期刊
JOURNAL OF CHEMICAL PHYSICS
卷 135, 期 14, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.3645000
关键词
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资金
- National Institutes of Health [GM58187]
We consider the diffusion-influenced rate coefficient of ligand binding to a site located in a deep pocket on a protein; the binding pocket is flexible and can reorganize in response to ligand entrance. We extend to this flexible protein-ligand system a formalism developed previously [A. M. Berezhkovskii, A, Szabo, and H.-X. Zhou, J. Chem. Phys. 135, 075103 (2011)] for breaking the ligand-binding problem into an exterior problem and an interior problem. Conformational fluctuations of a bottleneck or a lid and the binding site are modeled as stochastic gating. We present analytical and Brownian dynamics simulation results for the case of a cylindrical pocket containing a binding site at the bottom. Induced switch, whereby the conformation of the protein adapts to the incoming ligand, leads to considerable rate enhancement. (C) 2011 American Institute of Physics. [doi:10.1063/1.3645000]
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