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首页> 外文期刊>Journal of Molecular Biology >Local propensities and statistical potentials of backbone dihedral angles in proteins
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Local propensities and statistical potentials of backbone dihedral angles in proteins

机译：蛋白质骨架中二面角的局部倾向和统计潜力

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The following three issues concerning the backbone dihedral angles of protein structures are presented. (1) How do the dihedral angles of the 20 amino acids depend on the identity and conformation of their nearest residues? (2) To what extent are the native dihedral angles determined by local (dihedral) potentials? (3) How to build a knowledge-based potential for a residue's dihedral angles, considering the identity and conformation of its nearest residues? We find that the dihedral angle distribution for a residue can significantly depend on the identity and conformation of its adjacent residues. These correlations are in sharp contrast to the Flory isolated-pair hypothesis. Statistical. potentials are built for all combinations of residue triplets and depend on the dihedral angles between consecutive residues. First, a low-resolution potential is obtained, which only differentiates between the main populated basins in the dihedral angle density plots. Minimization of the dihedral potential for 125 test proteins reveals that most native alpha-helical residues (89%) and a large fraction of native beta-sheet residues (47%) adopt conformations close to their native one. For native loop residues, the percentage is 48%. It is also found that this fraction is higher for residues away from the ends of alpha or beta secondary structure elements. In addition, a higher resolution potential is built as a function of dihedral angles by a smoothing procedure and continuous functions interpolations. Monte Carlo energy minimization with this potential results in a lower fraction for native beta-sheet residues. Nevertheless, because of the higher flexibility and entropy of beta structures, they could be preferred under the influence of non-local interactions. In general, most alpha-helices and many beta-sheets are strongly determined by the local potential, while the conformations in loops and near the end of beta-sheets are more influenced by non-local interactions. (C) 2004 Elsevier Ltd. All rights reserved.
机译：提出了以下三个有关蛋白质结构的骨架二面角的问题。 （1）20个氨基酸的二面角如何取决于它们最接近的残基的身份和构象？ （2）天然二面角在多大程度上由局部（二面角）电势确定？ （3）如何考虑残基的最接近残基的身份和构象，为残基的二面角建立基于知识的潜力？我们发现，一个残基的二面角分布可以极大地取决于其相邻残基的身份和构象。这些相关性与弗洛里孤立对假说形成鲜明对比。统计。对残基三联体的所有组合建立电位，并取决于连续残基之间的二面角。首先，获得了低分辨率的潜力，该潜力仅在二面角密度图中区分了主要的人口盆地。 125种测试蛋白的二面角潜力最小化表明，大多数天然α-螺旋残基（占89％）和很大一部分天然β-sheet残基（占47％）都采用接近其天然构象的构象。对于天然环残基，该百分比为48％。还发现对于远离α或β二级结构元件的末端的残基，该分数更高。此外，通过平滑过程和连续函数插值，可将更高的分辨率潜力作为二面角的函数。具有这种潜力的蒙特卡洛能量最小化导致天然β-折叠残基的分数降低。但是，由于β结构具有更高的灵活性和熵，在非本地相互作用的影响下，它们可能是首选。通常，大多数α-螺旋和许多β-折叠均由局部电位决定，而环和β-折叠末端附近的构象受非局部相互作用的影响更大。 （C）2004 Elsevier Ltd.保留所有权利。

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