DFT Study on Nitrite Reduction Mechanism in Copper-Containing

Article pubs.acs.org/biochemistry

DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase Masami Lintuluoto*,† and Juha M. Lintuluoto‡ †

Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan ‡ Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan S Supporting Information *

ABSTRACT: Dissimilatory reduction of nitrite by coppercontaining nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle. The proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, and these two events are understood to couple. Proton-coupled electron transfer is one of the key processes in enzyme reactions. We investigated the geometric structure of bound nitrite and the mechanism of nitrite reduction on CuNiR using density functional theory calculations. Also, the proton transfer pathway, the key residues, and their roles in the reaction mechanism were clarified in this study. In our results, the reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite.

D

bound to three His residues and a water molecule, which is substituted to nitrite.7−11 A nitrite molecule is suggested to bind to the T2 Cu site in an η2-O,O side-on manner based on the crystal structures of nitrite bound CuNiRs and involved in a hydrogen bond network composed of bound waters, and the second coordination sphere highly conserved Asp and His residues is suggested to be essential for the catalytic activity.7−10,12,13 These noncoordinated Asp and His residues are assumed to play important roles in not only the catalytic process but also electron transfer from the spectroscopic experiments with mutants.7 The presence of the hydrophobic residues Ile or Val above the nitrite binding site is supposed to be important to prevent the binding of non-nitrite ligands13−17 and to bind the nitrite η2-O,O side-on form.18,19 The Ile residue above the nitrite binding site is highly conserved among all CuNiRs, whereas a few exceptions have been reported to encode the Val residue at this position.20,21 EPR experimental and DFT results show that the NO side-on is a more favorable conformation than the end-on on Cu T2 site in CuNiR, whereas the end-on structure on the monocuclear Cu(I) NO complexes is more favorable.14−17 The Ile residue above the T2 Cu site plays a main role in the observation of favorable NO side-on structure in CuNiR due to the steric effect.14−17

enitrification, including dissimilatory reduction of nitrate or nitrite to produce gaseous dinitrogen by prokaryotic organisms, is a part of the important geobiochemical nitrogen cycle.1 Denitrification balances the amount of nitrogen content in soil, waters, and the atmosphere.2,4 However, the amount of nitrogen in the soil and aqueous ecosystems has been increasing because of excessive human activities.2,3 Therefore, numerous studies have been focused to understand the mechanism of bacterial denitrification for remediating the human impact on ecosystems.2,4 Nitrite is initially reduced to nitric oxide by dissimilatory nitrite reductases (NiRs) followed by conversion to dinitrogen or nitrous oxide.1 There are two types of NiRs: the copper- and the iron-containing ones. Recent genomic analyses have revealed that a wide variety of organisms from all three taxonomic domains contain at least one gene encoding coppercontaining NiR (nirK).5,6 The copper-containing NiRs (CuNiRs) are homotrimeric enzymes as shown in Figure 1 (a). Each monomer contains two different Cu sites: type 1 (T1) and type 2 (T2). The T1 Cu site, which is the initial site of reduction by an electron donor, is located at monomer subunits, and the T2 Cu site, which is the site of nitrite reduction, is located at the monomer−monomer interface. The T1 Cu site is ligated by two His, a Cys, and a Met residue and connected to the T2 Cu via Cys-His peptide, which is the pathway for the rapid intramolecular electron transfer over 12.5 Å as shown in Figure 1 (b). The T2 site of the resting form is © XXXX American Chemical Society

Received: May 19, 2015 Revised: December 7, 2015

A

DOI: 10.1021/acs.biochem.5b00542 Biochemistry XXXX, XXX, XXX−XXX

Article

Biochemistry

Figure 1. (a) C135A with nitrite of GtNiR (PDB ID: 3WKP) (b) T1 and T2 Cu sites with surrounding residues. Cys135 was substituted for Ala of C135A.

in Scheme 1 (b, iv′).25 Ghosh and co-workers investigated the geometric and electronic structures and reduction mechanism of nitrite bound at the T2 Cu site in NiR from Rhodbacter sphaeroides (RsNiR) by using a combination of spectroscopy and DFT calculations.12 They showed that the protonation of nitrite to form HONO triggers electron transfer from the T2 Cu site to nitrite as shown in Scheme 1 (c). In this study, we investigated the geometric structure of the nitrite-bound T2 Cu site in GtNiR using DFT calculations. Two types of nitrite-stable bound forms have been reported: η1O end-on and η2-O,O side-on forms.12,20 We examined that the nitrite-bound forms at the T2 Cu site depend on both the various protonation states of catalytic residues and the oxidation state of Cu and investigated the role of the hydrophobic residues above the nitrite-bound site on the controlling the nitrite-bound forms. We also investigated the reaction mechanism of the nitrite reduction on the T2 Cu site using DFT calculations. Our results indicated that the reduction of the T2 Cu site promotes the protonation of nitrite, and the hydrogen bond network involving the Asp98, His244, water, and nitrite acts not only to stabilize the conformation of the nitrite bound form but also to promote the proton transfer from Asp98 to nitrite. The conformation of the hydrogen bond network involving the protonated Asp98 and His244 becomes most favorable for the protonation of nitrite. Protonation of nitrite bound on the T2 Cu site does not occur before the reduction of the Cu T2 site or the protonation of Asp98 and His244. Our results indicate that the water molecule in this hydrogen bond network has an important role in the proton transfer from Asp98 to nitrite and the cleavage of the NO bond.

The high-resolution crystal structures of a soluble domain of thermophilic Geobacillus CuNiR from Geobacillus thermodenitrif icans NG80-2 (GtNiR), which is one of a genus of an extremophilic Gram-positive bacterium, has been reported and has a complete set of all genes needed for absolute denitrification.20 The complex structures of WT with the formate and C135A mutant with the nitrite have been successfully determined. The complex structure of C135A with the nitrite shows a unique monodentate Cu(II)-nitrite complex at the T2 Cu site, and the Val residue is encoded above the nitrite binding site. The reaction mechanism of CuNiR has been investigated by a great number of spectroscopic, kinetics, and crystallographic studies.7−9,11−13,22,23 The proposed mechanisms for the reduction of nitrite to form NO and H2O involve electron transfer from the T1 to T2 Cu sites and the protonation of nitrite to form a HONO intermediate in which the proton is proposed to be supplied by the Asp catalytic residue.7,8,11,12,22−25 The intramolecular electron transfer event has been suggested to couple to proton transfer; however, the order of the two events remains under debate. There are a couple of supposed mechanisms for the order of proton and electron transfer as shown in Scheme 1. The binding of nitrite to the T2 Cu site was proposed to induce electron transfer from T1 to T2 Cu sites followed by the proton transfer from the Asp catalytic residue as shown in Scheme 1(a),7 whereas proton transfer from Asp to nitrite to form HONO was proposed to be followed by the electron transfer as shown in Scheme 1 (b).24 Several mechanisms have been suggested for O-NO bond cleavage followed by the formation of leaving NO and water bound to the T2 Cu site. The second proton was needed for the formation of water molecule binding at the T2 site, which is the resting state, and leaving NO. The catalytic His residue was proposed to supply the second proton to reform the resting state as shown in Scheme 1 (a, iv),7 whereas the second proton from the catalytic His residue might move via WAT1 as shown

