Properties of polyproline II, a secondary structure element implicated in protein-protein interactions
Properties of polyproline II, a secondary structure element implicated in protein-protein interactions
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DOI：
10.1002/prot.20327
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发表时间：
2005-03-01
影响因子：
2.9
通讯作者：
Lovell, SC
中科院分区：
文献类型：
--
作者：
Cubellis, MV;Caillez, F;Lovell, SC
聚脯氨酸II（PPII）构象是蛋白质骨架的重要二级结构类型。它的特殊之处在于，由于空间位阻的限制，它的主链上的氢键给体和受体不能轻易地被满足。它不能以类似于α-螺旋的方式形成局部氢键，并且它不能以类似于β-链的方式容易地满足聚脯氨酸构象中相邻残基的氢键结合潜力。在这里，我们描述了使用HOMSTRAD数据库的结构对齐的蛋白质的聚脯氨酸构象的分析。这使我们不仅可以从比以前大得多的数据库中确定氨基酸倾向，而且还可以研究聚脯氨酸构象中氨基酸的保守性以及构象本身的保守性。虽然脯氨酸在聚脯氨酸螺旋中很常见，但不含脯氨酸的螺旋占总数的46%。没有其他氨基酸似乎是非常优选的;甘氨酸和芳香族氨基酸对PPII具有低倾向性。因此，PPII主链的氢键键合势主要由水分子和主链的其他部分满足。侧链与主链的相互作用大多是非局部的。有趣的是，增加数量的不满意的H-键供体和受体（与a-螺旋和P-链相比），使PPII构象非常适合参加蛋白质-蛋白质相互作用。(C)2005 Wiley-Liss，Inc.
The polyproline II (PPII) conformation of protein backbone is an important secondary structure type. It is unusual in that, due to steric constraints, its main-chain hydrogen-bond donors and acceptors cannot easily be satisfied. It is unable to make local hydrogen bonds, in a manner similar to that of a-helices, and it cannot easily satisfy the hydrogen-bonding potential of neighboring residues in polyproline conformation in a manner analogous to beta-strands. Here we describe an analysis of polyproline conformations using the HOMSTRAD database of structurally aligned proteins. This allows us not only to determine amino acid propensities from a much larger database than previously but also to investigate conservation of amino acids in polyproline conformations, and the conservation of the conformation itself. Although proline is common in polyproline helices, helices without proline represent 46% of the total. No other amino acid appears to be greatly preferred; glycine and aromatic amino acids have low propensities for PPII. Accordingly, the hydrogen-bonding potential of PPII main-chain is mainly satisfied by water molecules and by other parts of the main-chain. Side-chain to main-chain interactions are mostly nonlocal. Interestingly, the increased number of nonsatisfied H-bond donors and acceptors (as compared with a-helices and P-strands) makes PPII conformers well suited to take part in protein-protein interactions. (C) 2005 Wiley-Liss, Inc.