Salt bridges: geometrically specific, designable interactions.
Salt bridges: geometrically specific, designable interactions.
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盐桥：几何特异性，可设计的相互作用。
DOI：
10.1002/prot.22927
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发表时间：
2011-03
影响因子：
2.9
通讯作者：
DeGrado, William F.
中科院分区：
文献类型：
--
作者：
Donald, Jason E.;Kulp, Daniel W.;DeGrado, William F.
关键词：
盐桥经常出现在蛋白质中，提供构象特异性，有助于分子识别和催化。我们通过对蛋白质结构的大型数据库的调查，对蛋白质结构中的这些相互作用进行了全面的分析。Asp或Glu与His、Arg或Lys之间的盐桥显示出非常明确的几何偏好。确认了几个先前观察到的偏好，并发现了先前未识别的其他偏好。探讨了盐桥在序列和空间上对不同分离的偏好、蛋白质内和蛋白质-蛋白质界面的几何偏好、网络盐桥中的协同性、金属结合位点内的包裹体、对酸性电子的偏好、形成时明显的构象侧链熵减少以及埋藏程度。盐桥发生在距离较近的序列分离的残基之间比距离较远的序列分离要频繁得多，但在较近的距离，在特定的分离位置仍然有强烈的盐桥偏好。还发现了涉及三个或更多成员的特定类型的复杂盐桥。当我们观察到盐桥的形成倾向和盐桥残基在蛋白质序列中的位置之间的密切关系时，我们讨论了盐桥在动力学影响蛋白质折叠和热力学稳定天然构象方面可能发挥的作用。我们还开发了一种定量方法来选择合适的晶体结构分辨率和B因子截止值。对这些几何和序列相关性的详细了解应该有助于从头设计和预测算法。
Salt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously observed preferences are confirmed and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, cooperativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction upon formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but at close distances there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms.
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