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1
Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels.扩散影响的配体在生物大分子和跨膜通道中的埋藏部位的结合。
J Chem Phys. 2011 Aug 21;135(7):075103. doi: 10.1063/1.3609973.
2
Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins.通过非特异性结合蛋白质的构象转变快速搜索 DNA 上的特定位点。
Proc Natl Acad Sci U S A. 2011 May 24;108(21):8651-6. doi: 10.1073/pnas.1101555108. Epub 2011 May 4.
3
Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change.蛋白质-配体结合耦合构象变化的动力学理论与模拟。
J Chem Phys. 2011 Mar 14;134(10):105101. doi: 10.1063/1.3561694.
4
A theory for the proton transport of the influenza virus M2 protein: extensive test against conductance data.流感病毒 M2 蛋白质子传输的理论：对电导数据的广泛检验。
Biophys J. 2011 Feb 16;100(4):912-21. doi: 10.1016/j.bpj.2011.01.002.
5
Crystal structure of unliganded TRAP: implications for dynamic allostery.无配体 TRAP 的晶体结构：对动态变构的启示。
Biochem J. 2011 Mar 15;434(3):427-34. doi: 10.1042/BJ20101813.
6
Rate theories for biologists.生物学家的率论。
Q Rev Biophys. 2010 May;43(2):219-93. doi: 10.1017/S0033583510000120. Epub 2010 Aug 9.
7
Diffusion-Influenced Transport of Ions across a Transmembrane Channel with an Internal Binding Site.离子通过具有内部结合位点的跨膜通道的扩散影响输运。
J Phys Chem Lett. 2010 Jul 1;1(13):1973-1976. doi: 10.1021/jz100683t.
8
From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions.从诱导契合到构象选择：结合机制的连续体受构象转变时间尺度控制。
Biophys J. 2010 Mar 17;98(6):L15-7. doi: 10.1016/j.bpj.2009.11.029.
9
Role of secondary sialic acid binding sites in influenza N1 neuraminidase.流感 N1 神经氨酸酶中次级唾液酸结合位点的作用。
J Am Chem Soc. 2010 Mar 10;132(9):2883-5. doi: 10.1021/ja9073672.
10
Theory of free energy and entropy in noncovalent binding.非共价键结合中的自由能与熵理论
Chem Rev. 2009 Sep;109(9):4092-107. doi: 10.1021/cr800551w.

扩散影响的理论和模拟，随机门控配体与埋藏部位结合。

Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites.

机构信息

Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.

出版信息

J Chem Phys. 2011 Oct 14;135(14):145101. doi: 10.1063/1.3645000.

DOI:10.1063/1.3645000
PMID:22010732
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3215080/
Abstract

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.

摘要

我们考虑位于蛋白质深口袋内的配体与位点结合的扩散影响的速率系数；结合口袋是灵活的，并可以响应配体进入而重新组织。我们将以前开发的[ A. M. Berezhkovskii，A. Szabo 和 H.-X. Zhou，J. Chem. Phys. 135, 075103 (2011)]的形式主义扩展到这个灵活的蛋白质 - 配体系统中，用于将配体结合问题分解为外部问题和内部问题。瓶颈或盖子和结合位点的构象波动被建模为随机门控。我们为包含底部结合位点的圆柱形口袋的情况提供了分析和布朗动力学模拟结果。诱导开关，即蛋白质的构象适应进入的配体，导致相当大的速率增强。