Murphy L R, Wallqvist A, Levy R M
Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
Protein Eng. 2000 Mar;13(3):149-52. doi: 10.1093/protein/13.3.149.
Protein design experiments have shown that the use of specific subsets of amino acids can produce foldable proteins. This prompts the question of whether there is a minimal amino acid alphabet which could be used to fold all proteins. In this work we make an analogy between sequence patterns which produce foldable sequences and those which make it possible to detect structural homologs by aligning sequences, and use it to suggest the possible size of such a reduced alphabet. We estimate that reduced alphabets containing 10-12 letters can be used to design foldable sequences for a large number of protein families. This estimate is based on the observation that there is little loss of the information necessary to pick out structural homologs in a clustered protein sequence database when a suitable reduction of the amino acid alphabet from 20 to 10 letters is made, but that this information is rapidly degraded when further reductions in the alphabet are made.
蛋白质设计实验表明，使用特定的氨基酸子集可以产生可折叠的蛋白质。这就引发了一个问题：是否存在一个最小的氨基酸字母表，可用于折叠所有蛋白质。在这项工作中，我们将产生可折叠序列的序列模式与通过序列比对来检测结构同源物的序列模式进行类比，并利用它来推测这种简化字母表可能的大小。我们估计，包含10至12个字母的简化字母表可用于为大量蛋白质家族设计可折叠序列。这一估计基于这样的观察结果：当将氨基酸字母表从20个适当减少到10个字母时，在聚类蛋白质序列数据库中挑选结构同源物所需的信息几乎没有损失，但当进一步减少字母表时，这些信息会迅速退化。
