Statistical analysis of predominantly transient protein-protein interfaces
Statistical analysis of predominantly transient protein-protein interfaces
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DOI：
10.1002/prot.20593
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发表时间：
2005-11-01
影响因子：
2.9
通讯作者：
Helms, V
中科院分区：
文献类型：
--
作者：
Ansari, S;Helms, V
统计分析了170个已知结构的蛋白质-蛋白质界面的残基和二级结构组成、配对偏好和侧链-主链相互作用频率。由于主要集中在瞬时蛋白质-蛋白质界面上，结果强调了以前关于蛋白质-蛋白质界面的发现，但也展示了瞬时界面的一些新的有趣的方面。这项研究中发现的界面残留物组成与其他研究结果有很好的相关性。平均而言，疏水残基和极性残基之间的接触是不利的，带电残基倾向于成对的电荷互补。二级结构组成分析表明，螺旋和P-折叠都不是主要分布在界面上。对二级结构元素配对偏好的分析表明，相同元素之间具有较高的亲和力，暗示着紧密堆积。此外，在更严格的条件下测量的侧链和主链相互作用频率的结果表明，侧链-主链相互作用的发生率很高。仔细观察给定侧链和主链相互作用的螺旋和P-折叠结合频率，强调了紧密堆积的相关性。界面的极性随界面尺寸的减小而增大。这些类型的信息可能对蛋白质-蛋白质对接研究中的复合体评分或仅从序列预测蛋白质-蛋白质界面有用。
A non-redundant set of 170 protein-protein interfaces of known structure was statistically analyzed for residue and secondary-structure compositions, pairing preferences and side-chain-backbone interaction frequencies. By focussing mainly on transient protein-protein interfaces, the results underline previous findings for protein-protein interfaces but also show some new interesting aspects of transient interfaces. The residue compositions at interfaces found in this study correlate well with the results of other studies. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity. Secondary structure composition analysis shows that neither helices nor P-sheets are dominantly populated at interfaces. Analyzing the pairing preferences of the secondary structure elements revealed a higher affinity within the same elements and alludes to tight packings. In addition, the results for the side-chain and backbone interaction frequencies, which were measured under more stringent conditions, showed a high occurrence of side-chain-backbone interactions. Taking a closer look at the helix and P-sheet binding frequencies for a given side-chain and backbone interaction underlined the relevance of tight packings. The polarity of interfaces increased with decreasing interface size. These types of information may be useful for scoring complexes in protein-protein docking studies or for prediction of protein-protein interfaces from the sequences alone.