Structural position correlation analysis (SPCA) for protein family.
Structural position correlation analysis (SPCA) for protein family.
复制标题
蛋白质家族的结构位置相关分析 (SPCA)
DOI：
10.1371/journal.pone.0028206
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Huang RB
中科院分区：
文献类型：
--
作者：
Du QS;Meng JZ;Wang CH;Long SY;Huang RB
背景同一家族中具有相似生物学功能的蛋白质，其氨基酸组成可能有很大差异，但它们必须具有相似的三维结构，并保持稳定的中心区域。在保守结构区，类似的生物学功能由两个或三个催化残基与关键位置上的几个功能残基协作执行。通信信号在位置网络中进行，调节蛋白质家族中的生物功能。方法采用结构位置相关分析（SPCA）的方法，分析结构片段（或位置）之间的相关关系。SPCA的基本假设是：在一个蛋白质家族中，结构保守性比序列保守性更重要，局部结构变化可能包含生物功能进化的信息。标准蛋白质P（0）定义于蛋白质家族中，其由最常见的氨基酸组成，并具有蛋白质家族的平均结构。SPCA的基本变量是标准蛋白质P（0）和家族中单个蛋白质Pi之间的结构位置位移。结构位置被组织为片段，片段是蛋白质家族结构位移中的稳定单元。蛋白质成员的生物学功能差异是由单个蛋白质Pi相对于标准蛋白质P（0）的位置结构位移决定的。采用相关性分析法对网段之间的通信网络进行分析。结论结构位置相关性分析（SPCA）能够发现蛋白质家族中结构片段（或位置）之间的相关关系，这是基于氨基酸序列和频率的方法所不能发现的。SPCA方法揭示了蛋白质家族中结构片段（或位置）之间的功能通讯网络，很好地说明了蛋白质家族中的远距离变构相互作用，为蛋白质工程研究提供了有价值的信息。
Background The proteins in a family, which perform the similar biological functions, may have very different amino acid composition, but they must share the similar 3D structures, and keep a stable central region. In the conservative structure region similar biological functions are performed by two or three catalytic residues with the collaboration of several functional residues at key positions. Communication signals are conducted in a position network, adjusting the biological functions in the protein family. Methodology A computational approach, namely structural position correlation analysis (SPCA), is developed to analyze the correlation relationship between structural segments (or positions). The basic hypothesis of SPCA is that in a protein family the structural conservation is more important than the sequence conservation, and the local structural changes may contain information of biology functional evolution. A standard protein P(0) is defined in a protein family, which consists of the most-frequent amino acids and takes the average structure of the protein family. The foundational variables of SPCA is the structural position displacements between the standard protein P(0) and individual proteins Pi of the family. The structural positions are organized as segments, which are the stable units in structural displacements of the protein family. The biological function differences of protein members are determined by the position structural displacements of individual protein Pi to the standard protein P(0). Correlation analysis is used to analyze the communication network among segments. Conclusions The structural position correlation analysis (SPCA) is able to find the correlation relationship among the structural segments (or positions) in a protein family, which cannot be detected by the amino acid sequence and frequency-based methods. The functional communication network among the structural segments (or positions) in protein family, revealed by SPCA approach, well illustrate the distantly allosteric interactions, and contains valuable information for protein engineering study.
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