Measuring residue associations in protein structures. Possible implications for protein folding.
Measuring residue associations in protein structures. Possible implications for protein folding.
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测量蛋白质结构中的残基关联。
DOI：
10.1006/jmbi.1994.1365
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发表时间：
1994
影响因子：
5.6
通讯作者：
Brocchieri,L
中科院分区：
文献类型：
--
作者：
Karlin,S;Zuker,M;Brocchieri,L
我们提出了一些基于所有原子（主链和侧链）坐标的平均、最小和最大距离或仅关于侧链原子坐标的蛋白质结构中残基之间的距离度量。D1-distance （D1-distance）是指给定结构中残基对的侧链（主链和侧链）原子之间的平均距离。其中Dm-distance （Dm-distance）是指侧链原子之间的最小距离（残基对中所有原子之间的非平凡最小距离）。对于每个距离测量，对代表性蛋白质结构，所有氨基酸类型的关联值和紧密排序进行平均和规范化。结果证实了半胱氨酸与半胱氨酸之间、疏水残基之间和带相反电荷残基之间的侧链相互作用的预期关联。几个令人惊讶的关联被观察到(1)芳香残基酪氨酸和色氨酸，但苯丙氨酸没有；(2)多个组氨酸残基；(3)精氨酸对赖氨酸、天冬氨酸对谷氨酸、丙氨酸对甘氨酸、天冬酰胺对谷氨酰胺的不对称性；(4) α-碳距离与侧链距离不存在相关性。所有原子sd1距离吸引以空间关系为主，甘氨酸和丙氨酸与所有氨基酸明显接近，而大残基与所有残基类型都不相关。相反，对于最小侧链距离对应的紧密排序，甘氨酸和丙氨酸是最不相关的。然而，在d1距离上，丙氨酸与除色氨酸外的所有疏水残基都非常接近。这些距离偏好显示了几乎所有残基类型对酪氨酸的普遍吸引力，酪氨酸和色氨酸在阳离子-芳香相互作用中的突出作用，以及组氨酸在功能上的多功能性。这些主要发现为蛋白质折叠的早期和中期阶段提供了一个新的视角。
We propose a number of distance measures between residues in protein structures based on average, minimum and maximum distances of all atom (backbone and side-chain) coordinates or with respect to side-chain atom coordinates only. Thed1-distance (D1-distance) refers to the average distance between side-chain (backbone and side-chain) atoms of a residue pair in a given structure. Thedm-distance (Dm-distance) refers to the minimum distance between side-chain atoms (non-trivial minimum distance between all atoms of a residue pair). For each distance measure, averaging and normalizing over representative protein structures, association values and closeness orderings for all amino acid types are determined. The expected associations of side-chain interactions between oppositely charged residues, among hydrophobic residues and of cysteine with cysteine are confirmed. Several surprising associations are observed relative to (1) the aromatic residues tyrosine and tryptophan, but not phenylalanine; (2) multiple histidine residues; (3) asymmetries of arginineversuslysine, aspartateversusglutamate, alanineversusglycine, and asparagineversusglutamine; (4) absence of correlations of α-carbon distances with side-chain distances. The all atomsD1-distance attractions are dominated by steric relationships, with glycine and alanine significantly close to all amino acids, whereas large residues are under-associated with all residue types. In contrast, for the closeness ordering corresponding to the minimum side-chaindm-distance, glycine and alanine are among the least associated. However, in thed1-distance alanine is significantly close to all hydrophobic residues with the exception of tryptophan. Thedm-distance preferences display a pervasive attraction for tyrosine by almost all residue types, the prominence of tyrosine and tryptophan in cation-aromatic interactions, and the versatility of histidine in functionality. The principal findings suggest a new perspective on the early and intermediate stages of protein folding.