Editorial pubs.acs.org/JPCB
Editorial - Virtual Issue of JPCB on Biophysics
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n case you ever wondered if there is a special meaning (beyond simple alphabetic ordering) to the letter B in the title of the Journal of Physical Chemistry B, the answer is “no”, or at least not explicitly. Implicitly, the letter B plays a central role in the journal. In this Virtual Issue, we highlight the “B” in JPC with a survey of recent articles on Biomolecules and Biomaterials. JPC B publishes some of the most innovative work in the field of Biophysics from authors around the world. The selected 25 articles demonstrate that modern physical chemistry possesses sharp spectroscopic and computational tools that can address prominent biophysical and biochemical questions, such as What is the role of water in the hydration shell of proteins or lipid membranes? What is the interplay between protein aggregation and formation of f ibrils? How does cholesterol modulate lipid f lip-flop in cell membranes? Why does urea denature proteins? What keeps bases stacked in DNA? How to label DNA to increase radiation damage to cancer cells? We believe that you will find this Virtual Issue interesting to read. Inside of it, you will discover inspirational answers to the above Biophysical questions and much more. A brief description of each paper is given below. 1. Engineering a pH-Regulated Switch in the Major LightHarvesting Complex of Plants (LHCII): Proof of Principle. J. Phys. Chem. B 2016, 120 (49), 12531− 12535. DOI: 10.1021/acs.jpcb.6b11541. Protein engineering the C-terminus of the main LHC of plants regulates the excited-state lifetime solely via protonation, demonstrating that the protein template of LHCs can be modified to activate reversible quenching mechanisms. The results have implications for photosynthetic organisms that employ feedback mechanisms to avoid photodamage. 2. Long-Lived Intermediates in a Cooperative Two-State Folding Transition. J. Phys. Chem. B 2016, 120 (47), 12040−12046. DOI: 10.1021/acs.jpcb.6b08932. Using a polyproline structure, cooperativity in a twostate protein folding reactant ↔ product transition is studied using ion mobility spectrometry, revealing a longlived intermediate, which is interesting for a two-state transition. 3. Human Islet Amyloid Polypeptide Assembly: The Key Role of the 8−20 Fragment. J. Phys. Chem. B 2016, 120 (46), 11905−11911. DOI: 10.1021/acs.jpcb.6b09475. Ion mobility mass spectrometry and atomic force microscopy are used to study the aggregation of a key sequence of the human islet amyloid polypeptide implicated in type 2 diabetes. 4. Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides. J. Phys. Chem. B 2016, 120 (44), 11395−11404. DOI: 10.1021/acs.jpcb.6b08678. Infrared (IR) absorption frequencies of isotope-labeled amide bonds probe local electrostatic environments and structures. Using empirical frequency maps to relate the spectroscopic data to atomistic structural models, the structural distributions of intrinsically disordered proteins is studied. © 2017 American Chemical Society
5. Water in Contact with a Cationic Lipid Exhibits Bulklike Vibrational Dynamics. J. Phys. Chem. B 2016, 120 (38), 10069−10078. DOI: 10.1021/acs.jpcb.6b07085. The water dynamics at the surface of a positively charged lipid monolayer is found to have dynamics similar to the bulk, as measured by ultrafast 2D sumfrequency generation spectroscopy. The results have implications for water at cell surfaces. 6. Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements. J. Phys. Chem. B 2016, 120 (34), 8905−8913. DOI: 10.1021/acs.jpcb.6b06129. Considerations about NMR transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance that provide information about molecular motions occurring on nanosecond to millisecond (ns−ms) time scales. 7. A Two-Step Method for smFRET Data Analysis. J. Phys. Chem. B 2016, 120 (29), 7128−7132. DOI: 10.1021/ acs.jpcb.6b05697. Analyzing single molecule FRET experiments is problematic when dynamics occurs on the millisecond time scale. A new method is presented that significantly reduces the effort of trajectory analyses to find hidden rate constants. 8. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets. J. Phys. Chem. B 2016, 120 (26), 5810−5816. DOI: 10.1021/acs.jpcb.5b09981. New crystal structures of a segment of the human islet amyloid polypeptide are reported that show that it can adopt out-of-register β sheets with steric zippers, which may be a canonical structural motif for amyloid aggregates. 9. Conformational Landscape and the Selectivity of Cytochrome P450cam. J. Phys. Chem. B 2015, 119 (22), 6620−6627. DOI: 10.1021/acs.jpcb.5b03896. Evidence that a conformational landscape that includes heterogeneity and dynamics is central to understanding P450 activity. 10. Quantifying the Distribution of the Stoichiometric Composition of Anticancer Peptide Lycosin-I on the Lipid Membrane with Single Molecule Spectroscopy. J. Phys. Chem. B 2016, 120 (12), 3081−3088. DOI: 10.1021/acs.jpcb.5b12618. TIRF single molecule microscopy is used to study a peptide toxin on a lipid bilayer to study the monomer/ oligomer size distribution. 11. Structural Origins of Cholesterol Accelerated Lipid Flip-Flop Studied by Sum-Frequency Vibrational Spectroscopy. J. Phys. Chem. B 2016, 120 (12), 3157− 3168. DOI: 10.1021/acs.jpcb.6b01254. Published: February 9, 2017 913
DOI: 10.1021/acs.jpcb.6b12749 J. Phys. Chem. B 2017, 121, 913−914
The Journal of Physical Chemistry B
