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本文引用的文献

1
Static and dynamic correlations in water at hydrophobic interfaces.疏水界面处水的静态和动态相关性。
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20130-5. doi: 10.1073/pnas.0809029105. Epub 2008 Dec 11.
2
Dewetting and hydrophobic interaction in physical and biological systems.物理和生物系统中的去湿与疏水相互作用。
Annu Rev Phys Chem. 2009;60:85-103. doi: 10.1146/annurev.physchem.58.032806.104445.
3
Mechanism of fast peptide recognition by SH3 domains.SH3结构域快速识别肽段的机制。
Angew Chem Int Ed Engl. 2008;47(40):7626-30. doi: 10.1002/anie.200801856.
4
A dry ligand-binding cavity in a solvated protein.溶剂化蛋白质中的干性配体结合腔。
Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6296-301. doi: 10.1073/pnas.0709844105. Epub 2008 Apr 21.
5
Solvation of proteins: linking thermodynamics to geometry.蛋白质的溶剂化作用：将热力学与几何学联系起来。
Phys Rev Lett. 2007 Sep 21;99(12):128101. doi: 10.1103/PhysRevLett.99.128101. Epub 2007 Sep 17.
6
Application of the level-set method to the implicit solvation of nonpolar molecules.水平集方法在非极性分子隐式溶剂化中的应用。
J Chem Phys. 2007 Aug 28;127(8):084503. doi: 10.1063/1.2757169.
7
Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations.通过计算机模拟研究甲烷疏水相互作用的水性质及平均力势与纳米尺度口袋
J Chem Phys. 2007 Aug 7;127(5):054505. doi: 10.1063/1.2749250.
8
Surface tension of the most popular models of water by using the test-area simulation method.通过使用测试区域模拟方法对最流行的水模型的表面张力进行研究。
J Chem Phys. 2007 Apr 21;126(15):154707. doi: 10.1063/1.2715577.
9
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.利用蛋白质-配体结合中的疏水包封进行分子识别的基序。
Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):808-13. doi: 10.1073/pnas.0610202104. Epub 2007 Jan 4.
10
Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?通过隐式溶剂模拟预测蛋白质-配体结合亲和力：先导化合物优化的工具？
J Med Chem. 2006 Dec 14;49(25):7427-39. doi: 10.1021/jm061021s.

去湿控制配体与疏水口袋的结合。

Dewetting-controlled binding of ligands to hydrophobic pockets.

机构信息

Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California 92093, USA.

出版信息

Phys Rev Lett. 2009 Oct 30;103(18):187801. doi: 10.1103/PhysRevLett.103.187801.

DOI:10.1103/PhysRevLett.103.187801
PMID:19905832
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2832595/
Abstract

We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting-dewetting transitions in the weakly solvated pocket. The transitions lead to bimodal solvent fluctuations which govern magnitude and range of the pocket-ligand attraction. A recently developed implicit water model, based on the minimization of a geometric functional, captures the sensitive aqueous interface response to the concave-convex pocket-ligand configuration semiquantitatively.

摘要

我们报告了一个通用疏水口袋-配体（主体-客体）系统的原子分子动力学模拟和隐溶剂分析的联合研究。接近的配体在弱溶剂化口袋中诱导了复杂的润湿-去湿转变。这些转变导致溶剂波动的双峰分布，从而控制口袋-配体吸引力的大小和范围。最近开发的基于几何函数最小化的隐式水分子模型，对凹-凸口袋-配体构型对半定量地捕捉到了敏感的水界面响应。