Computational alanine scanning mutagenesis - An improved methodological approach
Computational alanine scanning mutagenesis - An improved methodological approach
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DOI：
10.1002/jcc.20566
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发表时间：
2007-02-01
影响因子：
3
通讯作者：
Ramos, Maria J.
中科院分区：
文献类型：
--
作者：
Moreira, Irina S.;Fernandes, Pedro A.;Ramos, Maria J.
蛋白质-蛋白质界面残基的丙氨酸扫描诱变可以应用于多种蛋白质复合物，以了解热点的结构和能量特征。结合自由能已经通过经验方法如分子力学/泊松-玻尔兹曼表面积（MM-PBSA）和更严格的计算方法如自由能摄动（FEP）和热力学积分（TI）得到了合理的精度。这项工作的主要目标是发展一种改进的方法，以更少的计算成本，准确预测野生型和丙氨酸突变复合物之间结合自由能的差异（δ δ G（结合））。该方法应用于3个配合物，在一组46个突变中获得平均无符号误差为0.80 kcal/mol。本文提出的计算方法在丙氨酸突变导致结合自由能> 2.0 kcal/mol（热点和热点）增加的残基中获得了80%的总体成功率和82%的成功率。这种完全原子化的计算方法包括使用广义玻恩模型在连续介质中执行的计算分子动力学模拟协议。一组三种不同的内部介电常数，以模拟当不同类型的氨基酸突变为丙氨酸时界面的不同松弛程度，必须用于蛋白质，这取决于突变的氨基酸的类型。该方法允许对蛋白质-蛋白质界面进行系统的扫描诱变，并且能够预测诱变的实验结果，从而指导新的实验研究。(C) 2006 Wiley期刊有限公司
Alanine scanning mutagenesis of protein-protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot-spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild-type and alanine mutated complexes (Delta Delta G(binding)). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm- and hot-spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein-protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations. (C) 2006 Wiley Periodicals, Inc.