Analysis of side-chain orientations in homologous proteins.
Analysis of side-chain orientations in homologous proteins.
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同源蛋白质中侧链方向的分析。
DOI：
10.1016/0022-2836(87)90520-1
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发表时间：
1987
影响因子：
5.6
通讯作者：
M. Karplus
中科院分区：
文献类型：
--
作者：
N. Summers;William D. Carlson;M. Karplus
比较了序列同源性从16%到60%的7对蛋白质的拓扑等价残基的侧链构象。包括相同残基和突变残基。对于同源性大于40%的蛋白质，发现每对蛋白质中至少80%的相同残基的侧链取向和75%或更多的突变残基具有匹配的γ原子二面角(±40°)；这种比较并不是严格基于χ角度。此外，如果在γ位置获得匹配，则侧链的δ原子(S)匹配的概率很高。对于同源性低于25%的蛋白质，其百分比稍低。观察到的保守取代的趋势基本上与注意到的突变残基的趋势相同。侧链可及性不影响相同残基的匹配概率；然而，较难获得的突变残基对的匹配概率比暴露残基高10%至20%。错配经常与大的B因子、某些类型的氨基酸替换或侧链势能面上出现多个最小值有关，并且最有可能发生在某些小残基(Ser、Thr、Val)。对所有结果的分析使得在同源蛋白质建模中制定一套侧链定位规则成为可能。
The side-chain conformations of topologically equivalent residues in seven pairs of proteins ranging in sequence homology from 16% to 60% are compared. Both identical and mutated residues are included. For proteins with greater than 40% homology, it is found that at least 80 % of the side-chain orientations of identical residues and 75 % or more of the mutated residues in each pair of proteins have matching γ atom dihedral angles (± 40 °); the comparison is not based strictly onχ1angles. Further, if a match is obtained at the γ position, there is a high probability of matching for the δ atom(s) of the side-chain. For proteins with less than 25% homology the percentages are somewhat lower. Trends observed for conservative substitutions are essentially the same as those noted for mutated residues in general. Side-chain accessibility does not affect the probability of matches of identical residues; however, less accessible pairs of mutated residues have 10 to 20% higher matching probabilities than do exposed residues. Mismatches can frequently be related to largeB-factors, certain types of amino acid substitutions, or the appearance of multiple minima on the side-chain potential energy surfaces and are most likely to occur for certain small residues (Ser, Thr, Val). Analysis of all the results makes possible the formulation of a set of rules for side-chain positioning in the modeling of homologous proteins.