Structural dynamics of protein backbone φ angles: extended molecular dynamics simulations versus experimental 3 J scalar couplings
Structural dynamics of protein backbone φ angles: extended molecular dynamics simulations versus experimental 3 J scalar couplings
复制标题
DOI：
10.1007/s10858-009-9341-z
复制
发表时间：
2009-09-01
影响因子：
2.7
通讯作者：
Blackledge, Martin
中科院分区：
文献类型：
--
作者：
Markwick, Phineus R. L.;Showalter, Scott A.;Blackledge, Martin
(3) J 标量耦合报告了肽和蛋白质中骨架 phi 角的构象平均，因此代表了研究溶液中结构和动力学细节的潜在强大工具。我们使用加速分子动力学提供的增强采样或使用长时标轨迹 (200 ns)，将广泛的实验数据集与无约束分子动力学模拟预测的 J 耦合进行了比较。预测沿主干存在的动态波动与残余偶极耦合分析一致，与实验 (3) J 标量耦合兼容，提供比高分辨率静态结构更好的这些实验参数的再现。
(3) J scalar couplings report on the conformational averaging of backbone phi angles in peptides and proteins, and therefore represent a potentially powerful tool for studying the details of both structure and dynamics in solution. We have compared an extensive experimental dataset with J-couplings predicted from unrestrained molecular dynamics simulation using enhanced sampling available from accelerated molecular dynamics or using long timescale trajectories (200 ns). The dynamic fluctuations predicted to be present along the backbone, in agreement with residual dipolar coupling analysis, are compatible with the experimental (3) J scalar couplings providing a slightly better reproduction of these experimental parameters than a high-resolution static structure.