Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II

65-POS Board 18 A Molecular Dynamics Study of the Allosteric Mechanism of Pyruvate Kinase Ankita Naithani 1 , Prof. Burak Erman 2 , Prof. Malcolm D. Walkinshaw 1 , Dr. Paul Taylor 1 . 1 University of Edinburgh, Edinburgh, United Kingdom, 2 Koc University, Istanbul, Turkey. There is a growing body of interest to understand the regulation of proteins by “allosteric communication” between different ligand binding sites. Pyruvate kinase from Leishmania mexicana catalyzes the final reaction of glycolysis and is allosterically activated by fructose-2, 6- bisphosphate (FBP). The presence of this allosteric site 40 Å away from the active site makes it an ideal target to study allosteric mechanisms and identify potential communication pathways. We have carried out Molecular Dynamics Simulations to enhance our knowledge of allostery and also gain insight into the structural and dynamical properties at the atomic level. Our preliminary results provide new and promising insights into the classical Monod-Wyman- Changeux model of allostery. 66-POS Board 19 A Kinetic Model of Proton Transport in a Multi-Redox Center Protein: Cytochrome c Oxidase Johannes Srajer, Renate Naumann . AIT Austrian Institute of Technology, Vienna, Austria. Chemical reaction kinetics is employed to explore the stepwise electron and proton transfer reactions of cytochrome c oxidase (C c O) from R. sphaeroides . Proton transport coupled to electron transport is investigated in terms of a series of coupledprotonation-dependent redox reactions. Thereby, we assume fixed rather than shifting dissociation constants of the redox sites. Proton transport can thus be simulated particularly when separate proton uptake and release sites are assumed rather than the same proton pump site for every ET step. In order to test these assumptions, we make use of a model system introduced earlier, which allows to study direct ET of redox enzymes by electrochemistry. A four-electron transfer model of C c O has been used, according to which electrons are transferred from the electrode to Cu A . Thereafter, electrons are transferred along the sequence heme a , heme a 3 and Cu B . We consider protonation equilibria of the oxidized and reduced species for each of the four centers. Moreover, we add oxygen/H 2 O as the terminal (fifth) redox couple including protonation of reduced oxygen to water. Finally we arrive at a kinetic model comprising five protonation-dependent redox couples. Simulations are compared with fast-scan voltammetry data obtained in the absence and presence of oxygen. These results are corroborated by fitting time-resolved FTIR spectra modulated by electrochemical excitation to the model. Summarizing, we can show that proton transport can be modeled in terms of protonation-dependent redox kinetics.

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