Salt bridge stability in monomeric proteins
Salt bridge stability in monomeric proteins
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DOI：
10.1006/jmbi.1999.3218
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发表时间：
1999-11-12
影响因子：
5.6
通讯作者：
Nussinov, R
中科院分区：
文献类型：
--
作者：
Kumar, S;Nussinov, R
在这里，我们提出了连续的静电计算的结果来自36个非同源的高分辨率单体蛋白质晶体结构的222个非等价盐桥的数据集。我们数据集中的大多数盐桥都是稳定的，无论它们是被掩埋还是暴露，孤立还是网络化，氢键还是非氢键。在我们的数据集中，三分之一的盐桥被埋在蛋白质核心中，其余的暴露在溶剂中。水的介电性质与疏水蛋白质内部成本的差异埋盐桥大去溶剂化处罚。然而，由于没有溶剂屏蔽，盐桥侧链之间以及盐桥与其蛋白质环境中的电荷之间的静电相互作用在内部也更强。即使是掩埋盐桥的大的去溶剂化惩罚也经常被补偿，主要是通过盐桥侧链之间的静电相互作用。在网状盐桥中，盐桥侧链之间的静电相互作用以及盐桥与其蛋白质环境之间的静电相互作用具有相似的量级。特别是，这项工作的一个主要发现是，盐桥的几何形状是决定盐桥稳定性的一个关键因素。具有相互作用的侧链带电基团的有利几何定位的盐桥可能在蛋白质结构中的任何地方稳定。我们进一步发现，大多数的盐桥之间形成的残基是相对接近彼此的序列。(C)北京：科学出版社.
Here, we present the results of continuum electrostatic calculations on a dataset of 222 non-equivalent salt bridges derived from 36 non-homologous high-resolution monomeric protein crystal structures. Most of the salt bridges in our dataset are stabilizing, regardless of whether they are buried or exposed, isolated or networked, hydrogen bonded or non-hydrogen bonded. One-third of the salt bridges in our dataset are buried in the protein core, with the remainder exposed to the solvent. The difference in the dielectric properties of water versus the hydrophobic protein interior cost buried salt bridges large desolvation penalties. However, the electrostatic interactions both between the salt-bridging side-chains, and between the salt bridges and charges in their protein surroundings, are also stronger in the interior, due to the absence of solvent screening. Even large desolvation penalties for burying salt bridges are frequently more than compensated for, primarily by the electrostatic interactions between the salt-bridging side-chains. In networked salt bridges both types of electrostatic interactions, those between the salt-bridging side-chains, and those between the salt bridge and its protein environment, are of similar magnitudes. In particular, a major finding of this work is that salt bridge geometry is a critical factor in determining salt bridge stability. Salt bridges with favorable geometrical positioning of the interacting side-chain charged groups are likely to be stabilizing anywhere in the protein structure. We further find that most of the salt bridges are formed between residues that are relatively near each other in the sequence. (C) 1999 Academic Press.