Fornili Arianna, Autore Flavia, Chakroun Nesrine, Martinez Pierre, Fraternali Franca
Randall Division for Cellular and Molecular Biophysics, King's College London, London, UK.
Methods Mol Biol. 2012;819:375-92. doi: 10.1007/978-1-61779-465-0_23.
The effects of solvation on molecular recognition are investigated from different perspectives, ranging from methods to analyse explicit solvent dynamical behaviour at the protein surface to methods for the implicit treatment of solvent effects associated with the conformational behaviour of biomolecules. The here presented implicit solvation method is based on an analytical approximation of the Solvent Accessible Surface Area (SASA) of solute molecules, which is computationally efficient and easy to parametrise. The parametrised SASA solvation method is discussed in the light of protein design and ligand binding studies. The POPS program for the SASA computation on single molecules and complex interfaces is described in detail. Explicit solvent behaviour is described here in the form of solvent density maps at the protein surface. We highlight the usefulness of that approach in defining the organisation of specific water molecules at functional sites and in determining hydrophobicity scores for the identification of potential interaction patches.
从不同角度研究了溶剂化对分子识别的影响，范围从分析蛋白质表面明确溶剂动力学行为的方法到与生物分子构象行为相关的溶剂效应的隐式处理方法。本文提出的隐式溶剂化方法基于溶质分子溶剂可及表面积（SASA）的解析近似，计算效率高且易于参数化。根据蛋白质设计和配体结合研究讨论了参数化的SASA溶剂化方法。详细描述了用于单分子和复杂界面SASA计算的POPS程序。这里以蛋白质表面溶剂密度图的形式描述了明确的溶剂行为。我们强调了该方法在定义功能位点特定水分子的组织以及确定用于识别潜在相互作用区域的疏水性评分方面的有用性。