■

MATERIALS AND METHODS Initial coordinates of the nitrite complex model of GtNiR, in which the nitrite is bound to the T2 Cu site in the η1-O end-on form, were derived from the X-ray structures of C135A with nitrite (PDB ID: 3WKP)20 as shown in Figure 2. Hydrogen atoms were added to each residue in the standard manner by B


Article

Biochemistry Scheme 1. Nitrite Reduction Mechanisms for CuNiRs Proposed in the Preceding Studiesa

a

(a) Electron Transfer from T1 to T2 is followed by the protonation of nitrite. Second proton transfer from His catalytic residue occurs to form the resting state. (b) Protonation of nitrite is followed by the electron transfer from T1 to T2. Second proton is supplied from outside to form the resting state. (c) The protonation of nitrite to form HONO triggers the electron transfer from the T2 Cu site to nitrite.

The combination study of spectroscopy and the computational method showed that the nitrite binds to the T2 Cu site of NiR from Rhodbacter sphaeroides (RsNiR) in η2-O,O side-on form.12 Therefore, we compared the geometrical structures of the nitrite bound form in RsNiR and GtNiR. The model used for RsNiR (PDB ID: 1AS6) was constituted from three His coordinated to the T2 Cu site, two catalytic residues, two water molecules, and Ile257, which exists above the nitrite. B3LYP functional was used for geometry optimization and single point calculations. 6-311G(d) for Cu, N, and O atoms and 6-31G(d) for C and H atoms were used in the geometry optimizations. Unless otherwise specified, the geometries of the primary chain were fixed during the geometry optimization, whereas those of the side chain, waters, nitrite, and the T2 Cu site were fully optimized. Single point calculations were performed using these optimized structures with 6-311+G(d).

assuming a standard protonation state under physiological pH conditions. The model included the T2 Cu site, the nitrite, three His residues coordinated to the T2 Cu site, and the second sphere residues Asp98, His244, and Val246. Additionally, two water molecules were included; one is labeled WAT1 occupying an intermediate position between Asp98 and His244 and another is labeled WAT2 and seems to interact with Asp98 in the initial coordinates of the X-ray structure. We used five models to represent the various protonation states of Asp98 and His244 residues as shown in Scheme 2. Model A in Scheme 2 represents the standard protonation state under physiological pH conditions. In most CuNiRs, Nδ1 proton of catalytic histidine residue is proposed to interact with glutamine or threonine residues to prevent reorientation of the catalytic histidine plane.11,20 We supposed that the Nδ1 of His244 is protonated throughout the nitrite reduction. C


Article

Biochemistry

pKa values from the Gibbs free energy difference ΔG for the deprotonation by using the equations AH → A− + H+

(1)

ΔG = −RT ln K a

(2)

−

where AH, A are protonated, deprotonated His244 and Asp98, respectively. The deprotonation free energy difference is estimated by using the Born−Haber thermodynamic cycle as shown in eq 3 ΔG = ΔGg + ΔGsol(A−) + ΔGsol(H+) − ΔGsol(AH) (3)

where ΔGg is the free energy difference on the deprotonation of AH in the gas phase, and ΔGsol(A−), ΔGsol(H+), and ΔGsol(AH) are the solvation free energies for A−, proton, and AH, respectively. The values of ΔGsol(A−) and ΔGsol(AH) are calculated by using the PCM model. The ΔGsol(H+) estimated by the experimental and computational methods are in the range between −254 and −270 kcal/mol.27−35 We used the value −260 kcal/mol for ΔGsol(H+), which is adopted from the literature.27−31 The value of −6.32 kcal/mol was used for the gas phase free energy of proton at 298 K and standard pressure.36 All calculations were carried out by using Gaussian 09.37 Facio was used for the visualization of DFT calculation results.38 The differences between the η1-O and η2-O,O binding forms of nitrite are clearly present in the Cu−O(nitrite) bond lengths and the bond angles of Cu−O(nitrite)−N(nitrite) as shown in Table 1 and Table S1, where the bond lengths and bond angles of optimized nitrite bound structures are listed. It is difficult to

Figure 2. Initial geometry of the computational model used in this study derived from the X-ray structures of C135A with nitrite (PDB ID: 3WKP).20 Hydrogen atoms are not shown.

We used a PCM with an ε = 4.0 and 78.39 as an implicit solvent model to represent an environment of protein bulk26 and aqueous solution, respectively. We also investigated to the effect of the polarization p function on proton transfer by using 6-311+G(d,p). We calculated the Gibbs free energy and pKa values by using smaller models in which the imidazole and formate groups were substituted with His and Asp amino residues, respectively, and removed Ile257 from the model shown in Figure 2 to reduce the computational costs. The geometries optimized with the larger models as shown in Figure 2 were used for free energy calculations at the B3LYP/6-311G+(d) level. We estimated the

Scheme 2. Computational Models Used to Examine the Various Protonation States of Asp98 and His244 Residuesa

a

(A) Standard protonation state of His244 and Asp98 residues under physiological pH conditions, (B) protonated His244 and deprotonated Asp98, (C and D) deprotonated His244 and protonated Asp98, and (E) protonated His244 and protonated Asp98. D


Article

Biochemistry

evaluate the difference between the two binding forms by using the bond length Cu−O only, but there is a clear difference in the bond angle Cu−O−N. The angles of Cu−O−N in η1-O binding form are in the range of 113.8−128.0°, and the angles of Cu−O−N in η2-O,O binding form are in the range of 84.1− 107.2°. We used the bond angle of Cu−N−O and the bond length Cu−O to distinguish the two different binding forms.

