectroscopy. The limit of detection was as low as 0.1 ppb, and the response was completed within 10 min. In another interesting example, Kim et al.900 reported a novel method for H2O2 detection based on a single plasmonic nanoprobe via cyt c-mediated plasmon resonance energy transfer (PRET). Dynamic spectral changes were observed in the fingerprint quenching dip of a single NP as plasmonic nanoprobe in response to changes in the redox state of cyt c, induced by H2O2. On the basis of changes in the spectral profile of the single plasmonic nanoprobe, H2O2 was successfully detected in the wide concentration range from 100 mM to 10 nM, including physiologically relevant micromolar and nanomolar concentration. Selectivity in the presence of other biologically relevant metal ions and small molecules was also achieved. Because of the use of single NPs as sensing probes, devices based on this approach may be good candidates for achieving dynamic, high spatial resolution monitoring of ROS in extra- and intracellular environments.

enhancement, as well as high selectivity and sensitivity. A linear relationship was observed between the fluorescence intensity and concentration of trypsin from 0 to 1 mM and from 10 to 400 mM (DL = 1.4 nM). A similar response was reported for the detection of trypsin by using negatively charged CdTe QDs890 and by using fluorescence-based assays.891,892 More recently, a novel fluorescent sensing platform has been developed for protein kinase (CK2) based on phosphorylationinduced formation of a cyt c−peptide complex893 (Figure 33).

Figure 33. Schematic illustration of the cyt c-peptide sensing platform for the detection of CK2 activity and inhibition based on phosphorylation against CPY degradation. Reprinted with permission from ref 893. Copyright 2016 Royal Society of Chemistry.

Both the effective suppression of CPY digestion upon phosphorylation and the high quenching capacity of cyt c contributed to sensitive and selective screening of CK2 activity. In comparison with previous phosphorecognizing antibodybased methods or graphene oxide-based kinase assays, this approach was much more cost-effective and simple. Given the key roles of kinases in many biological processes, this fluorescent peptide/cyt c sensing platform shows great potential in kinase-related drug discovery and clinical diagnostics. 6.3.2. Colorimetric Biosensors. A portable oxidative stress sensor was developed by Koman et al.894,895 that contained cyt c as the sensing element, which enabled the detection of H2O2 down to a detection limit of 40 nM. This low detection limit was achieved by introducing cyt c into a random medium that enables multiscattering, thus enhancing the optical trajectory through the cyt c spot, thereby increasing the optical absorbance of cyt c by a factor of 4.6. A contact microspotting technique was used to produce reproducible and reusable cyt c spots, which were stable for several days. Using this device, the release of H2O2 from the green alga Chlamydomonas reinhardtii was detected when exposed to either 180 nM functionalized CdSe/ZnS core−shell QDs or to 10 mg/L TiO2NPs. Suarez et al.896 also determined H2O2 with the same strategy using inserts made of glass fiber membrane and placing them into microplate wells as the multiple scattering matrix. A similar approach was employed for the detection of thiols directly from a gas sample.897 Recently, Zhang et al.898 developed a simple, rapid, label-free, and sensitive trypsin colorimetric sensor by employing cyt c as an enzyme substrate and 3,3′,5,5′-tetramethylbenzidine (TMB) as a chromogenic reagent. It was found that cyt c hardly catalyzes H2O2-mediated TMB oxidation to produce a blue solution. On the other hand, the hydrolysate of cyt c by trypsin displays an intense catalytic effect on the aforementioned reaction, resulting in the formation of a blue solution

