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First Principle Calculations of intra- and inter-molecular ET in iron-sulfur proteins

Project ETISP2
Research Area Computational biochemistry
Principal Investigator(s) Prof. Michiel Sprik
Institution(s)
  • Department of Chemistry, University of Cambridge, UK
  • Institute of Physical Chemistry, University of Zurich, Switzerland

Abstract

Combining first principle density functional and QM/MM calculations with classical molecular dynamics simulation, various aspects of the electron transfer (ET) in ferredoxin, an aqueous iron-sulfur protein, are investigated within the context of Marcus theory. The hallmark of our approach is that we try to cover both the large system sizes needed for accurate computation and analysis of redox potentials and reorganization free energies and the long time scales needed to converge the statistics of the protein fluctuations. In the case of the study of the electrochemical properties of a single ferredoxin this is achieved by calculation of the electronic structure and total energy of the entire model system (protein+solvent) for configurations sampled from nanosecond time scale classical (force field based) molecular dynamics simulation. For the even larger models of ferredoxin coupled a biological redox partner, the same procedure is applied to a QM/MM region of a comparable large size. The aim of this study is to gain insight in the interplay between short range chemical effects, such as replacement of ligands or residues in the proximity of the redox center, and long range effects, such as protein conformation and the regulation of solvent access to the redox center. (Note that this is a follow up proposal to ETISP, which was granted Enabling Effort only, last year.)

 

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