Topham C M, Srinivasan N, Blundell T L
Department of Crystallography, Birkbeck College, University of London, UK.
Protein Eng. 1997 Jan;10(1):7-21. doi: 10.1093/protein/10.1.7.
An approach to the prediction of mutant stability is described using knowledge of amino acid replacements that are tolerated within the families of homologous proteins of known 3-D structure. Amino acid variations in families of homologous proteins are converted to propensity and substitution tables; these provide quantitative information about the existence of an amino acid in a structural environment and the probability of replacement by any other amino acid. The tables are used to calculate a 'stability difference score', analogous to the difference in free energy between a mutant and the wild type. The method has been developed and tested using the high-resolution structures for T4 lysozyme and 159 site-specific mutants. We show that differences in stability scores are correlated with experimentally observed free energy differences and differences in melting temperature. Blind tests, using only structural information derived from the parent wild-type crystal structures, on a combined set of 83 staphylococcal nuclease and 68 barnase mutants showed a correlation of 0.80 in the predicted stability changes with experimental thermodynamic data. Approximately 86% of the predictions were correctly classified as destabilizing or stabilizing.
本文描述了一种预测突变体稳定性的方法，该方法利用了已知三维结构的同源蛋白家族中可耐受的氨基酸替换信息。同源蛋白家族中的氨基酸变异被转化为倾向表和替换表；这些表提供了关于氨基酸在结构环境中存在的定量信息以及被任何其他氨基酸替换的概率。这些表用于计算“稳定性差异得分”，类似于突变体与野生型之间的自由能差异。该方法已使用T4溶菌酶的高分辨率结构和159个位点特异性突变体进行了开发和测试。我们表明，稳定性得分的差异与实验观察到的自由能差异以及解链温度差异相关。对83个葡萄球菌核酸酶和68个核糖核酸酶抑制剂突变体的组合集进行的盲测，仅使用来自亲本野生型晶体结构的结构信息，结果显示预测的稳定性变化与实验热力学数据的相关性为0.80。大约86%的预测被正确分类为不稳定或稳定。