6.4. Synthetic Receptors

Although cyt c is a relatively small protein, its structure is too complicated to be easily recognized by common synthetic receptors. In a review by Shinoda et al.,901 an overview of the molecular recognition of cyt c by synthetic receptors was done emphasizing examples exhibiting in vivo and in vitro nonbiological functions, and two examples were largely covered: (i) crown ether receptors interacting with cationic residues via multiple crown ether complexations and (ii) dendrimer receptors strongly binding with a negatively charged patch via complementary electrostatic interactions. These designed receptors offered effective cyt c recognition to generate nonbiological catalytic activity and in cell functions.902−908 Although Ru complexes and porphyrins have also received considerable attention,909−912 here we present more recent contributions in the field with special emphasis on calix[n]arenes and molecular imprinting and its applications. 6.4.1. Calix[n]arenes. Calix[n]arenes are one of the most widely studied classes of organic supramolecular hosts due to their relatively simple synthesis and the possibility to selectively modify them in a controlled manner. Calix[n]arenes consist of phenol rings bridged by methylenes that possess a unique basket-like cavity that can be controlled by changing the number of phenol units, thus allowing the construction of synthetic receptors.913,914 These synthetic receptors were successfully designed for the selective recognition of cyt c,903,915−918 allowing its nanomolar specific detection.915 Recently, p-sulfonato-calix[4]arene was shown to act as “molecular glue” for the assembly and crystallization of cyt c on SAM-modified Au electrodes (Figure 34). The crystals were characterized by cyclic voltammetry, and 13429


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Figure 34. (A) Cyt c-p-sulfonato-calix[4]arene crystals are ordered assemblies with defined interheme distances. (B) Cyt c-PASA multilayers are heterogeneous mixtures of protein−polymer contacts. Reprinted with permission from ref 919. Copyright 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Figure 35. Schematic representation of the epitope-oriented surface imprinting approach for preparation of MIP ultrathin films. Reprinted with permission from ref 922. Copyright 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

exceptionally high concentrations of electroactive cyt c were obtained. This study revealed high electroactivity accompanied by fast interprotein ET in crystals, which may have implications for the construction of novel bioelectronic devices.919 6.4.2. Molecular Imprinting. Molecular imprinting is a method for making selective binding sites in synthetic polymers using a molecular template. Target molecules can be used as templates for imprinting cross-linked polymers. After the template removal, the selectivity of the polymer depends on various factors such as the size and shape of the cavity and rebinding interactions. Molecularly imprinted polymers (MIPs) are rapidly becoming viable alternatives to antibodies and enzymes in sensor technology, chromatography, bioanalysis, and biocatalysis as they offer many advantages in terms of shelf life, stability, robustness, cost, and ease of preparation.920 However, affinities and catalytic activities obtained are in general relatively low, and, therefore, great efforts are directed toward improving the performance of this approach. Ö zcan et al.921 reported novel surface-imprinted beads for selective separation of cyt c by N-methacryloyl-(L)-histidinecopper(II) [MAH-Cu(II)]. They combined molecular imprinting with the ability of histidine to chelate metal ions to create ligand exchange beads suitable for the binding of cyt c as it is a surface histidine exposed protein. L-Histidine imprinted metalchelate beads could be used several times without considerable loss of cyt c adsorption capacity and could be used for cyt c separation by fast protein liquid chromatography. Dechtrirat et al.922 presented a novel strategy to prepare a selective ultrathin MIP film directly on a gold-based transducer surface for peptide and protein detection in aqueous solution (Figure 35). This was demonstrated using a combination of epitopes and an electrochemical surface imprinting approach. The synthetic nona-peptide derived from the surfaced exposed C-terminus of cyt c (residues 96−104) was selected as template for the imprinting. The resulting MIP film was able to selectively capture the template peptide and the corresponding target protein. Other authors have also obtained cyt c selective MIPs with promising results and high imprinting factors.923−926 More recently, novel methods combining the high selectivity of molecular imprinting technology with the fluorescence properties of upconversion nanoparticles (UCNPs)927 and QDs928 were proposed for cyt c sensing. In one case, UCNPs@ MIP were obtained by coating in situ cyt c imprinted materials to the surface of the carboxyl-modified UCNPs through sol−gel technique. The UCNPs@MIP showed selective recognition for

cyt c among other proteins.927 In the other case, a thermosensitive carbon dots/SiO2/MIP receptor was obtained, which showed a low DL of 89 nM and good reproducibility.928 Therefore, these new methods for protein sensing are very promising for future developments. 6.5. Biosensors for Cyt c Detection

The role of cyt c as apoptosis biomarker and its relevant role in the comprehension of certain diseases have resulted in a large variety of techniques to detect cyt c in various conditions.929 Standard techniques include flow cytometry, Western Blot, and enzyme-linked immunosorbent assay (ELISA).930−932 Recently, several electrochemical immunosensor platforms have been proposed for the detection of cyt c.933−935 A novel electrochemical immunosensor was developed for in situ analysis of cyt c in the cytosol by Wen et al.934 (Figure 36). AuNP−

