Electron transport is the essential mechanism for energy flow in respiration and photosynthesis. The mechanisms for electron transfer by proteins are still the subject of much debate. The research proposed here is to study electron transfer proteins by computational techniques such as molecular dynamics simulations. In these methods, the motions of individual atoms in a protein are modeled. This research is aimed at simulations of iron-sulfur proteins, which are a class of electron transfer proteins which are well characterized experimentally but not by simulations. Most of the initial studies will focus on the rubredoxins, which have a single iron. Preliminary steps will involve simple studies of the structure and dynamics of rubredoxin via molecular dynamics simulations. The next step will be to study how the protein environment influences the iron-sulfur site. The magnitudes and fluctuations of the distances the electron must travel and the polarization field at the active site can be calculated from the simulation. Comparison with simulations of analogs of the active site in solution can provide insight into how the protein environment alters the transfer process from what it would be for a simple compound with the same iron-sulfur site. Also, simulations of homologous rubredoxins, for which there are x-ray structures, can be used to determine how specific amino acid changes can influence the transfer. The eventual goal will be to develop methods for studying the quantum mechanical phenomena of electron transfer. One study will involve using path integral simulations of the transfer electron in the environment of the protein. Another approach will be to consider electron transfer as a two-level system. In this case, an important quantity to calculate is the interaction energy between the protein environment and the electron density (in the wavefunction representation of the electron) in the oxidized and reduced states.
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