TCB Publications - Abstract

Marco Nonella and Klaus Schulten. Molecular dynamics simulation of electron transfer in proteins: Theory and application to QA → QB transfer in the photosynthetic reaction center. Journal of Physical Chemistry, 95:2059-2067, 1991.

NONE91 Electron transfer (ET) from the primary menaquinone $Q_{A}$ to the secondary ubiquinone $Q_{B}$ i.e., $Q_{A}^{-}Q_{B}$ $\rightarrow$ $Q_{A}Q_{B}^{-}$, in the photosynthetic reaction center of Rhodopseudomonas viridis has been simulated by using the method of molecular dynamics accounting for the classical motion of a protein's nuclear degrees of freedom, the redistribution of charge accompanying electron transfer being described quantum chemically. We outline the role of classical nuclear degrees of freedom in electron transfer, identifying the essential dynamic properties that should be determined from molecular dynamics simulations in order to characterize electron transfer. These quantities, all related to the energy difference $\Delta$E(t)=$E_{p}$(t)-$E_{R}$(t) of virtual forward (electron tries to jump forward before ET) and backward (electron tries to jump backward after ET) electron transfer, R and P denoting the states $Q_{A}^{-}Q_{B}$ and $Q_{A}Q_{B}^{-}$, respectively, are as follows: the variance of $\Delta$E(t) and the average value of $\Delta$E(t) before and after transfer, i.e., $\sum_{R}$ (6.9kcal/mol), $\langle$$\Delta$E $\rangle$$ _{R}$ (22 kcal/mol) and $\sum$$_{p}$ (8.8 kcal/mol),$\langle$$\Delta$E$\rangle$$_{p}$ (-25 kcal/mol), respectively; the relaxation time of the energy-energy correlation function $\langle$($\Delta$E(t) - ($\Delta$E)$ _{R}$)($\Delta$E(0) - ($\Delta$E)$ _{R}$)$\rangle$$ _{R}$ (120 fs); the time describing the relaxation of $\Delta$E(t) from an average value $\langle$$\Delta$E$\rangle$$ _{R}$ to an average value $\langle$$\Delta$E$\rangle$$_{p}$ immediately after electron transfer (200 fs). The quantities in brackets are the respective simulation results. We determined also the free enthalpy difference of the transfer $Q_{A}^{-}Q_{B}$ $\rightarrow$ $Q_{A}Q_{B}^{-}$(-3.4 kcal/mol). Our simulations indicate that the motion of the non-heme iron of the reaction center is not coupled to the $Q_{A}$$^{-}Q_{B}$ $\rightarrow$ $Q_{A}Q_{B}^{-}$ transfer. Interaction energies of $Q_{B}$ in different charge states with the protein environment have been calculated and reflect a stronger binding of $Q_{B} ^{-}$ and $Q_{B} ^{2-}$ compared to that of $Q_{B}$.

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