Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center

Rabenstein, Björn; Ullmann, G. Matthias; Knapp, Ernst‐Walter

doi:10.1007/s002490050174

Cited by 86 publications

(101 citation statements)

References 49 publications

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“…A similar procedure was used for the basic groups of arginines and lysines, where instead of removing a proton explicitly in the deprotonated state the charges of all protons at the corresponding basic group were diminished symmetrically by a total unit charge. For cofactors and residues whose protonation states are not considered in the CHARMM22 parameter set, we used appropriate charges that were computed before (23). Because phyllo-Q has the same aromatic ring structure as menaquinone except for the non-polar phytol chain, the charges computed for the latter were used (23).…”

Section: Methodsmentioning

confidence: 99%

Redox Potential of Quinones in Both Electron Transfer Branches of Photosystem I

Ishikita

Knapp

2003

Journal of Biological Chemistry

106

151

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Section: Methodsmentioning

confidence: 99%

Redox Potential of Quinones in Both Electron Transfer Branches of Photosystem I

Ishikita

Knapp

2003

Journal of Biological Chemistry

106

151

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“…The Metropolis criterion is evaluated at the given temperature to accept or reject the move. The efficiency of the sampling is increased by a special treatment of pairs (double moves 41 ) or triplets (triple moves 102 ) of titratable sites that interact by more than a certain energy threshold. In the case of a double (resp.…”

Section: Calculation Of the Titration Profilementioning

confidence: 99%

The Influence of a Transmembrane pH Gradient on Protonation Probabilities of Bacteriorhodopsin: The Structural Basis of the Back-Pressure Effect

CALIMET¹

2004

Journal of Molecular Biology

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Bacteriorhodopsin pumps protons across a membrane using the energy of light. The proton pumping is inhibited when the transmembrane proton gradient that the protein generates becomes larger than four pH units. This phenomenon is known as the back-pressure effect. Here, we investigate the structural basis of this effect by predicting the influence of a transmembrane pH gradient on the titration behavior of bacteriorhodopsin. For this purpose we introduce a method that accounts for a pH gradient in protonation probability calculations. The method considers that in a transmembrane protein, which is exposed to two different aqueous phases, each titratable residue is accessible for protons from one side of the membrane depending on its hydrogen-bond pattern. This method is applied to several ground-state structures of bacteriorhodopsin, which residues already present complicated titration behaviors in the absence of a proton gradient. Our calculations show that a pH gradient across the membrane influences in a non-trivial manner the protonation probabilities of six titratable residues which are known to participate in the proton transfer: D85, D96, D115, E194, E204, and the Schiff base. The residues connected to one side of the membrane are influenced by the pH on the other side because of their long-range electrostatic interactions within the protein. In particular, D115 senses the pH at the cytoplasmic side of the membrane and transmits this information to D85 and the Schiff base. We propose that the strong electrostatic interactions found between D85, D115, and the Schiff base as well as the interplay of their respective protonation states under the influence of a transmembrane pH gradient are responsible for the back-pressure effect on bacteriorhodopsin.

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“…Inside proteins, the value of the dielectric constant is estimated to be as low as ⑀ P ϭ 4, although this value is still a matter of debate and differs depending on the type of application and model description used (14,24,34). Therefore, a basic factor in midpoint potential tuning is the transfer of a cofactor group from aqueous solution to its position in the protein.…”

Section: Tuning Heme Redox Potentialsmentioning

confidence: 99%

“…We determined the heme redox potentials, as well as the protonation pattern of all titratable residues, by calculating the difference in electrostatic energies between heme model systems in solvent and in protein environment from the solutions of the linearized Poisson-Boltzmann equation (13,14,22,23) and by applying a Monte Carlo (MC) titration method to generate the equilibrium protonation and redox pattern (24).…”

mentioning

confidence: 99%

Tuning Heme Redox Potentials in the Cytochrome c Subunit of Photosynthetic Reaction Centers

Voigt

Knapp

2003

Journal of Biological Chemistry

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The photosynthetic reaction center (RC) from Rhodopseudomonas viridis contains four cytochrome c hemes. They establish the initial part of the electron transfer (ET) chain through the RC. Despite their chemical identity, their midpoint potentials cover an interval of 440 mV. The individual heme midpoint potentials determine the ET kinetics and are therefore tuned by specific interactions with the protein environment. Here, we use an electrostatic approach based on the solution of the linearized Poisson-Boltzmann equation to evaluate the determinants of individual heme redox potentials. Our calculated redox potentials agree within 25 meV with the experimentally measured values. The heme redox potentials are mainly governed by solvent accessibility of the hemes and propionic acids, by neutralization of the negative charges at the propionates through either protonation or formation of salt bridges, by interactions with other hemes, and to a lesser extent, with other titratable protein side chains. In contrast to earlier computations on this system, we used quantum chemically derived atomic charges, considered an equilibrium-distributed protonation pattern, and accounted for interdependencies of site-site interactions. We provide values for the working potentials of all hemes as a function of the solution redox potential, which are crucial for calculations of ET rates. We identify residues whose site-directed mutation might significantly influence ET processes in the cytochrome c part of the RC. Redox potentials measured on a previously generated mutant could be reproduced by calculations based on a model structure of the mutant generated from the wild type RC.

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Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center

Cited by 86 publications

References 49 publications

Redox Potential of Quinones in Both Electron Transfer Branches of Photosystem I

Redox Potential of Quinones in Both Electron Transfer Branches of Photosystem I

The Influence of a Transmembrane pH Gradient on Protonation Probabilities of Bacteriorhodopsin: The Structural Basis of the Back-Pressure Effect

Tuning Heme Redox Potentials in the Cytochrome c Subunit of Photosynthetic Reaction Centers

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