Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis
Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis
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DOI：
10.1016/s0022-2836(03)00214-6
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发表时间：
2003-04-11
影响因子：
5.6
通讯作者：
Slotboom, DJ
中科院分区：
文献类型：
--
作者：
Lolkema, JS;Slotboom, DJ
提出了一种基于亲水谱分析的膜蛋白分类方案，将蛋白质家族聚类为结构类。蛋白质家族的平均亲水谱被作为蛋白质三维结构的指纹，因此，能够检测到比氨基酸序列更遥远的进化关系。开发了一种程序，其中亲水剖面分析最初用作NCBI蛋白质数据库BLAST搜索中的过滤器。通过将29个二级转运蛋白家族分类为单一结构类（称为ST[3]），可以证明该程序的强度。对数据库的详尽搜索显示，这29个家族包含568个独特的序列。这些蛋白主要来自原核生物，ST[3]中的大多数转运蛋白转运有机和无机阴离子，少数转运蛋白是Na+/H+反转运蛋白。所有的能量耦合模式（正态、反态、单态）都存在于结构类ST[3]中。讨论了该类中未表征转运蛋白的分类与结构/功能预测的相关性。2003爱思唯尔科学有限公司版权所有。
A classification scheme for membrane proteins is proposed that clusters families of proteins into structural classes based on hydropathy profile analysis. The averaged hydropathy profiles of protein families are taken as fingerprints of the 3D structure of the proteins and, therefore, are able to detect more distant evolutionary relationships than amino acid sequences. A procedure was developed in which hydropathy profile analysis is used initially as a filter in a BLAST search of the NCBI protein database. The strength of the procedure is demonstrated by the classification of 29 families of secondary transporters into a single structural class, termed ST[3]. An exhaustive search of the database revealed that the 29 families contain 568 unique sequences. The proteins are predominantly from prokaryotic origin and most of the characterized transporters in ST[3] transport organic and inorganic anions and a smaller number are Na+/H+ antiporters. All modes of energy coupling (symport, antiport, uniport) are found in structural class ST[3]. The relevance of the classification for structure/function prediction of uncharacterised transporters in the class is discussed. (C) 2003 Elsevier Science Ltd. All rights reserved.