Figure 36. Schematic representation of the preparation of AuNPpolydopamine (PDA) electrochemical immunosensors for the detection of cyt c. Reprinted with permission from ref 934. Copyright 2014 The Royal Society of Chemistry.

polydopamine composites were used to detect the changes in the expression level of cyt c in the cytosol upon curcumininduced apoptosis. Using the proposed method, a linear range (0.1−100 mM) for cyt c with a detection limit of 0.03−0.01 mM was achieved. Moreover, this method could detect as low as 100 cells expressing cyt c with results in good agreement with standard flow cytometry analysis. The developed electrochemical immunosensor offered a simple and rapid approach for sensitive evaluation of apoptosis markers with considerable 13430


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specificity and reproducibility, being of great importance in clinical diagnosis and therapeutic research. Pandiaraj et al.933 proposed two nanocomposite-based electrochemical immunosensor platforms for the detection of cyt c with nanomolar detection limits: (i) SAM on Au NPs in polypyrrole (PPy) grafted screen-printed electrodes (SPE) and (ii) CNTs integrated PPy/SPE. The overall analytical performance of GNP/PPy-based immunosensor (detection limit 2 nM; linear range: 2 nM to 150 mM) was better than that of the anticyt c/ CNT/PPy (detection limit 10 nM; linear range: 10 nM to 50 mM). Furthermore, the measurement of cyt c release in cell lysates of cardiomyocytes using the GNP/PPy-based immunosensor gave an excellent correlation with standard ELISA methods. Similar strategies were also employed by replacing antibodies with aptamers.936−943 Ocaña et al.936 reported a label-free impedimetric aptasensor for the recognition of cyt c at picomolar concentration levels based on an epoxy−graphite composite electrode. When the protein interacted with the immobilized aptamer on the aptasensor, it was detected by electrochemical impedance spectroscopy (EIS). The amount of protein was quantified by the observed increase of the ET resistance, employing the [Fe(CN)6]3−,4− redox marker. The aptasensor had a good detection range for cyt c between 50 pM and 50 nM, as well as a high sensitivity with a low detection limit of 63.2 pM, well below levels of this protein in serum. Cyt c was also detected by using a novel strategy for the enhancement of electrochemiluminescence (ECL) by combining CdSe QDs with graphene oxide-chitosan (GO-CHIT).944 The ECL sensor exhibited high ECL intensity, good biocompatibility, long-term stability, and high sensitivity for cyt c with a linear range from 4.0 to 324 uM and a DL of 1.5 μM. Furthermore, the ECL sensor could selectively sense cyt c from glucose and bovine serum albumin (BSA). Several authors successfully employed a similar strategy,945−950 including Hu et al., who developed a GO/PANi/CdSe nanocomposite that presented an impressive 50 nM to 0.1 mM linear range and 20 nM detection limit. Other strategies for cyt c detection include enzyme-based biosensors,951−954 resonance Rayleigh scattering sensors,955 localized SPR (LSPR) sensors, 956,957 surface-modified prisms,958 chemiluminiscence reactions,959 and fluorescent probes.960−965 Chen et al.960 reported a nanosensor constructed by assembly of a fluorophore-tagged DNA aptamer on PEGylated GO nanosheets used to detect cyt c released from mitochondria in apoptotic cells. The nanosensor could be selectively internalized in the cell and presented a very weak fluorescence signal due to effective quenching of the fluorophores on graphene surface. Upon formation of the aptamer−cyt c complex, the aptamer dissociates from the GO surface activating an intense fluorescence response. This enabled a direct visualization of cyt c translocation in apoptotic cells for the first time (Figure 37).960 Recently, Shamsipur et al.964 proposed two novel label-free fluorescence assays based on hemoglobin-stabilized gold nanoclusters (Hb/AuNCs) and aptamer-stabilized silver nanoclusters (DNA/AgNCs) for analysis of cyt c. The quenching processes observed were found to be based on the fluorescence resonance energy transfer mechanism from Hb/AuNCs to cyt c and photoinduced ET from DNA/AgNCs to the aptamer-cyt c complex. The linear range for cyt c was found to be 0−10 μM for Hb/ AuNCs and from 0 to 1 μM for DNA/AgNCs, with limits of detection of ∼15 nM. On the basis of the strong binding