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Sum-frequency generation spectroscopy is used to quantify the propensity for lipids to flip across a membrane bilayer in order to understand how the compression modulus of a membrane alters the kinetics of lipid translocation in membranes. Double Electron−Electron Spin Resonance Tracks Flavodoxin Folding. J. Phys. Chem. B 2015, 119 (43), 13507−13514. DOI: 10.1021/acs.jpcb.5b00856. A demonstration of using double electron−electron spin resonance (DEER) to study protein folding, evaluating the distance determination between paramagnetic spin-labels. Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation. J. Phys. Chem. B 2014, 118 (28), 7715−7729. DOI: 10.1021/jp409805p. Structurally and functionally very different proteins have similar solvation shells, and local factors are sufficient to rationalize the dynamical heterogeneity of the protein hydration layer. Unified Description of Urea Denaturation: Backbone and Side Chains Contribute Equally in the Transfer Model. J. Phys. Chem. B 2014, 118 (1), 107−114. DOI: 10.1021/ jp409934q. Despite conflicting views in the literature due to inconsistencies in the frequently applied transfer model, the protein denaturation action of urea is settled as coming about equally from interactions with the backbone and side chains of the protein. Preferential Solvation: Dividing Surface vs Excess Numbers. J. Phys. Chem. B 2014, 118 (14), 3922−3930. DOI: 10.1021/jp410567c. The excess solvation numbers of water and osmolyte molecules hold the key to protein assembly only if consistently obtained from experiment, which also points to limitations of traditional approaches such as the osmotic stress technique and solvent binding models. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions. J. Phys. Chem. B 2015, 119 (49), 15075−15088. DOI: 10.1021/acs.jpcb.5b04878. The open research project mnrlipids has collected a vast number of benchmarking molecular dynamics simulations yielding improvements in lipid force fields for membrane simulations, reproducing experimental NMR order parameters. Spontaneous Adsorption of Coiled-Coil Model Peptides K and E to a Mixed Lipid Bilayer. J. Phys. Chem. B 2015, 119 (12), 4396−4408. DOI: 10.1021/acs.jpcb.5b00434. An automated multiscale binding assay allows one to quantify the adsorption of the model fusion peptides to a mixed phospholipid/cholesterol membrane using coarsegrained molecular dynamics simulations. Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation. J. Phys. Chem. B 2015, 119 (26), 8227−8238. DOI: 10.1021/acs.jpcb.5b03948. The review article summarizes potential ways to efficient radio- and photodynamic cancer therapies via sensitizing cellular DNA to ultraviolet radiation or electrons. Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. J. Phys. Chem. B 2016, 120 (17), 4034−4046. DOI: 10.1021/acs.jpcb.6b02732.
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Infrared spectroscopy and molecular dynamics simulations show a linear correlation between nitrile IR frequencies and electric fields in a range of hydrogen-bonding environments fundamental to biomolecular functions. Advances in the Simulation of Protein Aggregation at the Atomistic Scale. J. Phys. Chem. B 2016, 120 (12), 2991− 2999. DOI: 10.1021/acs.jpcb.6b00059. The paper reviews atomistic simulations of protein aggregation, which is associated with Alzheimer’s disease, Parkinson’s disease, and type II diabetes but may also be used as the basis for developing nanoscale materials. Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix−Coil Transition and Helix−Helix Assembly in a Deca-Alanine Peptide. J. Phys. Chem. B 2016, 120 (1), 69−76. DOI: 10.1021/acs.jpcb.5b09881. Intrapeptide and peptide−peptide interactions favor while hydration forces disfavor the helix state of polyalanine over extended states and the paired helix bundle in the assembly of two peptides. Aggregation of Chameleon Peptides: Implications of alpha-Helicity in Fibril Formation. J. Phys. Chem. B 2016, 120 (26), 5874−5883. DOI: 10.1021/acs.jpcb.6b00830. The relationship between the inherent secondary structure and aggregation propensity of peptides with chameleon (context-dependent α- or β-structures) sequences is established, highlighting the role of α-helical intermediates in fibril formation. Unraveling Base Stacking Driving Forces in DNA. J. Phys. Chem. B 2016, 120 (26), 6010−6020. DOI: 10.1021/ acs.jpcb.6b01934. Thermodynamic analysis of molecular simulations shows that the dominant driving force stabilizing base stacking is the nonhydrophobic solvent entropy and not, as suggested previously, dispersion, electrostatics, or solvent hydrogen bonding. Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. J. Phys. Chem. B 2016, 120 (33), 8642−8653. DOI: 10.1021/acs.jpcb.6b03197. Hierarchical looping of chromatin fibers that can effectively bring distant regions of a gene together, satisfying connections reported by contact data and providing a structural mechanism for gene inhibition. Guanidinium Pairing Facilitates Membrane Translocation. J. Phys. Chem. B 2016, 120 (1), 143−153. DOI: 10.1021/acs.jpcb.5b10404. Direct pairing of cationic guanidinuim moieties occurs in aqueous solutions, despite the obvious electrostatic repulsion between like charges, and facilitates transport of cationic peptides across the cellular membrane.
Pavel Jungwirth Martin T. Zanni, Senior Editors AUTHOR INFORMATION
ORCID
Pavel Jungwirth: 0000-0002-6892-3288 Martin T. Zanni: 0000-0001-7191-9768 Notes
Views expressed in this editorial are those of the authors and not necessarily the views of the ACS.
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DOI: 10.1021/acs.jpcb.6b12749 J. Phys. Chem. B 2017, 121, 913−914