Table 1. Intermolecular Distances and Bond Length (Å) of Optimized Structures of Nitrite Bound to GtNiR in Protonation State E of Scheme 2 Cu(II) O1(nitrite)−Cu O2(nitrite)−Cu N−O1(nitrite) N−O2(nitrite) O1(nitrite)− Cδ2H(His244) O2(nitrite)− Cε1H(His100) O1(nitrite)− HOγ2(Asp98) O2(nitrite)−H (WAT2) H(WAT1)− HNε2(His244) H(WAT1)− Oγ2(Asp98) O(WAT1)− HOγ2(Asp98)

Cu(I)

monodentate

bidentate

monodentate

bidentate

1.97 2.77 1.30 1.21 2.52

2.49 2.00 1.26 1.26 2.77

1.99 2.75 1.29 1.23 1.95

2.10 2.56 1.29 1.23 2.77

2.60

2.79

2.45

3.11

3.27

1.84

2.51

1.74

none

none

1.95

1.91

1.74

1.70

1.66

1.70

1.79

1.84

1.82

1.79

2.89

3.23

3.76

3.16

■

RESULTS AND DISCUSSION Standard Protonation State of His244 and Asp98 Residues under Physiological pH Conditions. We first focused on revealing the role of the hydrophobic residue, which is Val246 for GtNiR and Ile257 for RsNiR, above the nitrite binding site under physiological pH conditions (A in Scheme 2). We compared the conformations of nitrite with and without hydrophobic residues Val246 or Ile257. The geometrical parameters of the only nitrite are optimized, and the other parameters are fixed during the optimization. The geometrical parameters of nitrite in complexes without hydrophobic residues are converged to the monodentate η1 end-on form in both Cu oxidation states of (I) and (II) (Figure S1). The optimized nitrite binding forms with hydrophobic residues are converged to the monodentate η1 and the bidentate η2 forms on Cu(I) and Cu(II) states, respectively (optimized structures

Figure 3. Optimized structures of nitrite binding forms under physiological pH conditions (A in Scheme 2). Val246 is omitted. The dashed lines denote the hydrogen bond network. Nitrite binds in (a) monodentate η1 end-on form on Cu(I) and (b) bidentate η2 side-on form on Cu(II). (c) Comparison of the coordination of nitrite and the environment around the T2 Cu site before and after reduction of the Cu T2 site. Optimized structures of bidentate η2 and monodentate η1 nitrite bound on Cu(II) and Cu(I) atoms are represented by red and green sticks, respectively. E


Article

Biochemistry

Figure 4. Optimized structures in neutral states [His244-Im-Nε2 and Asp98-CγOOH], Scheme 2 (C and D). Val246 is not shown. The dashed lines denote the hydrogen bond network. Nitrite binds by monodentate η1 end-on form for all models. (a) Nitrite bound on Cu(II) site in neutral state C. In neutral state D, nitrite bound on (b) Cu(I) and (c) Cu(II) sites. (d) Comparison of the coordination of nitrite and the environment around the T2 Cu site in neutral state D before and after reduction of the Cu T2 site. Optimized structures before and after reduction of the Cu T2 site are represented by red and green sticks, respectively.

(Af NiR)22 and Achromobacter cycloclastes (AcNiR),8 and His catalytic residues are observed in the “vertical” conformation in which the Nδ1 atom of histidine catalytic residues forms a hydrogen bond with Nγ1 of threonine, which is highly conserved in most CuNiR with few exceptions. Our previous X-ray experimental study and present calculational results suggests that, in GtNiR, the “horizontal” conformation of His244 may have responsibility to the nitrite unique η1 bound mode.20 Conformational Changes of Nitrite and Hydrogen Bond Network around the T2 Cu Site in the Various Protonation States of Asp98 and His244. Spectroscopic and kinetic experiments suggested that the protonation states of Asp98 and His244 have important meanings in the nitrite reduction mechanism.12,13 Therefore, we next investigated nitrite binding at the T2 Cu site in the various protonation states of Asp98 and His 244. We first added one excess proton to the hydrogen bond network system composed by Asp98, His244, and WAT1. Then, we supposed two different protonation states, neutral and charge-separated His244-Asp98 pairs, connecting to each other by WAT1 as shown in Scheme 2 (B−D). The Nε2 of His244 is protonated and the carboxyl group of Asp98 is deprotonated in B ([His244-Im-Nε2H+ and Asp98-CγOO−], respectively), which represents the charge-separated state, and His244 is deprotonated and Asp98 is protonated in C and D

for RsNiR are shown in Figure S2). The role of the hydrophobic residue above the T2 Cu site on the nitrite binding due to steric effect corresponds with the results of NO binding to CuNiR.14−17 Our DFT results indicate that not only the hydrophobic residues Val246 or Ile257 but also the oxidation state of the T2 Cu site determines the nitrite binding form. The geometrical parameters of the side chain of residues, the waters, the nitrite, and the T2 Cu site are fully optimized for the nitrite bound GtNiR complex. The optimized binding forms of nitrite are stabilized in the monodentate η1 and the bidentate η2 forms on Cu(I) and Cu(II) states, respectively, as shown in Figure 3 (a and b) and Table S2. The hydrogen bond networks composed of the nitrite, His244, Asp98, and two water molecules are formed in both binding forms. In the monodentate η1 nitrite bound to the Cu(I) site, the imidazole ring of His244 tilts toward the nitrite compared to that in the bidentate η2 form as shown in Figure 3 (c). Dihedral angles CαCβ-Cγ-Cδ2 of His244 are −91.23° and −114.58° for bindentate and monodentate nitrite bound complexes, respectively. Two conformations, “horizontal” and “vertical”, have been suggested for His catalytic residues.8,20,22 X-ray studies suggest that the Nδ1 atom of His244 in GtNiR forms a hydrogen bond with the carbonyl oxygen of Gln267, which is not included in our calculational models, and this interaction causes the “horizontal” conformation.20 Bidentate η2 side-on nitrite are observed in most CuNiRs, for example, CuNiRs from Alcaligenes faecalis F


Article

Biochemistry

Figure 5. Optimized structures of model E. Val246 is not shown. The dashed lines denote the hydrogen bond network. (a) Monodentate end-on bound form on Cu(II), (b) bidentate side-on bound form on Cu(II), and (c) bidentate side-on form on Cu(I). (d) Comparison of the coordination of the nitrite bidentate form and the environment around the T2 Cu site for model E before and after reduction of the Cu T2 site. Optimized structures before and after reduction of the Cu T2 site are represented by red and green sticks, respectively.

