Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
复制标题
DOI：
10.1021/ct500718s
复制
发表时间：
2015-01-01
影响因子：
5.5
通讯作者：
Barducci, Alessandro
中科院分区：
文献类型：
--
作者：
Palazzesi, Ferruccio;Prakash, Meher K.;Barducci, Alessandro
分子动力学(MD)在描述蛋白质无序状态方面发挥着重要作用，而蛋白质无序状态是许多生物过程中的关键因素。在这里，我们通过结合增强采样MD模拟和核磁共振数据来评估三种当前力场在模拟无序多肽方面的准确性。这些力场产生了显著不同的构象系综[Best和Mittal J.Phys.化学。B2010,114,14916-14923]提供了与实验的最佳一致性，通过添加ILDN校正进一步改进了[Lindorff-Larsen等人]。蛋白质2010、78、1950-1958]。
Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w [Best and Mittal J. Phys. Chem. B 2010, 114, 14916-14923] provides the best agreement with experiments, which is further improved by adding the ILDN corrections [Lindorff-Larsen et al. Proteins 2010, 78, 1950-1958].