An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation
An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation
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DOI：
10.1021/ja0319994
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发表时间：
2004-06-16
影响因子：
15
通讯作者：
Bax, A
中科院分区：
文献类型：
--
作者：
Grishaev, A;Bax, A
描述了一种新的多维势，其编码在高分辨率X射线结构的大型数据库内观察到的肽基骨架单元的相对空间排列。这种分析提供的详细描述提供了一个研究蛋白质中氢键的原子细节的机会。相应的平均力（PMF）势的规范是基于一组定义的物理原理，并进行了优化，以在应用于蛋白质结构优化时产生最大的优势。所观察到的各种模式的二级结构内的氢键的几何形状之间的复杂差异允许应用程序的PMF的蛋白质结构的验证和它们的细化。一个显着的改善几个方面的结构质量观察到以下应用程序的这种潜力的各种NMR衍生的模型，包括一个显着的减少骨架坐标均方根偏差相对于X-射线结构和相当大的改善Ramachandran地图统计。
A new multidimensional potential is described that encodes for the relative spatial arrangement of the peptidyl backbone units as observed within a large database of high-resolution X-ray structures. The detailed description afforded by such an analysis provides an opportunity to study the atomic details of hydrogen bonding in proteins. The specification of the corresponding potential of mean force (PMF) is based on a defined set of physical principles and optimized to yield the maximum advantage when applied to protein structure refinement. The observed intricate differences between hydrogen-bonding geometries within various patterns of secondary structure allow application of the PMF to both validation of protein structures and their refinement. A pronounced improvement of several aspects of structural quality is observed following the application of such a potential to a variety of NMR-derived models, including a noticeable decrease in backbone coordinate root-mean-square deviation relative to the X-ray structures and a considerable improvement in the Ramachandran map statistics.