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Description
Lipid membranes surrounding cells and various cell compartments anchor proteins with essential roles in the cell. Membrane-bound proteins are involved, for example, in cell signaling, transport of nutrients, and protein secretion. Understanding how membrane-bound proteins work in their physiological lipid membrane environment is thus important for biomedical applications.
Computer simulations allow us to study the motions of membrane proteins in hydrated lipid membrane environments, and to dissect interactions important for conformational dynamics. To characterize the role of lipids in membrane protein function we study GlpG, the rhomboid protease of Escherichia coli, a protease whose catalytic activity depends on lipids. Atomistic simulations of GlpG reveal a complex interplay between lipid and protein interactions, and suggest mechanisms by which lipid could shape early events along the reaction coordinate of GlpG.
Proton transfer is a chemical reaction essential for bioenergetics. A key open issue here is how dynamic protein/water hydrogen bond networks conduct protons along distances significantly longer than that of one hydrogen bond. To study proton transfer systems such as photosystem II and retinal proteins we develop algorithms for the analysis of dynamic hydrogen bond networks, and rely on combined quantum mechanics/molecular mechanics approaches.
