Musafia B, Buchner V, Arad D
Department of Molecular Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel.
J Mol Biol. 1995 Dec 8;254(4):761-70. doi: 10.1006/jmbi.1995.0653.
We developed an algorithm to analyze the distribution and geometry of simple and complex salt bridges in 94 proteins selected from the Protein Data Bank. In this study, the term "salt bridging" denotes both non-bonded and hydrogen-bonded paired electrostatic interactions between acidic carboxyl groups and basic amino groups in single or adjacent protein chains. We defined complex salt bridges as those joining more than two charged residues, including Asp, Glu, Lys and Arg, and excluding His. The survey related the following special features of complex salt bridges. (1) The abundance of complex salt bridges is high; one-third of all residues participating in salt-bridge formation were part of complex salt bridges. (2) The geometry of the interaction between acidic and basic residues is very similar in simple and complex salt bridges. Adding one residue to a simple interaction represents a minor change in the geometry but provides the molecule with a more complex interaction, a phenomenon that may explain the cooperative effect of salt bridges in proteins. Such moderate changes in salt-bridge networks can be generated stepwise and reversibly without trapping the protein in a local energetic minimum. (3) One important role of complex salt bridges is connecting protein subunits or joining two secondary structures to form quaternary structures, where they can connect as many as five secondary structure units. (4) Arginine serves as a key connector and/or a branching unit because its geometry allows three possible directions of interactions. The information gained from this study of complex salt bridges should enhance the understanding of protein structure.
我们开发了一种算法，用于分析从蛋白质数据库中选出的94种蛋白质中简单和复杂盐桥的分布及几何结构。在本研究中，“盐桥”一词表示单条或相邻蛋白质链中酸性羧基与碱性氨基之间的非键合和氢键配对静电相互作用。我们将复杂盐桥定义为连接两个以上带电残基的盐桥，这些残基包括天冬氨酸（Asp）、谷氨酸（Glu）、赖氨酸（Lys）和精氨酸（Arg），不包括组氨酸（His）。该调查涉及复杂盐桥的以下特殊特征。（1）复杂盐桥的丰度很高；参与盐桥形成的所有残基中有三分之一是复杂盐桥的一部分。（2）简单盐桥和复杂盐桥中酸性和碱性残基之间的相互作用几何结构非常相似。在简单相互作用中增加一个残基代表几何结构上的微小变化，但为分子提供了更复杂的相互作用，这一现象可能解释了蛋白质中盐桥的协同效应。盐桥网络中的这种适度变化可以逐步且可逆地产生，而不会使蛋白质陷入局部能量最小值。（3）复杂盐桥的一个重要作用是连接蛋白质亚基或连接两个二级结构以形成四级结构，在四级结构中它们可以连接多达五个二级结构单元。（4）精氨酸作为关键的连接体和/或分支单元，因为其几何结构允许三种可能的相互作用方向。从对复杂盐桥的这项研究中获得的信息应能增强对蛋白质结构的理解。
