AMINO-ACID SUBSTITUTION DURING FUNCTIONALLY CONSTRAINED DIVERGENT EVOLUTION OF PROTEIN SEQUENCES
AMINO-ACID SUBSTITUTION DURING FUNCTIONALLY CONSTRAINED DIVERGENT EVOLUTION OF PROTEIN SEQUENCES
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DOI：
10.1093/protein/7.11.1323
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发表时间：
1994-11-01
期刊：
影响因子：
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通讯作者：
GONNET, GH
中科院分区：
文献类型：
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作者：
BENNER, SA;COHEN, MA;GONNET, GH
在比对同源蛋白质序列时，通常假设在时间上随后的氨基酸取代独立于在时间上先前的氨基酸取代发生，即突变模式在低和高序列差异下相似。这个假设在这里进行了检查，并以一种有趣的方式证明是不正确的。为在5至100个PAM单位（每100个比对位置的点可接受突变）的分歧处比对的蛋白质序列对构建单独的突变矩阵。由此，构建了归一化为250个PAM单位的相应对数几率（Dayhoff）矩阵。矩阵表明，遗传密码的影响，接受点突变强烈的分歧的早期阶段，而侧链的化学性质占主导地位，在更先进的阶段。
In aligning homologous protein sequences, it is generally assumed that amino acid substitutions subsequent in time occur independently of amino acid substitutions previous in time, i.e. that patterns of mutation are similar at low and high sequence divergence. This assumption is examined here and shown to be incorrect in an interesting way. Separate mutation matrices were constructed for aligned protein sequence pairs at divergences ranging from 5 to 100 PAM units (point accepted mutations per 100 aligned positions). From these, the corresponding log-odds (Dayhoff) matrices, normalized to 250 PAM units, were constructed. The matrices show that the genetic code influences accepted point mutations strongly at early stages of divergence, while the chemical properties of the side chains dominate at more advanced stages.