Simulation Studies of Protein Dynamics in Membranes

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Douglas Tobias of the University of California Irvine is supported by an award from the Theoretical and Computational Chemistry program within the Division of Chemistry with co-funding provided by the Molecular Biophysics program within the Division of Molecular and Cellular Biosciences to carry out research on the development of simulation methods for protein dynamics in membranes. Tobias and his group are concentrating on four projects: (1) MD simulations and single particle dynamics studies of bacteriorhodpsin in purple membranes and phospholipid bilayers; (2) a study of collective dynamics in membranes through normal mode analyses of bacteriorhodopsin; (3) comparison of the results from the first two projects on bacteriorhodopsin to maltose binding protein, a soluble protein; and (4) the development of a novel normal mode analysis using elastic network models for membrane proteins. Proper protein function requires motion of the protein macromolecule over a wide range of time and length scales. Both temperature and the solvent environment, a combination of water and fat-like lipid molecules, affect the dynamic motion of these molecules. The supported work is revealing details about these complex molecules and developing new computational techniques for simulating their motion. It is having a broader impact both through insights revealed about the functioning of biological systems and through the work of Tobias and his students in an interdisciplinary environment. The group is associated with the interdepartmental TEMPO group which brings together researchers interested in Theory and Experiments on Membrane Protein Organization, the Center for Biomembrane Systems and the Center of Excellence in Theoretical Chemistry, all at UC-Irvine.