([His244-Im-Nε2 and Asp98-CγOOH], respectively), representing the neutral state. Monodentate and bidentate nitrite bound forms at the Cu(II) site show similar stabilities and geometries in both B and C, and the energy differences between the two forms bound at the Cu(II) site in B and C are approximately 1 kcal/ mol (∼3 kcal/mol in Gibbs free energy differences). The neutral state C is more stable than the charge-separated state B, and the energy difference between the two states are 10.2 and 9.3 kcal/mol (Gibbs free energy difference; 8.8 and 7.8 kcal/ mol) in the monodentate and bidentate forms at the Cu(II) site, respectively. The compensation effect by the surrounding water and the polar residues on the energy difference between the neutral and charge-separated state of Asp-His dyad of Dpath in cytochrome c was reported to be significant.39 WAT1 and His244 seem to interact with another water molecule connecting to the surrounding polar residues in the X-ray structure.20 There is a possibility of compensating for the energy difference between the neutral and charge-separated states by including the surrounding water molecules around WAT1 and His244. Our calculation results may overestimate the energy differences between the two states; however, we think that our results are qualitatively correct. The structures and energetics of nitrite bound complexes on the T2 Cu(I) site are nearly identical to those on the T2 Cu(II) site. Figure 4 (a) shows the optimized structure of the monodentate nitrite binding forms on T2 Cu(II) site in the neutral state C. Asp98 interacts with two water molecules but not with nitrite, and the nitrite contacts only the Cγ2H of

His244. The distances between hydrogen of WAT2 and Oδ2 of Asp98 and between O of nitrite and Cδ2H of His244 are 1.90 and 2.50 Å, respectively. We next examine the protonation state of D in Scheme 2 as shown in Figure 4 (b and c). Bidentate bound form in neutral state D does not exist on either of the Cu oxidation states. There is no energy difference between the monodentate nitrite binding complexes in neutral states C or D at the T2 Cu(II) site. The rotation of CγOO of Asp98 around the Cβ−Cγ axis is supposed to occur easily to let the proton point toward and interact with nitrite. This result is coincident with the high Bvalue and disorder associated with catalytic Asp of various CuNiRs.11 On the T2 Cu(II) site, the hydrogen bond network in neutral state D is different from that in C as shown in Figure 4 (c); Oδ1 and Oδ2H of Asp98 interact with only WAT1 in D, whereas Oδ1 and Oδ2H of Asp98 interact with WAT1 and WAT2 in C, respectively. Hydrogen bond network in neutral state D is significantly changed by the reduction of the T2 Cu site as shown in Figure 4 (b and c). The conformations on Cu(I) and (II) states are almost the same except for the location of WAT2. WAT2 interacts with both Asp98 and nitrite in Cu(I) state, whereas it interacts with the nitrite only in the Cu(II) state. The structures of nitrite and His134 coordinated to the T2 Cu site are changed by the reduction of Cu as shown in Figure 4 (d). His134 is connected to the T1 Cu site via Cys135; therefore, this conformation change by the reduction of T2 Cu site may have some influence on the electron transfer from T1 to T2 sites. G


Article

Biochemistry Scheme 3. Mechanisms for the Nitrite Reduction on the T2 Cu Site Investigated in This Studya

a In mechanism A, the reaction starts from I in which Asp98 is protonated identically to that in Scheme 2 D. In mechanisms B−D, the reaction starts from III in which both Asp98 and His244 are protonated identically to those in Scheme 2 E. The values beneath each structure denote the relative free energy on Cu(I), and the energy barriers in Gibbs free energy on Cu(I) are shown on the left side of or beneath the arrows. The values in the parentheses denote the relative energy and the energy barrier on Cu(II).

state E are over 3 Å. These conformation changes from D to E by the protonation of His244 make Asp98 interact with nitrite more effectively. The distances between O1 of nitrite and Oδ1 of Asp98 in crystal structures of nitrite binding complexes, where O1 of nitrite is the oxygen atom closest to the Asp98, vary between 3.4 and 2.6 Å.8,10,22 The distance between O1 of nitrite and Oδ1 of Asp98 in protonate state E ([His244-ImNε2H+ and Asp98-CγOOH]) is more appropriate to the crystal structural data compared to that in neutral state D ([His244Im-Nε2 and Asp98-CγOOH]). Structures of nitrite in the bidentate form on both Cu oxidation states are asymmetric in which two O−Cu distances are different as shown in Table 1. Cu−O1 distance, where O1 interacts with the Oδ1 of Asp98, is longer than Cu−O2 on the T2 Cu(II) site, whereas Cu−O2 is longer than O1−Cu on the T2 Cu(I) site. Our results are coincident with the crystal

We add another proton to neutral state D to build the protonation state E. In E, both Asp98 and His244 are protonated. On the T2 Cu(II) site, the bidentate nitrite bound form exists as stable as the monodentate nitrite binding form, and the energy difference between the two nitrite forms is 1.6 kcal/mol (2.1 kcal/mol in Gibbs free energy difference). On the T2 Cu(I) site, the bidentate nitrite binding form is more stable by 7.1 kcal/mol (7.5 kcal/mol in Gibbs free energy difference) than the monodentate form. Hydrogen bond networks in the protonated state E are different from those in the neutral state D as shown in Figure 5. In the bidentate form, nitrite moves to interact with Asp98 more effectively compared to that in the monodentate form. The distances between HOδ2 of Asp98 and O1 atom of nitrite bidentate forms on the Cu(II) and Cu(I) T2 site in protonated state E are 1.84 and 1.74 Å, respectively, as shown in Table 1, whereas those in the neutral state D and those of monodentate in protonated H


Article

Biochemistry

Figure 6. Energy landscapes for the mechanisms C and D in Gibbs free energy values. The black and red lines denote mechanism C on Cu(I) and (II) T2 sites, and the blue line denotes mechanism D on Cu(I) T2 sites.

+ Asp98-CγOO− → His244-Im-Nε2 + Asp98-CγOOH) between models B and D are 1.3 and −0.5 on Cu(I) and Cu(II), respectively. In model D, the bidentate state is not stable; however, adding another proton to His244 makes the bidentate nitrite more stable than monodentate by 1.6 and 7.1 kcal/mol (2.1 and 7.5 kcal/mol in Gibbs free energy) on the Cu(I) and (II) states, respectively. The pKa values of deprotonation from His244 and Asp98 in model E are 6.8 and 8.1 on Cu(I), respectively, whereas those values on Cu(II) are very acidic at 3.2 and 2.7, respectively. The protonation of both catalytic residues occurs more easily on Cu(I). Model E is more favorable at low pH on Cu(II); our results are in agreement with the EPR and other DFT calculation results by Ghosh and co-workers.12 The protonation of His244 changes the conformation of the hydrogen bond network and makes the distances between HOδ2 of Asp98 and O1 atom of nitrite bidentate shorter than before the protonation (over 3 Å to 1.84 and 1.74 Å on Cu(II) and (I), respectively). The protonation state of His244 has a significant effect to stabilize the bidentate form of nitrite, and this result coincides with the pH dependency of the catalytic activity and mutant genesis studies, which suggest that the catalytic His residue associates the nitrite binding by controlling the position of the catalytic Asp residue through the hydrogen network.7,20,25 In the protonated Asp98 and protonated His244, the reduction of the T2 Cu site makes the distance between HOδ2 of Asp98 and O atom of nitrite shorter from 1.84 to 1.74 Å, and this conformational change might make the proton transfer more easily. Reaction Mechanism of the Nitrite Reduction on the T2 Cu Site. We first examined the proton transfer from Asp98 to nitrite to form HONO bound on the Cu T2 site. Supposed mechanisms are shown in Scheme 3. In structure I as reactant of mechanism A, Asp98 is protonated and His244 is neutral identically to those of model D in Scheme 2. Structure II resulting from the protonation of nitrite is unstable on the Cu(I) site, and the same protonation reaction on the Cu(II) site is 34.0 kcal/mol endothermic. For structure III as a reactant of mechanisms B−D, both Asp98 and His244 are protonated the same as those in model E in Scheme 2. In mechanism B,

