Improved dihedral-angle restraints for protein structure refinement
Improved dihedral-angle restraints for protein structure refinement
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DOI：
10.1107/s0021889802018265
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发表时间：
2003-02-01
影响因子：
6.1
通讯作者：
Priestle, JP
中科院分区：
文献类型：
--
作者：
Priestle, JP
由于典型蛋白质晶体的衍射分辨率相对较低，因此通常采用立体化学限制来进行结构细化，以增加有效的观察次数。键长和键角的明确定义值可从小分子晶体结构中获得。由于小分子晶体结构中的强晶体接触可能会扭曲二面角，因此二面角不存在这样的值。本文探讨了在超高分辨率蛋白质结构（1.2埃或更好）的二面角分布作为一种手段，分析人口的二面角在蛋白质中的频率，并比较这些与目前使用的立体化学的限制，在一个更广泛使用的分子动力学细化包，X-PLOR，及其继任者，CNS。在这些程序中使用的限制和什么是实际上看到的高分辨率蛋白质结构之间的差异进行检查，并从这些检查中得到一组改进的二面角约束参数。
Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Angstrom or better) as a means of analysing the population frequencies of dihedral angles in proteins and compares these with the stereochemical restraints currently used in one of the more widely used molecular-dynamics refinement packages, X-PLOR, and its successor, CNS. Discrepancies between the restraints used in these programs and what is actually seen in high-resolution protein structures are examined and an improved set of dihedral-angle restraint parameters are derived from these inspections.