Structure validation by Cα geometry:: φ,ψ and Cβ deviation
Structure validation by Cα geometry:: φ,ψ and Cβ deviation
复制标题
DOI：
10.1002/prot.10286
复制
发表时间：
2003-02-15
期刊：
影响因子：
--
通讯作者：
Richardson, DC
中科院分区：
文献类型：
--
作者：
Lovell, SC;Davis, IW;Richardson, DC
几何验证周围的Calpha的描述，一个新的Cbeta措施和更新的Ramachandran图。观察到的C β原子从理想位置的偏差提供了一个单一的措施封装，主要的结构验证信息中包含的键角失真。C β偏差对由错配构象或不适当的精细化限制引起的侧链和主链之间的不相容性敏感。一个新的phi，psi图使用密度依赖性平滑的81,234非甘氨酸，非Pro，和非前Pro残基与B < 30从500高分辨率蛋白质显示尖锐的边界在关键的边缘和大的空白区域和区域之间的清晰划定，允许但不赞成。一个这样的区域是靠近+75度，-60度的γ-转角构象，被常见的结构验证程序视为禁止;然而，它发生在良好结构的有序部分，它在功能位点附近过度表达，并且应变部分被γ-转角氢键补偿。还为Pro、prePro和Gly定义了Fcb和允许的phi、psi区域（这很重要，因为Gly phi、psi角度更允许，但确定的准确度较低）。这些精确的经验分布的细节在以前的理论计算中预测得很差，包括α-螺旋左边的区域，这在能量上是有利的，但很少发生。解释这种差异的一个建议因素是，拥挤的两个肽NH允许捐赠只有一个H键。Hu等人[Proteins 2002（this issue）]使用混合量子力学和分子力学对Ala和Gly二肽进行的新计算非常符合我们的非重复数据。要在用户上传的文件上运行我们的几何评估，请参见MOLPROBITY（http：//kinemage. biochem.duke.edu）或RAmPAGE（http：//www-cryst.bioc.cam.ac.uk/rampage）。(C)2003 Wiley-Liss，Inc.
Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the, major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain And backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75degrees,-60degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, prePro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage. biochem.duke.edu) or RAmPAGE (http://www-cryst. bioc.cam.ac.uk/rampage). (C) 2003 Wiley-Liss, Inc.