Major factors of protein evolution revealed by eigenvalue decomposition analysis

IMECH-IR > 力学所知识产出(1956-2008)

	Major factors of protein evolution revealed by eigenvalue decomposition analysis
	Liu X(刘鑫); Zhang LM; Yin J; Zhao YP(赵亚溥)
会议录名称	Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
	2008
会议名称	2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008
会议日期	July 14, 2008 - July 17, 2008
会议地点	Las Vegas, NV, United states
摘要	Here we attempt to characterize protein evolution by its dominant factors. These factors are revealed by top eigenvectors in the spectrums of eigenvalue decomposition analysis. To reduce the bias induced by closely related sequences in the database, we introduce a parameter, sequence identity by which proteins with sequence identity below certain level are involved in analysis. It is found that, with drop of sequence identity level, residue feature mainly conserved in mutation changes from hydrophobicity to volume. The transition point is at sequence identity 45%. As residue hydropho-bicity no longer governs residue substitution, it is a doubt whether importance of hydrophobic interaction declines in conserving the family representative properties among remote homologues. So, we also investigate the contribution of hydrophobic interaction in near and remote homologues. In aligned homologues, hydrophobic interaction systems inbuilt in these proteins are aligned too; and can be deemed to be similar and substitutable with each other. With a comparison of aligned hydrophobic interaction systems, we can catch the representative character of hydrophobic interaction for the corresponding protein family. Here top weighted feature in the substitution of hydropho-bic interaction systems is revealed as a function of sequence identity. It is found that a shift happens to the type of physical quantity which governs the substitution of hydrophobic interaction. The number of hydrophobic residue is the dominantly unchangeable part in aligned hydrophobic interactions as sequence identity > 30%. Below this point, state of internal hydrophobic force which characterizes the residue-residue pairwise interaction is primarily conserved. With view of this shift, intrinsic requirement of protein evolution is sought in the discussion section.
关键词	Eigenvalue Decomposition Analysis Hydrophobic Interaction Protein Evolution Remote Homologues Sequence Analysis And Alignment
ISBN号	1601320558
收录类别	EI
语种	英语
文献类型	会议论文
条目标识符	http://dspace.imech.ac.cn/handle/311007/60315
专题	力学所知识产出(1956-2008)
推荐引用方式 GB/T 7714	Liu X,Zhang LM,Yin J,et al. Major factors of protein evolution revealed by eigenvalue decomposition analysis[C]Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008,2008.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
CaEi082.pdf（1129KB）	会议论文		开放获取	CC BY-NC-SA	浏览下载