Department of Biochemistry, University of Washington, Seattle, WA 98105, USA.
Proteins. 2011 Mar;79(3):830-8. doi: 10.1002/prot.22921. Epub 2010 Dec 3.
The prediction of changes in protein stability and structure resulting from single amino acid substitutions is both a fundamental test of macromolecular modeling methodology and an important current problem as high throughput sequencing reveals sequence polymorphisms at an increasing rate. In principle, given the structure of a wild-type protein and a point mutation whose effects are to be predicted, an accurate method should recapitulate both the structural changes and the change in the folding-free energy. Here, we explore the performance of protocols which sample an increasing diversity of conformations. We find that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that the resolution of the force field is matched to the resolution of the sampling method. Methods involving backbone sampling can in some cases closely recapitulate the structural changes accompanying mutations but not surprisingly tend to do more harm than good in cases where structural changes are negligible. Analysis of the outliers in the stability change calculations suggests areas needing particular improvement; these include the balance between desolvation and the formation of favorable buried polar interactions, and unfolded state modeling.
预测由于单个氨基酸取代而导致的蛋白质稳定性和结构变化既是对大分子建模方法的基本检验，也是一个当前的重要问题，因为高通量测序以越来越快的速度揭示序列多态性。原则上，给定野生型蛋白质的结构和要预测其影响的点突变，准确的方法应该再现结构变化和折叠自由能的变化。在这里，我们探索了采样越来越多样化构象的方案的性能。我们发现，使用涉及非常不同构象采样量的方案，在预测稳定性变化方面可以达到惊人相似的性能，只要力场的分辨率与采样方法的分辨率相匹配。涉及骨架采样的方法在某些情况下可以很好地再现伴随突变的结构变化，但在结构变化可以忽略不计的情况下，并不奇怪地往往弊大于利。对稳定性变化计算中的离群值的分析表明需要特别改进的领域；这些包括去溶剂化和形成有利的埋藏极性相互作用之间的平衡，以及展开状态建模。
