Simulation of the Electron Transfer between the Tetraheme Subunit and the Special Pair of the Photosynthetic Reaction Center Using a Microstate Description

Abstract

Charge transfer through biological macromolecules is essential for many biological processes such as, for instance, photosynthesis and respiration. Protons or electrons are transferred between titratable residues or redox-active cofactors, respectively. Transfer rates between these sites depend on the current charge configuration of neighboring sites. Here, we formulate the kinetics of charge-transfer systems in a microstate formalism. A unique transfer rate constant can be assigned to the interconversion of microstates. Mutual interactions between sites participating in the transfer reactions are naturally taken into account. The formalism is applied to the kinetics of electron transfer in the tetraheme subunit and the special pair of the reaction center of Blastochloris viridis. It is shown that continuum electrostatic calculations can be used in combination with an existing empirical rate law to obtain electron-transfer rate constants. The re-reduction kinetics of the photo-oxidized special pair simulated in a microstate formalism is shown to be in good agreement with experimental data. A flux analysis is used to follow the individual electron-transfer steps.

On the interaction of two different types of ligands binding to the same molecule part I: basics and the transfer of the decoupled sites representation to systems with n and one binding sites

“…This problem is of biophysical interest as proteins involved in electron transfer are often located in membranes with pH-gradient. Moreover, it can be applied to any other transporter molecule with proton binding sites or receptors with different types of ligands which are frequently a subject of investigation [3,8,9,13,18,19]. Also from a mathematical point of view this transfer is not trivial as one has to deal with polynomials of the polynomial ring in two variables C [ , κ].…”

Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

“…The kinetics of charge transfer reactions can be simulated by a master equation approach. The rate constants which are required for such simulations can be calculated using electrostatic methods (Sham et al 1999;Ferreira and Bashford 2006;Becker et al 2007). Thus, combined with a master equation approach, continuum electrostatics also offers a possibility to access the non-equilibrium behavior of biomolecular systems.…”

“…7a; Becker et al 2007). The comparison with the experimental data (Ortega and Mathis 1993) shows that continuum electrostatic calculations can be used in combination with the empirical rate law of Eq.…”

A mathematical view on the decoupled sites representation

“…Thus, it can affect the catalytic center of an enzyme, the affinity to the substrate (or to another type of ligand), and the tertiary structure of macromolecules such as proteins and nucleic acids (Garcia-Moreno 1995). Moreover, electron or proton transport chains in oxidation processes and photosynthesis can be described by binding properties of the carrier proteins (Becker et al 2007;Medvedev and Stuchebrukhov 2006;Till et al 2008). Certainly, the mathematical description of titration curves of individual sites of macromolecules is much more complicated than that of small molecules with only one binding site.…”