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Computational Modeling in the Chemical Sciences

Arneh Babakhani
Chemistry Department, UCSD


A wide range of functions, such as proton transport and cell signaling,illustrate the importance of transmembrane proteins in biological phenomena. Elucidatingthe chemical and biochemical behavior of these proteins is the subject of much research. Tothis end, many experimental techniques have been employed to study membrane-proteinsystems, including spectroscopic and calorimetric methods. Computational methods includingimplicit membrane models, coarse-grained, and all-atom molecular dynamics (MD)simulations6 have complemented the experimental work. The all-atom method treats nearlyevery atom of the system in an explicit fashion, meaning that each atom is parameterized andsimulated according to the MD equations. Standard software packages can execute these all-atomMD simulations.

Many large transmembrane protein receptors play vital roles in clinical applications. For instance, the nicotinic acetylcholine receptor (nAChR) can serve as a useful target in the efforts of smoking cessation, counter drug addiction and pain management. Yet, there are no highresolutionstructures of nAChR, thus making it a difficult pharmacological target. There existseveral resolved structures of the acetylcholine binding protein (AChBP), which is an aqueous protein that mimics the binding and activity of the extra-cellular domain in nAChR. Thus, weintend to use AChBP as the target, to identify new small-molecule ligands that could becomepotential pharmaceuticals against nAChR. Such ligands may also help distinguish between thechemical features of AChBP and the various subtypes of nAChR.

Monday, June 2, 2008
11:00AM AP&M 2402