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Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns
Wen Lu ,Hai-yan Liu*
Author NameAffiliation
Wen Lu Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China 
Hai-yan Liu* Hefei National Laboratory for Physical Sciences at Microscale, Key Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China 
Abstract:
Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to nonnative local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.
Key words:  Protein, Local structure pattern, Sequence-structure correlation, Hydrogen bonding
FundProject:
已知结构的短肽段的不同位点之间氨基酸残基的相关性
卢文,刘海燕*
摘要:
构筑了一个9个残基长度的短肽段库,根据短肽段的结构把它们分成不同的簇,用卡方分析每个簇,鉴别不同位点之间的相关性.同时还构筑了一个序列比对的评分函数,这个评分函数不但包含单个位点的信息,也包含不同位点之间相关性的信息.结果表明, 位点之间的相关性能够提供一些新颖的信息,这些信息一般都与短肽段不同位点之间的相互作用有关,相关性信息的引入能够明显的提高短肽段结构的预测准确度.
关键词:  蛋白质,短肽段,结构相关性,氢键
DOI:10.1360/cjcp2007.20(1).71.7
分类号: