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REVIEW

From discrete protein kinetics to continuous Brownian dynamics: A new perspective

Department of Applied Mathematics, University of Washington, Seattle, Washington 98195-2420, USA

Reprint requests to: Hong Qian, Department of Applied Mathematics, University of Washington, Seattle, WA 98195-2420; e-mail: qian{at}amath.washington.edu; fax: (206) 685-1440.

Abstract

This article presents a comparative analysis of two sets of data from recent experiments on kinetics of (i) protein unfolding by mechanical force and (ii) channel gating with membrane electric potential. Both situations necessitate a continuous Brownian-dynamic view of protein conformational kinetics. We show that the discrete approach traditional to biochemical kinetics is insufficient for understanding dynamics of protein molecules in an aqueous solution or lipid membrane with varying conditions under which the major activation barrier can disappear. A semiquantitative analysis based on Brownian dynamics in a continuous energy landscape offers a more comprehensive description for motions of biological macromolecules.

Keywords: Energy landscape; folding; force; gating; channel protein; membrane potential

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