structural data of Cu(II)−nitrite complexes in which Cu−O1 are longer than Cu−O2.8,10,22 Optimized structures of the nitrite bidentate form and the environment around the T2 Cu site before and after reduction of T2 Cu site are almost the same, except for the conformation of His134 bound to the T2 Cu site as shown in Figure 5 (d). Dihedral angle Cu-Nε-Cδ-Nγ of His134 in the Cu reduced state is 168.9°, whereas in the Cu oxidized state, it is 150.7°. This conformation change of His134 by the reduction of the T2 Cu site is supposed to have correlation to the electron transfer from T1 to T2 sites. Our results indicate that the binding form of nitrite depends on not only the oxidation state of the T2 Cu site but also the protonation state of Asp98 and His244. We performed the calculation of pKa values for the His and Asp residues in each model. We first tested our calculation’s reliability by calculating the values of pKa for the deprotonation of His and Asp residues in water. The values of pKa for His and Asp are examined to be 6.1 and 5.0, respectively, which are qualitatively in good agreement with the standard values of 6.5 and 3.9.40 Although the Born−Haber thermodynamic cycle has been used for the estimation of pKa, the ab initio prediction of pKa is still very difficult. The error of 1 kcal in Gibbs free energy difference translates to an error of approximately 0.73 in the estimated pKa. The error in the estimation of Gibbs free energy of DFT has been reported as 2−3 kcal.41 The size of our models also affects the estimation of pKa due to the localization of charge on amino residues, the hydrogen bonding, and so on. However, the calculation of pKa based on the Born−Haber cycle has shown reasonable qualitative results compared to the experimental results in the literature.27−35 Thus, we think the comparison of pKa among our calculational models is qualitatively correct. The values of pKa for the deprotonation of His244 in model B are 7.2 and 9.0 on Cu(I) and Cu(II), respectively. The values of pKa for the deprotonation of Asp98 in model C are 11.1 and 8.7 on Cu(I) and Cu(II), respectively. As mentioned above, model D, [His244-Im-Nε2 and Asp98-CγOOH], is more stable than models B and C. The values of ΔpKa (His244-Im-Nε2H+ I


Article

Biochemistry

Figure 7. Optimized structure of HONO complex on the Cu(I) T2 site, which is structure V of mechanism C in Scheme 3. Val246 is not shown. The dashed lines denote the hydrogen bond network. (a) Top and (b) side view of nitrite binding complexes.

Figure 8. (a) Optimized structure of HONO complex on Cu(I) T2 site, which is structure VI of mechanism D in Scheme 3. (b) Transition state from structure III to VI on the Cu(I) site in mechanism D. Val246 is not shown. The dashed lines denote the hydrogen bond network.

His244 does not change its protonation state during the proton transfer from Asp98 to nitrite to form structure IV, and structure IV is not stable on either of the Cu oxidation states. In mechanisms C and D, the proton transfer from HNε2-His244 to Asp98 via WAT1 occurs at the same time as the proton transfer from Asp98 to nitrite. In mechanism C, structure V on the Cu(II) site is less stable by 8.3 kcal/mol (10.5 kcal/mol in Gibbs free energy) than structure III, whereas structure V on the Cu(I) site has almost the same stability as structure III. These results show that the proton of HNε2-His244 plays an important role not only to fix the appropriate position of Asp98 via the hydrogen bond network but also to promote the proton transfer from Asp98. The energy landscape of the reactions is shown in Figure 6. The activation energies of mechanism C are 35.8 and 47.8 kcal/mol (34.5 and 47.1 kcal/mol in Gibbs free energy) on Cu(I) and (II) sites, respectively. Structure VI, as a product in mechanism D, is not stable on the Cu(II) site, whereas structure VI on the Cu(I) site is 2.5 kcal/mol (3.7 kcal/mol in Gibbs free energy) less stable than structure III. The conformation of structure VI as a product in mechanism D is different from that of structure V in mechanism C as shown in Figures 7 and 8 and Table 2. HONO interacts with Cu by

Table 2. Intermolecular Distance and Bond Length (Å) of Optimized HONO in Structures V and VI of Scheme 3 and Transition State to Form Structure VI O(HONO) T2 Cu(I) N(HONO) T2 Cu(I) H−-ONO(HONO) HO−NO(HONO) HON−O(HONO) H(HONO)−O1γ2(Asp98) H−O2γ2(Asp98) O(WAT1)−HO2γ2(Asp98) H(WAT1)−-Nε2(His244) H(WAT1)−O(HONO)

structure V

structure VI

transition state

2.17 3.13 0.99 1.47 1.17 1.80 1.01 1.65 1.84 4.72

2.12 2.10 1.00 1.50 1.19 1.62 1.01 1.64 1.81 4.12

2.10 2.41 1.24 1.39 1.21 1.12 1.18 1.26 1.67 1.70

the protonated oxygen atom in structure V in which the binding is monodentate form, whereas HONO interacts by not only protonating oxygen but also nitrogen atoms in structure VI, which has a side-on binding form. The activation energy for mechanism D is 27.3 kcal/mol (25.4 kcal/mol in Gibbs free energy) on the Cu(I) T2 site. WAT1 interacts with nitrite in J