Figure 37. Schematic representation of fluorescence activation strategy for cyt c release imaging. Reprinted with permission from ref 960. Copyright 2015 American Chemical Society.

affinity of DNA aptamers for their target proteins, the DNA/ AgNCs probe was successfully applied to the quantitative determination of cyt c in cell lysates, which opens a new avenue to early diagnostics and drug screening with high sensitivity. As compared to the conventional Western blot method, these methods present several advantages as they are of low cost, the fluorescent probes are sensitive and easy to prepare, and the overall time for the detection and quantitation of cyt c from isolated mitochondria is only 20 min. Finally, Poghossian et al.966 and Shen et al.957 have suggested promising alternative methods for cyt c detection. In the first case, a field-effect capacitive electrolyte−insulator−semiconductor modified with citrate-capped AuNPs was applied for a label-free electrostatic detection of charged molecules like cyt c by their intrinsic molecular charge. The proposed strategy detects the charge changes in AuNP/molecule inorganic/ organic hybrids induced by the molecular adsorption or binding events and was demonstrated using an Al−p-Si−SiO2−silane− AuNP structure for the label-free detection of positively charged cyt c.966 In the second case, a localized surface plasmon resonance (LSPR)-based sensor was proposed that showed better performance than the commercial propagating surface plasmon resonance (PSPR)-based sensors. The array of submicrometer gold mushrooms-like structures was used for detecting cyt c with detection limits down to 200 pM, showing this strategy as a promising candidate for label-free biomedical sensing.957

7. SUMMARY AND OUTLOOK The structural flexibility of cyt c is a key feature both for the regulation of the protein primary electron transport function and for enabling alternative conformations with different functionalities. In the first case, the native crystallographic structure is typically regarded as the redox competent species, but a number of recent in vitro studies show that the dynamical features of the protein may play a crucial role. This includes (i) subtle redox state-dependent differences of protein structure and flexibility that are thought to be determinant in binding and dissociation of interprotein ET complexes;19,115,118 (ii) the finding that low frequency vibrational modes of the heme group and of the CXXCH binding motif are strongly coupled and that this dynamical coupling is likely to minimize Marcus reorganization energy in interprotein ET;9,10,117 (iii) the dynamical behavior of interprotein complexes and how these dynamics critically affect the donor−acceptor electronic coupling;116,158 (iv) the observation that relatively weak 13431


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electrostatic interactions of cyt c induce subtle structural alterations that affect neither the secondary structure nor the heme axial ligation pattern but minimize the reorganization energy;146,465and (v) the discovery that biologically relevant electric fields strongly modulate the orientation and reorientation rates of cyt c in electrostatic complexes, thus modulating the electronic coupling.158 On the basis of these and other findings, detailed regulatory mechanisms of the ET dynamics of cyt c, in particular, and their possible extrapolation to biological electron−proton energy transduction, in general, have been envisioned,15 although validation or rebuttal of these hypothesis under in vivo conditions remains highly elusive. On the other hand, a growing body of evidence indicates that the structural flexibility of cyt c, particularly at the distal side of the heme plane, allows this protein to respond to cellular stressors, via changes in coordination, geometry, and redox properties of its heme center as well as conformational changes of the protein matrix to form alternative conformers. Among these perturbations, we can find local electric field effects, naturally occurring point mutations, specific cyt c−CL interactions, or post-translational modifications such as phosphorylation, acetylation, nitration, nitrosylation, and sulfoxidation. Clearly, our current understanding of structural, thermodynamic, and dynamical determinants of the canonical and alternative functions of cyt c needs to be revised in light of the recent findings that mitochondria might operate at temperatures significantly higher than commonly believed.38,39 There is evidence that some of the alternative cyt c conformers may reside outside the mitochondrion, at least transiently. Structural models and biological functions for some of these alternative conformations have been proposed, while others await further investigation.16,18,29,273 Moreover, some alternative conformers translocate more readily across compartments than the native form, raising the possibility that these species may act at the forefront of cellular decisions. Depending on the specific chemical modification, some of these protein variants may exhibit downshifted redox potentials with respect to the native form, enhanced or reduced peroxidase activity, and either higher or lower affinity toward relevant partners such as Apaf-1 and lipids, although most of these studies were performed in vitro.30,32,33 The recent finding that cyt c may translocate into the nucleus and interfere with nucleosome assembly44 underlines the need for investigating the interactions of native and alternative conformations of cyt c with other possible partner proteins in the cell, a subject that remains largely unexplored. Meanwhile, the interactions of cyt c with cardiolipin and other lipids, and the concomitant gain of peroxidase activity related to apoptosis and other pathways, remain matters of intense research not exempt from controversy.32,34,43,306,309,631,641 In general, the large body of evidence accumulated points out that molecular flexibility is an evolutionary maintained feature of cyt c that plays a key role in the different functions of this protein, which include sustaining and terminating life through respiratory and apoptotic activities. Moreover, features like tunable redox potentials and peroxidase activity, sensitivity to electric fields and other local physicochemical parameters, as well as translocation across cellular compartments suggest that native and alternative conformations of cyt c may have a function in redox sensing. Immunochemistry tools and the recent discovery of drugs that could selectively inhibit the peroxidase activity of cyt c may help to distinguish in vivo

