Patterns for prediction of hydration around polar residues in proteins.
Patterns for prediction of hydration around polar residues in proteins.
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DOI：
10.1006/jmbi.1993.1043
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发表时间：
1993-01
影响因子：
5.6
通讯作者：
S. Roe;M. Teeter
中科院分区：
文献类型：
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作者：
S. Roe;M. Teeter
七个非常高分辨率（< 1.4 A）蛋白质的原子坐标已被用于定义五个极性侧链（精氨酸、天冬氨酸、谷氨酸、天冬酰胺和谷氨酰胺）的水-氢键模板。测定的平均水分子位置与每个侧链预期的氢键立体化学一致。氮原子周围的氢键几何形状明显比氧原子周围更好地局部化，这可能是因为氮上的质子。一个预测算法写来定位水分子网站周围的这些侧链从蛋白质的坐标只进行了测试crambin以及两个高分辨率的蛋白质结构不包括在氢键数据库。从晶体学确定的这些结构的预测位置的均方根偏差优于这些结构的分辨率。该方法还成功地预测了两种蛋白质的X射线细化的水位置，表明预测的水分子在细化的收敛半径内。该方法具有实用性的X射线模型，以及用于分析酶的水合作用和功能。
The atomic co-ordinates of seven very high resolution (< 1.4 A) proteins have been used to define a water-hydrogen bond template for five polar side-chains (arginine, aspartic acid, glutamic acid, asparagine and glutamine). The average water molecule positions determined were consistent with the hydrogen bonding stereochemistry expected for each side-chain. Hydrogen bonding geometry around nitrogen atoms was significantly better localized than around oxygen atoms, perhaps because of the proton on nitrogen. A prediction algorithm written to locate water molecule sites around these side-chains from the protein co-ordinates only was tested for crambin as well as for two high resolution protein structures not included in the hydrogen bond data base. The root-mean-square deviation of the predicted positions from the crystallographically determined ones for these structures was better than the resolution of these structures. The method also successfully predicted water positions for X-ray refinement of two proteins, indicating that predicted water molecules are within the radius of convergence of refinement. This method has utility for X-ray models as well as for analysis of enzyme hydration and function.