Article

Biochemistry

These results show that the proton transfer from HεNHis244 to WAT1 promotes the proton transfer from Asp98 to nitrite to form the HONO so that there is no proton on εNHis244 to transfer to HONO, and the distances between εNHis244 and HONO are very long for proton transfer: 3.85 and 3.81 Å in structure V on the Cu(I) and (II) T2 sites, respectively, and 3.28 Å in structure VI on Cu(I). Our results also show that HO−NO bond cleavage and NO desorption from structures V and VI occurs by 13.9 and 16.3 kcal/mol (15.2 and 16.2 kcal/mol in Gibbs free energy), respectively, without the second proton. We concluded that His244 is not involved in the HO−NO bond cleavage and NO desorption. The β-LUMOs are composed of Cu d, nitrite π*, and His N nonbonding orbitals in both nitrite (structure III)- and HONO (structure V)-bound complexes on Cu(II) as shown in Figure 9. The contribution of Cu d, nitrite π*, and His N nonbonding orbitals in β-LUMO of the nitrite complex (structure III) are 64, 18, and 18%, respectively. This result is in agreement with the EPR and DFT studies for CuNiR.12 Because β-LUMO is contributed by dz2 type (36%), this induces the asymmetric binding mode of nitrite on Cu(II) T2 site in model E. Adding the Jahn−Teller effect, there is an interaction between Asp98-H and the oxygen of nitrite, and this interaction makes one Cu−O distance longer. The spin density of the Cu atom is 0.60 and 0.61 for nitrite and HONO complexes, respectively. The contributions of Cu d, nitrite π*, and His N nonbonding orbitals in β-LUMO of the HONO complex (structure V) are 65, 9, and 26%, respectively. The protonations of both His244 and Asp98 to form model E in Scheme 2 are very important for the stabilization and protonation of bound nitrite. Our calculated pKa values show that the single protonation of either His244 or Asp98 occurs on both Cu oxidation states. Model D is the most favorable structure among the single protonation states (models B−D in Scheme 2). Our calculated pKa values also show the protonation of His244 of model D to obtain model E (structure III in Scheme 3) is difficult to occur on Cu(II). This along with structure III (Scheme 3) on Cu(I), which is required for the protonation of bound nitrite, implies that the reduction of the T2 site should occur before structure III is formed. We summarize the sequence of events of nitrite reduction on the T2 Cu site as shown in Scheme 4. De Marothy and co-workers applied the DFT calculation to nitrite reduction.41 They supposed the higher pH range and used the smaller models for CuNiR, including Cu T2, three His residues coordinating to T2, and Asp catalytic residue without

the transition state for mechanism D as shown in Figure 8 (b) and Table 2. This interaction between WAT1 and nitrite stabilizes the transition state, and the activation energy becomes smaller compared to that in mechanism C. We also examined adding the excess proton via the proton channel from the outside of the protein to structure III. Adding the excess proton to the nitrite to form HONO is stabilized as shown in Figure S3. However, the pKa value of HONO deprotonation is negative on both oxidation states of the Cu T2 site; therefore, adding the excess proton is difficult. We investigated the effect of polarization p function on proton transfer by using 6-311+G(d,p) with PCM. The activation energies of mechanism C are 34.1 and 46.0 kcal/ mol on the Cu(I) and (II) sites, respectively, and the value for mechanism D is 23.1 kcal/mol on the Cu(I) T2 site. The energy differences between them with and without polarization p function are 2−4 kcal/mol, and the activation energy of mechanism D is reduced by 4.2 kcal/mol. Although including the polarization p function for investigating the proton transfer reduces the activation energy, we think that the qualitative results are not changed. Next, we examined HO−NO bond cleavage by following the formation of structures VII and VIII. The activation energies for structures V and VI are 13.9 and 16.3 kcal/mol (15.2 and 16.2 kcal/mol in Gibbs free energy), respectively. When the HO− NO bond of structure VI is elongated, the NO desorbs from Cu(I) and structure VII is formed instead of forming structure VIII. Structure VII is 5.1 kcal/mol (1.7 kcal/mol in Gibbs free energy) less stable than the nitrite bound complex structure III. The net atomic charge on the Cu(I) atom gradually increases from 1.00 to 1.13 during the proton transfer along mechanism D as shown in Table 3. Then, the change of the net atomic charge on Cu(I) from structure VI to VII seems to show the electron transfer from Cu(I) to HO. Table 3. Changes of the Net Atomic Charges During NO Desorption from the Cu(I) T2 Site along Mechanism D in Scheme 3 in which the Net Atomic Charges were Calculated without the Diffuse Basis Functions structure III transition state structure VI structure VII

T2 Cu(I)

O (nitrite)

1.00 1.06 1.13 1.34

−0.53

HO (HONO)

NO

−0.15 −0.10 −0.55

−0.23 −0.17 −0.22 0

Figure 9. β-LUMOs of (a) nitrite (structure III) and (b) HONO (structure V) in model E on the Cu(II) T2 site. K


Article

Biochemistry Scheme 4. Mechanisms for Nitrite Reduction on the T2 Cu Site Concluded in This Studya

a

Nitrite binds on Cu(II) in model D of Scheme 2 followed by reduction of the T2 Cu site. Then, the protonation of His244 in model D occurs to form model E of Scheme 2. The nitrite reduction starts on Cu(I) in model E of Scheme 2, which is structure III of Scheme 3. The values beneath each structure denote the relative free energy on Cu(I), and the energy barriers in Gibbs free energy and values of pKa on Cu(I) are shown beneath the arrows.

η1-N binding forms has not yet been discussed.42 In our mechanism, the η2-O,O binding form binds on Cu(II) in model D followed by the reduction of the Cu T2 site. When the protonation of Asp98 occurs to achieve model E, the nitrite binds on Cu(I) in the η2-O,O binding form. There is no requirement or opportunity for conversion from η2-O,O to the η1-N binding form. A QM-MM study for the mechanism of heme-containing NiR showed that the protonation of two catalytic His residues plays an important role for stabilizing the nitrite binding on Fe.44 We found the same importance for the protonation states of His and Asp catalytic residues of CuNiR in this study. Zhao and co-workers reported that the values of activation energy obtained via Eyring plots at pH values between 5.0 and 7.5 were 8−19 kcal/mol.13 Our results show that the activation energy in Gibbs free energy is 25.4 kcal/mol. Ghosh and coworkers showed that the activation energy is 16 kcal by DFT calculation with almost the same size model12 and is also in good agreement with the experimental result. We think that our energy barrier is slightly high because the protonation of nitrite involves two proton transfers, which are from Asp98 to nitrite and from His244 to Asp98 at the same time. The proton pool exists around the WAT1 in GtNiR, which is the minor proton channel in general CuNiRs. Those water molecules build the hydrogen bond network, including the other amino acid residues. This hydrogen bond network may support the proton transfer from His244 to Asp98. Li et al. confirmed the solvent effect by including the explicit 500 water molecules and reported that including the explicit water molecules changed the energy barrier by approximately 4 kcal/mol.42 Not only the water molecules but also the protein environment also may affect the energy barrier. Although including the solvent effect, size of models, and level of calculational method may change

