Dourado Daniel F A R, Flores Samuel Coulbourn
Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University, 751 24, Uppsala, Sweden.
Proteins. 2014 Oct;82(10):2681-90. doi: 10.1002/prot.24634. Epub 2014 Jul 5.
Substitution mutations in protein-protein interfaces can have a substantial effect on binding, which has consequences in basic and applied biomedical research. Experimental expression, purification, and affinity determination of protein complexes is an expensive and time-consuming means of evaluating the effect of mutations, making a fast and accurate in silico method highly desirable. When the structure of the wild-type complex is known, it is possible to economically evaluate the effect of point mutations with knowledge based potentials, which do not model backbone flexibility, but these have been validated only for single mutants. Substitution mutations tend to induce local conformational rearrangements only. Accordingly, ZEMu (Zone Equilibration of Mutants) flexibilizes only a small region around the site of mutation, then computes its dynamics under a physics-based force field. We validate with 1254 experimental mutants (with 1-15 simultaneous substitutions) in a wide variety of different protein environments (65 protein complexes), and obtain a significant improvement in the accuracy of predicted ΔΔG.
蛋白质 - 蛋白质界面的替换突变会对结合产生重大影响，这在基础和应用生物医学研究中都有重要意义。蛋白质复合物的实验表达、纯化和亲和力测定是评估突变影响的一种昂贵且耗时的方法，因此非常需要一种快速且准确的计算机模拟方法。当野生型复合物的结构已知时，可以利用基于知识的势函数经济地评估点突变的影响，这种方法不考虑主链的灵活性，但仅针对单突变体进行了验证。替换突变往往仅诱导局部构象重排。因此，ZEMu（突变体区域平衡）仅使突变位点周围的小区域具有灵活性，然后在基于物理的力场下计算其动力学。我们在多种不同的蛋白质环境（65种蛋白质复合物）中用1254个实验突变体（同时有1 - 15个替换）进行了验证，并在预测的ΔΔG准确性方面取得了显著提高。
