构建基于折叠核心的全α类蛋白取代矩阵  

Construction of All-alpha Protein Substitution Matrix Based on Fold Core

作　　者：刘晓辉[1] 李晓琴[1] 徐海松[1] 任文科[1] 

机构地区：[1]北京工业大学生命科学与生物工程学院,北京100124

出　　处：《中国生物化学与分子生物学报》2008年第8期761-766,共6页Chinese Journal of Biochemistry and Molecular Biology

基　　金：国家自然科学基金(No.30570427);北京市自然科学基金(No.4063035)资助项目~~

摘　　要：氨基酸残基取代矩阵是影响多序列比对效果的重要因素,现有的取代矩阵对低相似序列的比对性能较低.在已有的BLOSUM取代矩阵算法基础上,定义了基于蛋白质折叠核心结构的序列-结构数据块;提出一种新的基于全α类蛋白质折叠核心结构的氨基酸残基取代矩阵——TOPSSUM25,用于提高低相似度序列的比对效果.将矩阵TOPSSUM25导入多序列比对程序,对相似性小于25%的一组四螺旋束序列-结构数据块的测试结果表明,基于TOPSSUM25的多序列比对效果明显优于BLOSUM30矩阵;基于一个BAliBASE子集的比对检验也进一步表明,TOPSSUM25在全α类蛋白质的两两序列比对上优于BLOSUM30矩阵.研究结果可为进一步的阐明低同源蛋白质序列-结构-功能关系提供帮助.Amino acid substitution matrix is a key factor to protein sequence alignment. However, the existing matrices are not competent for aligning low-identity sequence. Based on the algorithm used to construct BLOSUM series, sequence-structure ＂blocks＂ are defined based on protein fold cores. We have constructed a new matrix, TOPSSUM25, based on all-α protein fold core structure of proteins to improve the alignment of low-identity sequences. Aligning a four updown helical bundle sequence-structure block （ 〈 25% sequence identity） based on TOPSSUM25 and BLOSUM30 respectively indicates that TOPSSUM25 is better than BLOSUM30 in multiple sequence alignment. The alignment test conducted on a BAliBASE subset also indicates that TOPSSUM25 gives better result in pairwise sequence alignment of all-α proteins. Our research indicates that some improvements could be managed to the protein sequence alignment under certain conditions, therefore might contribute to the understanding of relationship among sequence, structure and function.

关 键 词：蛋白质结构 折叠核心结构 低相似性 多序列比对 取代矩阵 

分 类 号：Q617[生物学—生物物理学] Q71