Department of Mathematics, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
Proteins. 2010 Aug 1;78(10):2322-8. doi: 10.1002/prot.22744.
Reduced amino acid alphabets are useful to understand molecular evolution as they reveal basal, shared properties of amino acids, which the structures and functions of proteins rely on. Several previous studies derived such reduced alphabets and linked them to the origin of life and biotechnological applications. However, all this previous work presupposes that only direct contacts of amino acids in native protein structures are relevant. We show in this work, using information-theoretical measures, that an appropriate alphabet reduction scheme is in fact a function of the maximum distance amino acids interact at. Although for small distances our results agree with previous ones, we show how long-range interactions change the overall picture and prompt for a revised understanding of the protein design process.
简化的氨基酸字母表对于理解分子进化非常有用，因为它们揭示了氨基酸的基本、共同特性，而蛋白质的结构和功能则依赖于这些特性。以前的一些研究得出了这样的简化字母表，并将其与生命起源和生物技术应用联系起来。然而，所有这些之前的工作都假设只有天然蛋白质结构中氨基酸的直接接触才是相关的。在这项工作中，我们使用信息论度量方法表明，适当的字母表简化方案实际上是氨基酸相互作用的最大距离的函数。虽然对于小距离，我们的结果与之前的结果一致，但我们展示了长程相互作用如何改变整体情况，并促使对蛋白质设计过程有一个修正的理解。
