Computer Simulations of Electron Transfer Proteins

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One of the most intriguing questions about electron transfer proteins is how the protein modifies the electron transfer properties of its redox site. This knowledge is crucial in understanding the molecular basis of a variety of metabolic processes, diseases involving these processes, and drug design targeting these processes. The overall goal is to understand the properties of electron transfer proteins at a molecular level. The focus is on the iron-sulfur proteins, which are ubiquitous proteins involved in fundamental processes such as respiration, photosynthesis, biosynthesis, and biodegradation. Our approach uses electrostatic potential calculations, molecular dynamics simulations, electronic structure calculations, and sequence analysis. Our studies cover three essential areas: (1) the reduction potentials (E),which determine the driving force for electron transfer, (2) the protein reorganization energy, which must play a role in how proteins can move electrons so efficiently and quickly, and (3) cluster conversion, which is important in the function and formation of many Fe-Sproteins. Studies will be mainly on the 2[4Fe-4S] ferredoxins and biotin synthase. The specific aimsare: Aim 1. The origins of differences in E due to polar groups in Fe-Sproteins will be determined. Our working model is that hydrogen bonds to the redox site affect E mainly by the electrostatics of the hydrogen bond donor dipole rather than by electronic perturbation. Aim 2. The nature of the reorganization energy of Fe-Sproteins will be determined. Our working model is that sequence differences can affect the reorganization energy via hydrogen bonds. Aim 3. The mechanisms of cluster conversion in Fe-S analogs and proteins will be determined . Our working model is that spin delocalization and redox state are important.