Ollikainen Noah, de Jong René M, Kortemme Tanja
Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America.
DSM Biotechnology Center, Alexander Fleminglaan 1, Delft, The Netherlands.
PLoS Comput Biol. 2015 Sep 23;11(9):e1004335. doi: 10.1371/journal.pcbi.1004335. eCollection 2015.
Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.
小分子与蛋白质之间的相互作用在调节和促进多种生物学功能中起着关键作用，然而，我们利用计算方法精确重新设计这些相互作用特异性的能力一直有限。除了能量函数不准确之外，一个主要困难是蛋白质 - 配体相互作用对细微构象变化极其敏感，再加上对配体、氨基酸侧链和蛋白质主链自由度的大构象搜索空间进行采样的计算问题。在这里，我们描述了两个用于评估重新设计蛋白质 - 配体相互作用计算方法准确性的基准：（i）预测改变酶特异性的突变，以及（ii）预测配体结合位点的序列耐受性。在发现当前最先进的“固定主链”设计方法在这些测试中表现不佳后，我们在Rosetta程序中开发了一种新的“耦合移动”设计方法，该方法将蛋白质序列的变化与蛋白质侧链和蛋白质主链构象的改变相结合，并允许配体刚体和扭转自由度的变化。我们在预测改变配体特异性的突变和结合位点序列方面都显示出显著提高的准确性。这些方法学上的改进对于蛋白质 - 配体设计的许多应用应该是有用的。该方法还为细微构象调整的作用提供了见解，这些调整不仅在工程应用中，而且在天然蛋白质进化中都能实现功能变化。