the His catalytic residue. The energy barrier of leaving NO is larger than the protonation of nitrite in their mechanism, and the largest energy barrier was 11.3 kcal/mol. The monodentate binding form as the stable nitrite form on both Cu oxide states was adopted due to the lack of hydrophobic residue above the Cu T2 site, and the role of the His residue was not discussed in their mechanism. Li et al. reported the energy barrier of nitrite reduction by CuNiR as 20 kcal/mol in their DFT study.42 They suggested that the reduction of the T2 Cu site was followed by nitrite reduction. The nitrite reduction in their reaction mechanism starts from the η1-N binding nitrite and the two protons transferred from Asp and His residues. As in our models, their models included the same amino residues and four water molecules. We therefore examined the η1-N binding form. The η1-N binding forms in model E of Scheme 2, [His244-Im-Nε2H+ and Asp98-CγOOH], are shown in Figure S5. They are almost as stable as the η2-O,O binding form on both Cu(I) and Cu(II), and the differences are less than 1 kcal/mol in Gibbs free energy. The spectroscopic and DFT study for the coppernitrito complexes also showed that the energy differences between these conformations are small.43 However, the η1-N binding forms in model D of Scheme 2, [His244-Im-Nε2 and Asp98-CγOOH], are very unstable compared to the η2-O,O binding form by 5.5 and 9.5 kcal/mol on Cu(I) and (II), respectively. Likewise, as discussed above, model D is required to achieve model E as shown in Scheme 4. Furthermore, the reduction of Cu T2 site should be followed by the protonation of Asp98 to achieve model E. Li et al. supposed that the nitrite binds to the Cu T2 site by the η2-O,O binding form followed by the electron transfer from the T1 to T2 site.42 They supposed that the protonation of nitrite starts from the η1-N binding form. However, the conversion between η2-O,O and L


Article

Biochemistry

A. (2008) Transformation of the Nitrogen Cycle: Recent Trends, Questions, and Potential Solutions. Science 320, 889−892. (4) Suzuki, S., Kataoka, K., Yamaguchi, K., Inoue, T., and Kai, Y. (1999) Coord. Chem. Rev. 190−192, 245−265. (5) Jones, C. M., Stres, B., Rosenquist, M., and Hallin, S. (2008) Phylogenetic Analysis of Nitrite, Nitric Oxide, and Nitrous Oxide Respiratory Enzymes Reveal a Complex Evolutionary History for Denitrification. Mol. Biol. Evol. 25, 1955−1966. (6) Kim, S.-W., Fushinobu, S., Zhou, S., Wakagi, T., and Shoun, H. (2009) Eukaryotic nirK Genes Encoding Copper-Containing Nitrite Reductase: Originating from the Protomitochondrion? Appl. Environ. Microbiol. 75, 2652−2658. (7) Suzuki, S., Kataoka, K., and Yamaguchi, K. (2000) Metal Coordination and Mechanism of Multicopper Nitrite Reductase. Acc. Chem. Res. 33, 728−735. (8) Antonyuk, S. V., Strange, R. W., Sawers, G., Eady, R. R., and Hasnain, S. S. (2005) Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism. Proc. Natl. Acad. Sci. U. S. A. 102, 12041− 12046. (9) Leferink, N. G. H., Han, C., Antonyuk, S. V., Heyes, D. J., Rigby, S. E. J., Hough, M. A., Eady, R. R., Scrutton, N. S., and Hasnain, S. S. (2011) Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry 50, 4121−4131. (10) Murphy, M. E. P., Turley, S., and Adman, E. T. (1997) Structure of Nitrite Bound to Copper-containing Nitrite Reductase from Alcaligenes faecalis. J. Biol. Chem. 272, 28455−28460. (11) Adman, E. T., Godden, J. W., and Turley, S. (1995) The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2− bound and with type II copper depleted. J. Biol. Chem. 270, 27458−27474. (12) Ghosh, S., Dey, A., Sun, Y., Scholes, C. P., and Solomon, E. I. (2009) Spectroscopic and Computational Studies of Nitrite Reductase: Proton Induced Electron Transfer and Backbonding Contributions to Reactivity. J. Am. Chem. Soc. 131, 277−288. (13) Zhao, Y., Lukoyanov, D. A., Toropov, Y. V., Wu, K., Shapleigh, J. P., and Scholes, C. P. (2002) Catalytic Function and Local Proton Structure at the Type 2 Copper of Nitrite Reductase: The Correlation of Enzymatic pH Dependence, Conserved Residues, and Proton Hyperfine Structure. Biochemistry 41, 7464−7474. (14) Periyasamy, G., Sundararajan, M., Hillier, I. H., Burton, N. A., and Mcdouall, J. J. (2007) The binding of nitric oxide at the Cu(I) site of copper nitrite reductase and of inorganic models: DFT calculations of the energetics and EPR parameters of side-on and end-on structures. Phys. Chem. Chem. Phys. 9, 2498−2506. (15) Fujisawa, K., Tateda, A., Miyashita, Y., Okamoto, K., Paulat, F., Praneeth, V. K. K., Merkle, A., and Lehnert, N. (2008) Structural and Spectroscopic Characterization of Mononuclear Copper(I) Nitrosyl Complexes: End-on versus Side-on Coordination of NO to Copper(I). J. Am. Chem. Soc. 130, 1205−1213. (16) Merkle, A., and Lehnert, N. (2009) The Side-On Copper(I) Nitrosyl Geometry in Copper Nitrite Reductase Is Due to Steric Interactions with Isoleucine-257. Inorg. Chem. 48, 11504−11506. (17) Silaghi-Dumitrescu, R. (2006) Copper-containing nitrite reductase: A DFT study of nitrite and nitric oxide adducts. J. Inorg. Biochem. 100, 396−402. (18) Boulanger, M. J., and Murphy, M. E. P. (2003) Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: Characterization of an active site isoleucine. Protein Sci. 12, 248−256. (19) Tocheva, E. I., Eltis, L. D., and Murphy, M. E. P. (2008) Conserved Active Site Residues Limit Inhibition of a CopperContaining Nitrite Reductase by Small Molecules. Biochemistry 47, 4452−4460. (20) Fukuda, Y., Tse, K. M., Lintuluoto, M., Fukunishi, Y., Mizohata, E., Matsumura, H., Takami, H., Nojiri, M., and Inoue, T. (2014) Structural insights into the function of a thermostable coppercontaining nitrite reductase. J. Biochem. 155, 123−135.

the value of the energy barrier and stabilization energy, we think the qualitative figure in this study will not change.

■

CONCLUSIONS We investigated the geometric structure of a nitrite-bound T2 Cu site in GtNiR by using the DFT calculation method. Two types of nitrite bound stable forms were found on the Cu T2 site: η1-O end-on and η2-O,O side-on forms. The nitrite binding conformation depends on both the oxidation state of Cu and the protonation states of Asp98 and His244 catalytic residues. The conformation of the hydrogen bond network composed by the nitrite, Asp98 and His244 residues, and two water molecules also changes depending on both the Cu oxidation state and the protonation state of the catalytic residues. The protonation state of Nε2-His244 has a significant effect not only to stabilize the bidentate form of nitrite, as has been suggested by the experimental results, but also to make the proton transfer from Asp98 to nitrite more efficient by reducing the distance between HOδ2 of Asp98 and the O atom of nitrite. The proton transfer from Asp98 to nitrite on Cu(I) is more favorable than that on Cu(II). HO−NO dissociation and desorption occur from HONO without second proton transfer to form a HO−Cu(II) complex. Electron transfer from the Cu(I) T2 site to HO occurs along the HO−NO dissociation and desorption.

