Protein space: A natural method for realizing the nature of protein universe
Protein space: A natural method for realizing the nature of protein universe
复制标题
蛋白质空间：认识蛋白质宇宙本质的自然方法
DOI：
10.1016/j.jtbi.2012.11.005
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发表时间：
2013-02-07
影响因子：
2
通讯作者：
Yau, Stephen S. -T.
中科院分区：
文献类型：
--
作者：
Yu, Chenglong;Deng, Mo;Yau, Stephen S. -T.
目前的方法不能告诉我们蛋白质宇宙的具体性质是什么。它们基于不同的氨基酸替换和多序列比对模型，这是一个NP-Hard问题，需要人工干预。蛋白质结构分析也为绘制蛋白质宇宙图提供了方向。不幸的是，现在人们只知道蛋白质三维结构的一小部分。此外，系统发育树的表示对于任何现有的树构建方法都不是唯一的。在这里，我们发展了一种新的方法来认识蛋白质宇宙的本质。我们证明了蛋白质宇宙可以被实现为60维欧氏空间中的蛋白质空间，使用基于氨基酸归一化分布的距离。每一种蛋白质都与蛋白质空间中的一个点一一对应，在那里具有相似性质的蛋白质保持紧密联系。因此，蛋白质空间中两点之间的距离代表了相应的两个蛋白质的生物距离。我们还提出了一种自然的图形表示来推断系统发育。基于蛋白质在蛋白质空间中的生物距离，这种表示是自然和独特的。这将解决蛋白质在蛋白质宇宙中如何分布的根本问题。(C)2012爱思唯尔有限公司。保留所有权利。
Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe. (C) 2012 Elsevier Ltd. All rights reserved.