Colonna-Cesari F, Sander C
Laboratoire d'Enzymologie Physico-Chimique et Moleculaire, Universite de Paris Sud, Orsay, France.
Biophys J. 1990 May;57(5):1103-7. doi: 10.1016/S0006-3495(90)82630-8.
Important properties of globular proteins, such as the stability of its folded state, depend sensitively on interactions with solvent molecules. Existing methods for estimating these interactions, such as the geometrical surface model, are either physically misleading or too time consuming to be applied routinely in energy calculations. As an alternative, we derive here a simple model for the interactions between protein atoms and solvent atoms in the first hydration layer, the solvent contact model, based on the conservation of the total number of atomic contacts, a consequence of the excluded-volume effect. The model has the conceptual advantage that protein-protein contacts and protein-solvent contacts are treated in the same language and the technical advantage that the solvent term becomes a particularly simple function of interatomic distances. The model allows rapid calculation of any physical property that depends only on the number and type of protein-solvent nearest-neighbor contacts. We propose use of the method in the calculation of protein solvation energies, conformational energy calculations, and molecular dynamics simulations.
球状蛋白质的重要特性，比如其折叠态的稳定性，敏感地依赖于与溶剂分子的相互作用。现有的估算这些相互作用的方法，例如几何表面模型，要么在物理上具有误导性，要么耗时过长，无法在能量计算中常规应用。作为一种替代方法，我们在此基于原子接触总数守恒（这是排除体积效应的结果），推导出了一种用于描述蛋白质原子与第一水化层中溶剂原子之间相互作用的简单模型——溶剂接触模型。该模型在概念上的优势在于，蛋白质 - 蛋白质接触和蛋白质 - 溶剂接触能用相同的方式处理；在技术上的优势在于，溶剂项成为原子间距离的一个特别简单的函数。该模型能够快速计算任何仅依赖于蛋白质 - 溶剂最近邻接触的数量和类型的物理性质。我们建议将该方法用于蛋白质溶剂化能的计算、构象能量计算以及分子动力学模拟。