■

ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.biochem.5b00542. Optimized nitrite bound structure of RsNiR, optimized HONO structure formed by the excess proton to model E, optimized structures of HONO and transition states in mechanisms C and D, which are not shown in Figures 7 and 8, η1-N binding form and intermediate HONO from the η1-N binding form, and detailed information regarding the nitrite binding structures and the hydrogen bond network in our models (PDF)

■

AUTHOR INFORMATION

Corresponding Author

*Tel: +81-75-703-5445. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

■

ACKNOWLEDGMENTS The computations in this work were performed using the Research Center for Computational Science, Okazaki, Japan. We acknowledge valuable discussions and comments with Dr. Yoshifumi Fukunishi, Dr. Yohta Fukuda, and Prof. Takeshi Inoue.

■

REFERENCES

(1) Zumft, W. G. (1997) Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev. 61 (4), 533−616. (2) Gruber, N., and Galloway, J. N. (2008) An Earth-system perspective of the global nitrogen cycle. Nature 451, 293−296. (3) Galloway, J. N., Townsend, A. R., Erisman, J. W., Bekunda, M., Cai, Z., Freney, J. R., Martinelli, L. A., Seitzinger, S. P., and Sutton, M. M


Article

Biochemistry

Cioslowski, J., Fox, D. J. (2009) Gaussian 09, revision D.01, Gaussian, Inc., Wallingford CT. (38) Suenaga, M. (2008) Development of GUI for GAMESS/FMO calculation. J. Comput. Chem., Jpn. 7, 33−53. (39) Kamiya, K., Boero, M., Shiraishi, K., Oshiyama, A., and Shigeta, Y. (2010) Energy compensation mechanism for charge-separated protonation states in aspartate-histidine amino acid residue pairs. J. Phys. Chem. B 114, 6567−6578. (40) Pace, C. N., Grimsley, G. R., and Scholtz, J. M. (2009) Protein Ionizable Groups: pKa Values and Their Contribution to Protein Stability and Solubility. J. Biol. Chem. 284, 13285−13289. (41) De Marothy, S. A., Blomberg, M. R. A., and Siegbahn, P. E. M. (2007) Elucidating the Mechanism for the Reduction of Nitrite by Copper Nitrite Reductase − A Contribution from Quantum Chemical Studies. J. Comput. Chem. 28, 528−539. (42) Li, Y., Hodak, M., and Bernholc, J. (2015) Enzymatic Mechanism of Copper-Containing Nitrite Reductase. Biochemistry 54, 1233−1242. (43) Lehnert, N., Cornelissen, U., Neese, F., Ono, T., Noguchi, Y., Okamoto, K., and Fujisawa, K. (2007) Synthesis and Spectroscopic Characterization of Copper(II)-Nitrito Complexes with Hydrotris(pyrazolyl)borate and Related Coligands. Inorg. Chem. 46, 3916−3933. (44) Marti, M. A., Crespo, A., Bari, S. E., Doctorovich, F. A., and Estrin, D. A. (2004) QM-MM Study of Nitrite Reduction by Nitrite Reductase of Pseudomonas aeruginosa. J. Phys. Chem. B 108, 18073− 18080.

(21) Boulanger, M. J., and Murphy, M. E. P. (2002) Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases. J. Mol. Biol. 315, 1111−1127. (22) Tocheva, E. I., Rosell, F. I., Mauk, A. G., and Murphy, M. E. P. (2004) Side-On Copper-Nitrosyl Coordination by Nitrite Reductase. Science 304, 867−870. (23) Merkle, A. C., and Lehnert, N. (2012) Binding and activation of nitrite and nitric oxide by copper nitrite reductase and corresponding model complexes. Dalton Trans. 41, 3355−3368. (24) Sundararajan, M., Hillier, I. H., and Burton, N. A. (2007) Mechanism of Nitrite Reduction at T2Cu Centers: Electronic Structure Calculations of Catalysis by Copper Nitrite Reductase and by Synthetic Model Compounds. J. Phys. Chem. B 111, 5511−5517. (25) Boulanger, M. J., and Murphy, M. E. P. (2001) Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate. Biochemistry 40, 9132−9141. (26) Simonson, T., and Brooks, C. L., III (1996) Charge Screening and the Dielectric Constant of Proteins: Insights from Molecular Dynamics. J. Am. Chem. Soc. 118, 8452−8458. (27) Wang, T., Brudvig, G., and Batista, V. S. (2010) Characterization of Proton Coupled Electron Transfer in a Biomimetic Oxomanganese Complex: Evaluation of the DFT/B3LYP Level of Theory. J. Chem. Theory Comput. 6, 755−760. (28) Hwang, S., and Chung, D. S. (2005) Calculation of the Solvation Free Energy of the Proton in Methanol. Bull. Korean Chem. Soc. 26, 589−593. (29) Reiss, H., and Heller, A. (1985) The absolute potential of the standard hydrogen electrode: a new estimate. J. Phys. Chem. 89, 4207− 4213. (30) Jang, Y. H., Sowers, L. C., Ç aǧin, T., and Goddard, W. A., III (2001) First Principles Calculation of pKa Values for 5-Substituted Uracils. J. Phys. Chem. A 105, 274−280. (31) Lim, C., Bashford, D., and Karplus, M. (1991) Absolute pKa calculations with continuum dielectric methods. J. Phys. Chem. 95, 5610−5620. (32) Tawa, G. J., Topol, I. A., Burt, S. K., Caldwell, R. A., and Rashin, A. A. (1998) Calculation of the aqueous solvation free energy of the proton. J. Chem. Phys. 109, 4852−4863. (33) Tissandier, M. D., Cowen, K. A., Feng, W. Y., Gundlach, E., Cohen, M. H., Earhart, A. D., Coe, J. V., and Tuttle, T. R., Jr. (1998) The Proton’s Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster-Ion Solvation Data. J. Phys. Chem. A 102, 7787−7794. (34) Bykov, D., and Neese, F. (2011) Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study. JBIC, J. Biol. Inorg. Chem. 16, 417−430. (35) Bykov, D., and Neese, F. (2012) Reductive activation of the heme iron−nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. JBIC, J. Biol. Inorg. Chem. 17, 741−760. (36) Fifen, J. J., Dhaouadi, Z., and Nsangou, M. (2014) Revision of the Thermodynamics of the Proton in Gas Phase. J. Phys. Chem. A 118, 11090−11097. (37) Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A., Jr., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, M. J., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, Ö ., Foresman, J. B., Ortiz, J. V., N


DFT Study on Nitrite Reduction Mechanism in Copper-Containing

Recommend Documents