Artur Galstyan

Oxygen-evolving Mn cluster in photosystem II: the protonation pattern and oxidation state in the high-resolution crystal structure.

Extensive quantum chemical DFT calculations were performed on the high-resolution (1.9 Å) crystal structure of photosystem II in order to determine the protonation pattern and the oxidation states of the oxygen-evolving Mn cluster. First, our data suggest that the experimental structure is not in the S(1)-state. Second, a rather complete set of possible protonation patterns is studied, resulting in very few alternative protonation patterns whose relevance is discussed. Finally, we show that the experimental structure is a mixture of states containing highly reduced forms, with the largest contribution (almost 60%) from the S(-3)-state, Mn(II,II,III,III).

Accurate redox potentials of mononuclear iron, manganese, and nickel model complexes*

Density functional theory (DFT) was combined with solution of the Poisson equation for continuum dielectric media to compute accurate redox potentials for several mononuclear transition metal complexes (TMCs) involving iron, manganese, and nickel. Progress was achieved by altering the B3LYP DFT functional (B4(XQ3)LYP‐approach) and supplementing it with an empirical correction term GX having three additional adjustable parameters, which is applied after the quantum‐chemical DFT computations. This method was used to compute 58 redox potentials of 48 different TMCs involving different pairs of redox states solvated in both protic and aprotic solvents. For the 58 redox potentials the root mean square deviation (RMSD) from experimental values is 65 mV. The reliability of the present approach is also supported by the observation that the energetic order of the spin multiplicities of the electronic ground states is fulfilled for all studied TMCs, if the influence from the solvent is considered as well.

Exploring the possible role of Glu286 in CcO by electrostatic energy computations combined with molecular dynamics.

Cytochrome c oxidase (CcO) is a central enzyme in aerobic life catalyzing the conversion of molecular oxygen to water and utilizing the chemical energy to pump protons and establish an electrochemical gradient. Despite intense research, it is not understood how CcO achieves unidirectional proton transport and avoids short circuiting the proton pump. Within this work, we analyzed the potential role of Glu286 as a proton valve. We performed unconstrained MD simulations of CcO with an explicit membrane for up to 80 ns. Those MD simulations revealed that deprotonated Glu286 (Glu286-) is repelled by the negatively charged propionic acid PRD of heme a3. Thus, it destabilizes a potential linear chain of waters in the hydrophobic cavity connecting Glu286 with PRD and the binuclear center (BNC). Conversely, protonated Glu286 (Glu286H) may remain in an upward position (oriented toward PRD) and can stabilize the connecting linear water chain in the hydrophobic cavity. We calculated the pKa of Glu286 under physiological conditions to be above 12, but this value decreases to about 9 under increased water accessibility of Glu286. The latter value is in accordance with experimental measurements. In the time course of MD simulation, we also observed conformations where Glu286 bridges between water molecules located on both sides (the D channel being connected to the N side and the hydrophobic cavity), which might lead to proton backflow.

Tuning electron transfer by ester-group of chlorophylls in bacterial photosynthetic reaction center

Accessory chlorophylls (BA/B) in bacterial photosynthetic reaction center play a key role in charge‐separation. Although light‐exposed and dark‐adapted bRC crystal structures are virtually identical, the calculated BA redox potentials for one‐electron reduction differ. This can be traced back to different orientations of the BA ester‐group. This tuning ability of chlorophyll redox potentials modulates the electron transfer from SP* to BA.

Can oxidation states and the protonation pattern of oxomanganese complexes be recognized from their structures

Multi-core oxomanganese complexes can adopt different oxidation states and protonation patterns depending on ligands and external conditions (for example, solvent, pH, and redox potential). An archetypical example of such complexes is the Mn4Ca cluster in the oxygen-evolving complex (OEC) of photosystem II (PSII). Despite the recent high-resolution crystal structure of PSII, some uncertainty about the oxidation state of the Mn centers and the protonation pattern of the oxygen atoms bridging the metals still exists. In this work, we construct a quantum-chemically based tool to “recognize” the oxidation state and the protonation pattern of oxomanganese complexes from their experimental structure. Combined with simple structural information, our tool can be employed as an empirical guideline to recognize the oxidation state and/or the protonation pattern of those oxomanganese complexes for which this information is not experimentally available.

