Department of Chemistry, College of Science and Health, William Paterson University, 300 Pompton Rd, Wayne, NJ 07470, USA.
Molecules. 2021 Mar 9;26(5):1484. doi: 10.3390/molecules26051484.
Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural "ensembles" first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, 82 (S2), 219-230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR "ensembles" capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.
蛋白质是分子机器，其功能需要灵活性。晶体学 B 因子和分子动力学 (MD) 模拟都可以在原子尺度上提供对蛋白质灵活性的深入了解。核磁共振 (NMR) 缺乏与 B 因子普遍对应的指标。然而，基于 NMR 的结构计算中原子坐标的收敛性不足也表明原子的移动性。本文描述了在 NMR 衍生结构“集合”中，重原子坐标不确定度的一种模式，该模式最早在 FindCore2 的开发中（以前称为 Expanded FindCore：DA Snyder、J Grullon、YJ Huang、R Tejero、GT Montelione，82 (S2)，219-230）被注意到，并证明了该模式存在于 MD 轨迹中的坐标方差中，但不存在于晶体学 B 因子中。这要么表明 MD 轨迹和 NMR“集合”捕获了 B 因子未捕获的肽键单元的运动行为，要么表明 NMR 和 MD 计算中都使用的力场存在共同的缺陷。
