Balance between a and β Structures in Ab Initio Protein Folding
Balance between a and β Structures in Ab Initio Protein Folding
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DOI：
10.1021/jp102575b
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发表时间：
2010-07-08
影响因子：
3.3
通讯作者：
Mittal, Jeetain
中科院分区：
文献类型：
--
作者：
Best, Robert B.;Mittal, Jeetain
尽管通过分子模拟在蛋白质折叠方面取得了初步的成功，但越来越明显的是，目前的能量函数（力场）倾向于支持α或β二级结构，因此力场的选择取决于蛋白质的结构类别。在这里，我们研究了折叠的肽主要是α（色氨酸笼）或β（GB I发夹）结构与修改后的版本的琥珀ff03力场，优化重现结构倾向的螺旋形成肽。使用广泛的复制交换分子动力学模拟从完全展开的配置开始，我们获得了正确的折叠结构的每一个肽，在接近一致的实验天然结构（
Despite initial successes in folding of proteins by molecular simulation, it is becoming increasingly evident that current energy functions (force fields) tend to favor either alpha or beta secondary structure, such that the choice of force field is governed by the structural class of the protein. Here, we study the folding of peptides with either predominantly alpha (Trp cage) or beta (GB I hairpin) structure with a modified version of the Amber ff03 force field, optimized to reproduce structural propensity in a helix-forming peptide. Using extensive replica exchange molecular dynamics simulations starting from completely unfolded configurations, we obtain the correct folded structure for each peptide, in close agreement with the experimental native structure (