Understanding Rubredoxin Redox Potentials: Role of H-Bonds on Model Complexes

The energetics of redox states in different models of rubredoxin-like iron-sulfur complexes (ISC) was computed using a combination of density functional and electrostatic continuum theories. In agreement with experiment, the calculated redox potential for the small ISC model [Fe(SCH2CH3)4](1-,2-) in acetonitrile was -813 mV [Galstyan, A. S.; Knapp, E. W. J. Comput. Chem. 2009, 30, 203-211] as compared to the measured value of -838 mV. Surprisingly the experimental values for rubredoxin (Rd) are much higher ranging between -87 and +39 mV. These large variations in redox potentials of ISC models and ISC in Rd are due to specific conformational symmetries adopted by the ligands due to both the protein environment and type and the number of H-bonds, and the dielectric environment. In a dielectric environment corresponding to proteins (ε = 20), the computed ISC redox potentials shift positive by about 64 mV for Fe-S···H-N and 95 mV for Fe-S···H-O H-bonds, correlating well with data estimated from experiments on ISC proteins. In aqueous solutions (ε = 80), a positive shift of 58 mV was computed for Fe-S···H-O H-bonds (using a model with the same ISC conformation as in Rd) in agreement with a measured value for Rd with partially solvent exposed ISC. The latter demonstrates the dependence of the ISC redox potentials on the environment (solvent or protein). For a model whose chemical composition is analog to the relevant part of ISC in a specific Rd, the computed redox potential of the model agrees with the measured value in Rd. This study allows to understand redox potential shifts for small ISC models and ISC in proteins.

Understanding Properties of Cofactors in Proteins: Redox Potentials of Synthetic Cytochromes b

Haehnel et al. synthesized 399 different artificial cytochrome b (aCb) models. They consist of a template-assisted four-helix bundle with one embedded heme group. Their redox potentials were measured and cover the range from -148 to -89 mV. No crystal structures of these aCb are available. Therefore, we use the chemical composition and general structural principles to generate atomic coordinates of 31 of these aCb mutants, which are chosen to cover the whole interval of redox potentials. We start by modeling the coordinates of one aCb from scratch. Its structure remains stable after energy minimization and during molecular dynamics simulation over 2 ns. Based on this structure, coordinates of the other 30 aCb mutants are modeled. The calculated redox potentials for these 31 aCb agree within 10 mV with the experimental values in terms of root mean square deviation. Analysis of the dependence of heme redox potential on protein environment shows that the shifts in redox potentials relative to the model systems in water are due to the low-dielectric medium of the protein and the protonation states of the heme propionic acid groups, which are influenced by the surrounding amino acids. Alternatively, we perform a blind prediction of the same redox potentials using an empirical approach based on a linear scoring function and reach a similar accuracy. Both methods are useful to understand and predict heme redox potentials. Based on the modeled structure we can understand the detailed structural differences between aCb mutants that give rise to shifts in heme redox potential. On the other hand, one can explore the correlation between sequence variations and aCb redox potentials more directly and on much larger scale using the empirical prediction scheme, which--thanks to its simplicity--is much faster.

PSII manganese cluster: protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations.

Photosystem II (PSII) is a membrane-bound protein complex that oxidizes water to produce energized protons, which are used to built up a proton gradient across the thylakoidal membrane in the leafs of plants. This light-driven reaction is catalyzed by withdrawing electrons from the Mn₄CaO₅-cluster (Mn-cluster) in four discrete oxidation steps [S₁-(S₄/S₀)] characterized in the Kok-cycle. In order to understand in detail the proton release events and the subsequent translocation of such energized protons, the protonation pattern of the Mn-cluster need to be elucidated. The new high-resolution PSII crystal structure from Umena, Kawakami, Shen, and Kamiya is an excellent basis to make progress in solving this problem. Following our previous work on oxidation and protonation states of the Mn-cluster, in this work, quantum chemical/electrostatic calculations were performed in order to estimate the pKa of different protons of relevant groups and atoms of the Mn-cluster such as W2, O4, O5 and His337. In broad agreement with previous experimental and theoretical work, our data suggest that W2 and His337 are likely to be in hydroxyl and neutral form, respectively, O5 and O4 to be unprotonated. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.

Crystal structure and modeling calculation of the columnar helix 2,6-Bis(imino)phenoxy iron(III) chloride

Abstract Crystal structure of novel bis(imino)phenoxychloro-iron(III) chloride demonstrated a columnar helix through hydrogen bonding of anion–cation molecules and intermolecular π–π interactions, along with the syntheses and characterization of the new compounds. A quantum-chemical single point calculations of the interaction energies were performed on the basis of the X-ray structural data.

Combined NMR and computational study for azide binding to human manganese superoxide dismutase.

Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the (15)N-labeled inhibitor azide ([(15)N(3)(-)]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy ((19)F-MAS and (15)N-CPMAS). Employing (19)F-(15)N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three (15)N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R(1)=4.85A between the (19)F-label of Tyf34 and the nearest (15)N of the azide and an azide-fluorotyrosine Tyf34 angle of 90 degrees were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide-Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-(19)F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.