Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins
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DOI：
10.1002/jcc.10420
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发表时间：
2004-04-15
影响因子：
3
通讯作者：
Sobolev, V
中科院分区：
文献类型：
--
作者：
Eyal, E;Najmanovich, R;Sobolev, V
使用接触表面积和原子的化学性质来同时预测固定蛋白质主链上多个氨基酸侧链的构象。表面互补性和溶剂可及表面的结合解释了范德华力和溶剂化自由能。评分函数特别适用于部分埋地侧链的建模。同时采用迭代和随机搜索方法。我们的程序（Sccomp-I和Sccomp-S）具有相对较快的执行时间，正确预测了92-93%的埋藏残基和82-84%的所有残基的X-1角，RMSD与侧链重原子相似为1.7埃。我们发现原子溶剂化参数和接触面参数（包括非互补原子之间的接触面参数）之间的差值是正的：即大多数蛋白质原子更喜欢与其他蛋白质原子表面接触，而不是与溶剂接触。这可能对应于最大限度地包装蛋白质的驱动力。考察了晶体填充、旋转体库的完备性和c - β原子的精确定位对侧链预测精度的影响。可以通过Web （http://sgedg.weizmann.ac.il/sccomp.html）访问Sccomp-S和Sccomp-I程序，它们可用于多个平台。(C) 2004 Wiley期刊有限公司
Contact surface area and chemical properties of atoms are used to concurrently predict conformations of multiple amino acid side chains on a fixed protein backbone. The combination of surface complementarity and solvent-accessible surface accounts for van der Waals forces and solvation free energy. The scoring function is particularly suitable for modeling partially buried side chains. Both iterative and stochastic searching approaches are used. Our programs (Sccomp-I and Sccomp-S), with relatively fast execution times, correctly predict X-1 angles for 92-93% of buried residues and 82-84% for all residues, with an RMSD of similar to1.7 Angstrom for side chain heavy atoms. We find that the differential between the atomic solvation parameters and the contact surface parameters (including those between noncomplementary atoms) is positive: i.e., most protein atoms prefer surface contact with other protein atoms rather than with the solvent. This might correspond to the driving force for maximizing packing of the protein. The influence of the crystal packing, completeness of rotamer library and precise positioning of C-beta atoms on the accuracy of side-chain prediction are examined. The Sccomp-S and Sccomp-I programs can be accessed through the Web (http://sgedg.weizmann.ac.il/sccomp.html) and are available for several platforms. (C) 2004 Wiley Periodicals, Inc.