between the canonical and secondary functions of this moonlighting protein. Deeper understanding of the factors that determine the structure and reactivity of cyt c will also help to further rationalize the flourishing area of designing cyt c-based electrochemical and optical sensors.

AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected]. ORCID

Daniel H. Murgida: 0000-0001-5173-0183 Present Address

́ Instituto de Investigaciones Bioquimicas de Buenos Aires, FILCONICET, Argentina. ∥

Notes

The authors declare no competing financial interest. Biographies Damian Alvarez-Paggi earned his bachelor degree in Molecular Biology and his Ph.D. in Physical Chemistry (2012) from the School of Sciences of the University of Buenos Aires. His doctoral work, performed under the supervision of Daniel Murgida, garnered several awards and centered on the elucidation of the regulatory mechanism of ET reactions involving cytochrome c and cytochrome c oxidase employing a combination of electrochemical, spectroelectrochemical, and spectroscopic techniques with classical molecular dynamics and quantum mechanical calculations. Since 2016 he is a CONICET Research Assistant at the Leloir Institute Foundation where he is studying the role of structure and dynamics of protein and nucleic acids complexes in viral assembly, function, and infection. Luciana Hannibal completed undergraduate studies in Biochemistry in 2004 at Universidad de la República, Montevideo, Uruguay, and received her Ph.D. in Cellular and Molecular Biology in 2009 at Kent State University, OH. Her doctoral work focused on the chemistry and metabolism of cobalamins. She performed postdoctoral training in the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, OH, on the structure and function of bacterial and mammalian nitric oxide synthases. In 2012 she was promoted to Research Associate to investigate heme trafficking in mammals. She joined the Division of Bioinorganic Chemistry at Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany, as a DAAD-sponsored visiting lecturer in 2014. Since 2015 she works in the Department of Pediatrics, Universitätsklinikum Freiburg, Germany. She is also an Adjunct Investigator at the Center for Free Radical and Biomedical Research, Universidad de la República, Uruguay. Her team investigates genetic diseases affecting the metabolism of cobalamin and heme in humans, including natural and engineered structural variants of cytochrome c. Her research on protein chemistry incorporates biophysical, cell biology, and redox “omics”. Maria Ana Castro received her Ph.D. in Chemistry in 2010 from the School of Sciences of the University of Buenos Aires. From 2010 to 2013 she was a PostDoc fellow at Dr. Murgida’s laboratory where she studied the regulatory mechanism of electron transfer reactions involving cytochrome c from a theoretical and experimental point of view. Since 2013 she is a CONICET Researcher in the same group, and her research is focused on the development of analytical techniques for ultrasensitive and specific analyte detection in complex matrixes based on surfaced enhanced resonant Raman spectroscopy (SERRS). 13432


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University of Buenos Aires and CONICET Researcher at the Institute of Physical Chemistry of Materials, Environment and Energy (INQUIMAE). His current research centers on understanding structure−dynamics−function relationships that determine redox and alternative functions of metalloproteins. His work uses a combination of experimental and theoretical methods, with focus on protein electrochemistry, spectroscopy, and time-resolved surface-enhanced vibrational spectroelectrochemistry.

