AMINO-ACID SUBSTITUTIONS IN STRUCTURALLY RELATED PROTEINS - A PATTERN-RECOGNITION APPROACH - DETERMINATION OF A NEW AND EFFICIENT SCORING MATRIX
AMINO-ACID SUBSTITUTIONS IN STRUCTURALLY RELATED PROTEINS - A PATTERN-RECOGNITION APPROACH - DETERMINATION OF A NEW AND EFFICIENT SCORING MATRIX
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DOI：
10.1016/0022-2836(88)90058-7
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发表时间：
1988-12-20
影响因子：
5.6
通讯作者：
HENAUT, A
中科院分区：
文献类型：
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作者：
RISLER, JL;DELORME, MO;HENAUT, A
从结构的角度研究了进化相关蛋白质中的氨基酸取代。我们在这里认为，如果在p1和p2结构叠加后，a1和a2C.a，则蛋白质p1中的氨基酸a1已经被结构相似的蛋白质p2中的a2氨基酸取代。原子之间的距离不超过1.2。用这种方法分析了11类32种蛋白质。这产生了2860个氨基酸对(取代)，并用多维统计方法进行了分析。主要结果如下：(1)根据观察到的氨基酸侧链的交换性，只有四个基团(强团)可被划分为：(I)Ile和Val，(Ii)Leu和Met，(Iii)Lys，Arg和Gln，(Iv)Tyr和Phe。其他残留物不能归类。(2)本研究确定的氨基酸间距离矩阵或评分矩阵不同于任何其他已发表的矩阵。(3)除了基于氨基酸侧链化学性质的距离矩阵可以归为一组外，所有已发表的距离矩阵都是不同的。(4)本研究确定的距离矩阵对于远缘关系蛋白质序列的比对是非常有效的。
Amino acid substitutions in evolutionarily related proteins have been studied from a structural point of view. We consider here that an amino acid a1 in a protein p1 has been replaced by the amino acid a2 in the structurally similar protein p2 if, after superposition of the p1 and p2 structures, the a1 and a2 C.alpha. atoms are no more than 1.2 .ANG. apart. Thirty-two proteins, grouped in 11 classes, have been analysed by this method. This produced 2860 amino acid pairs (substitutions), which were analysed by multi-dimensional statistical methods. The main results are as follows: (1) according to the observed exchangeability of amino acid side-chains, only four groups (strong clusters) could be delineated; (i) Ile and Val, (ii) Leu and Met, (iii) Lys, Arg and Gln, and (iv) Tyr and Phe. The other residues could not be classifed. (2) The matrix of distances between amino acids, or scoring matrix, determined from this study, is different from any other published matrix. (3) Except for the distance matrices based on the chemical properties of amino acid side-chains, which can be grouped together, all other published matrices are different from one another. (4) The distance matrix determined in this study seems to be very efficient for aligning distantly related protein sequences.