Statistical and energetic analysis of side-chain conformations in oligopeptides.
Statistical and energetic analysis of side-chain conformations in oligopeptides.
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寡肽侧链构象的统计和能量分析。
DOI：
10.1111/j.1399-3011.1983.tb02062.x
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发表时间：
1983
期刊：
影响因子：
--
通讯作者：
Scheraga,HA
中科院分区：
文献类型：
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作者：
Benedetti,E;Morelli,G;Némethy,G;Scheraga,HA
分析了258种寡肽晶体结构中侧链构象的分布。样品含有321个残基，其侧链延伸超过Cβ原子。统计学观察到的侧链二面角的偏好进行了总结，并与立体化学和能量约束。将这些分布与已知X射线结构的蛋白质中观察到的分布以及计算的氨基酸衍生物的最小能量构象进行比较。在所有三组数据中的分布是相似的，它们似乎主要受残留物内相互作用的影响。在没有β分支的侧链中，决定χ1的最重要的相互作用是Cγ H2基团与相邻肽基团原子之间的相互作用。因此，g-构象（χ1 <$60 °）最常出现在寡肽中围绕Cα-Cβ键的旋转中，其次是θ构象（χ1 <$180 °），而g+构象（χ1 <$60 °）最不受欢迎。在具有β分支的残基中，Cγ H2或Cγ H3基团与主链原子之间的空间排斥控制χ1的分布。伸展（t）构象非常有利于在无支链侧链中围绕Cβ-Cγ Cγ-Cδ键旋转，因为t构象的能量低于烃链中的g +g-构象。对观察到的侧链构象的研究导致了对经验构象能量计算中使用的能量参数之一的改进。
The distributions of side‐chain conformations in 258 crystal structures of oligopeptides have been analyzed. The sample contains 321 residues having side chains that extend beyond the Cβ atom. Statistically observed preferences of side‐chain dihedral angles are summarized and correlated with stereochemical and energetic constraints. The distributions are compared with observed distributions in proteins of known X‐ray structures and with computed minimum‐energy conformations of amino acid derivatives. The distributions are similar in all three sets of data, and they appear to be governed primarily by intraresidue interactions. In side chains with no β‐branching, the most important interactions that determine χ1 are those between the CγH2group and atoms of the neighboring peptide groups. As a result, theg‐conformation (χ1 ⋍ ‐60°) occurs most frequently for rotation around the Cα‐Cβ bond in oligopeptides, followed by thetconformation (χ1 ⋍ 180°), while theg+ conformation (χ1 ⋍ 60°) is least favored. In residues with β‐branching, steric repulsions between the CγH2or CγH3groups and backbone atoms govern the distribution of χ1. The extended (t) conformation is highly favored for rotation around the Cβ‐Cγ Cγ‐Cδ bonds in unbranched side chains, because thetconformer has a lower energy than theg+g‐ conformers in hydrocarbon chains. This study of the observed side‐chain conformations has led to a refinement of one of the energy parameters used in empirical conformational energy computations.