Santiago Oviedo-Rouco received his bachelor degree in chemistry from the School of Sciences of the University of Buenos Aires, Argentina. Since 2016 he is a Ph.D. student at Dr. Murgida’s laboratory. His research focuses on the structural and dynamic properties of non-native functions of cytochrome c. Veronica Demicheli obtained her Ph.D. in Chemistry in May 2012 working at the Department of Biochemistry, Facultad de Medicina, Universidad de la República, Uruguay, where she is now an Assistant Professor. She is also an investigator at the Center for Free Radical and Biomedical Research, Universidad de la República, Uruguay. Her research is focused in the study of nitro-oxidative modifications on the structure and function of mitochondrial proteins, in particular cytochrome c and manganese-superoxide dismutase and the effect that nitration and the interaction with mitochondrial lipids has on the activity and structure of these proteins.

ACKNOWLEDGMENTS Financial support by ANPCyT (PICT2015-0133, PICT20111249) and UBACyT (20020130100206BA) to D.H.M. and by A g e n c i a N a c i o n a l d e I n v e s t i g a c i ó n I n n o v a c i ó n (FCE_2014_104233), Universidad de la República (CSIC and Espacio Interdisciplinario, UdelaR), to R.R is gratefully acknowledged. L.H. acknowledges intramural funding support from the Department of Pediatrics, Medical Center, University of Freiburg. Additional support was obtained from Programa de Desarrollo de Ciencias Básicas (PEDECIBA), Centro de Biologiá Estructural del Mercosur (CeBEM), CONICET, SNM-MINCYT, and Ridaline through Fundación Manuel Pérez (Facultad de Medicina, Universidad de la República). S.O.-R. and F.T. were partially supported by fellowships from CONICET (Argentina) and Universidad de la República (CAP_Uruguay), respectively. D.A.-P., M.A.C., and D.H.M. are CONICET staff members.

Veronica Tórtora obtained her Ph.D. in Biology in December 2014 working at the Department of Biochemistry, Facultad de Medicina, Universidad de la República, Uruguay. Currently, she is an Assistant Professor and investigator at the Center for Free Radical and Biomedical Research, Universidad de la República, Uruguay. Her research is focused on the study of the effect of oxidative modifications on the structure and function of iron-containing mitochondrial proteins. Specifically, she studies the impact of oxidants on aconitase and cytochrome c structure and function. Florencia Tomasina received her bachelor’s degree in Biochemistry in 2012 from the School of Sciences of the Universidad de la República, Uruguay. Since 2013 she is a Ph.D. student at the laboratory of Dr. Rafael Radi in the Department of Biochemistry, Facultad de Medicina, and the Center for Free Radical and Biomedical Research Universidad de la República, Uruguay. Her research focuses on biochemical and immunochemical studies on alternative conformations of cytochrome c.

ABBREVIATIONS 5cHS five-coordinate high spin 6cHS six-coordinate high spin 6cLS six-coordinate low spin AcMet N-acetylmethionine Apaf-1 apoptosis protease activating factor 1 AuNCs gold nanoclusters AuNP gold nanoparticle BDD boron-doped diamond BOD bilirubin oxidase CcO cytochrome c oxidase CcP cytochrome c peroxidase CcR cytochrome c reductase CD circular dichroism CK2 casein kinase II CL cardiolipin CNTs carbon nanotubes CpdI compound one Cryo-EM cryo-electron microscopy CYMAL cyclohexyl-methyl-β-D-maltoside Cyt c cytochrome c Cyts c cytochromes c DD dynamic docking DET direct electron transfer DFT density functional theory DL detection limit DLPA dilauroylglycerophosphate DOPA dioctadecenoylglycerophosphate DOPC dioleoylglycerophosphocholine DOPG dioleoylglycerophosphoglycerol DOPS dioctadecenoylglycerophosphoserine DPPA dipalmitoylglycerophosphate DPPC dipalmitoylphosphatidylcholine DPPE dipalmitoylglycerophosphoethanolamine DPPG dipalmitoylglycerophosphorylglycerol

Rafael Radi received his M.D. (1988) and Ph.D. (1991, in Biochemistry) at the Universidad de la República, Montevideo, Uruguay. He was a postdoctoral fellow at the University of Alabama at Birmingham, AL, working with Bruce A. Freeman and Joseph S. Beckman. He has been tenured faculty at the Department of Biochemistry, Facultad de Medicina, Universidad de la República, Uruguay, for three decades and is now its Professor and Chairman. He is the Director of the Center for Free Radical and Biomedical Research at the same University. Radi is a foreign member of the U.S. National Academy of Sciences and Howard Hughes Medical Institute alumni. His research interests have focused on the biochemistry of free radical and redox processes in oxidative stress and signaling, mitochondrial dysfunction, and oxidative post-translational modifications of proteins. He has applied rapid kinetic techniques, bioanalytical and immunochemical methods, electron paramagnetic resonance studies, and structural biology approaches to unravel the molecular basis of oxidative processes in disease states and has made efforts in the development, characterization, and evaluation of redox-based therapeutics in vitro and in vivo. Daniel H. Murgida received his Ph.D. in Chemistry in 1997 from the Department of Organic Chemistry, School of Sciences, University of Buenos Aires, Argentina. He was a Visiting Scientist at the University of Parma, Italy; Humboldt Fellow at the Max Planck Institute for Radiation Chemistry, Mülheim, Germany; Staff Scientist at the Institute of Chemical and Biological Technology (ITQB), Oeiras, Portugal; Assistant Professor at the Technical University of Berlin, Germany; and Visiting Professor at ITQB. In 2007 he returned to Argentina where he is a Professor at the Department of Inorganic, Analytical, and Physical Chemistry from the School of Sciences of the 13433


Chemical Reviews DPPS DSPA DSPG E0 ECL EIS EPR GCE GD GO GOD GQDs GS GuHCl H/S HCCS HcySH H-cyt c HDA hh-cyt c HS HSQC Ht HX I Im IR Iso-1-cyt c ISP kET LSPR mAb MCCE MD MIPs MpITO MS MWCNTs NMR NPs Pa PANi PCB PCNF Pd PDDA PEG PFS poly-TTCA PPy PRE PRET QDs QM/MM RMSD ROS RTIL SAM SASA SBA-15 SD SDS

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SEIRA SERR SO SPE SPR TMB UCNPs λ ω-UDM

dipalmitoylphosphatidylserine dioctadecanoylglycerophosphate dioctadecanoylglycerophosphoglycerol standard reduction potential electrochemiluminescence electrochemical impedance spectroscopy electron paramagnetic resonance glassy carbon electrode gated docking graphene oxide glucose oxidase graphene quantum dots ground state guanidine hydrochloride enthalpy/entropy cytochrome c heme lyase homocysteine human cytochrome c electronic coupling matrix elements horse heart cytochrome c high spin heteronuclear single quantum correlation Hydrogenobacter thermophilus hydrogen exchange ionic strength imidazole infrared isoform 1 of yeast cytochrome c iron−sulfur protein electron transfer rate constant localized surface plasmon resonance monoclonal antibody multiconformer continuum electrostatics molecular dynamics molecularly imprinted polymers mesoporous indium tin oxide mass spectrometry multiwalled carbon nanotubes nuclear magnetic resonance nanoparticles Pseudomona aeruginosa polyaniline polychlorinated biphenyl porous carbon nanofiber Paracoccus denitrificans poly(diallyldimethylammonium chloride) polyethylene glycol poly(ferrocenylsilane) polyterthiophene carboxylic acid polypyrrole paramagnetic relaxation enhancements plasmon resonance energy transfer quantum dots quantum mechanics/molecular mechanics root-mean-square deviation reactive oxygen species room-temperature ionic liquid self-assembled monolayer solvent-accessible surface area Santa Barbara amorphous ordered mesoporous silica particles simple docking sodium dodecyl sulfate

surface-enhanced infrared absorption surface-enhanced resonance Raman superoxide screen-printed electrodes surface plasmon resonance 3,3′,5,5′-tetramethylbenzidine upconversion nanoparticles electron transfer reorganization energy undecyl-β-maltoside

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