Amino acid contact energy networks impact protein structure and evolution

被引:16
|
作者
Yan, Wenying [1 ]
Sun, Maomin [1 ,2 ]
Hu, Guang [1 ]
Zhou, Jianhong [1 ]
Zhang, Wenyu [1 ]
Chen, Jiajia [1 ,3 ]
Chen, Biao [1 ]
Shen, Bairong [1 ]
机构
[1] Soochow Univ, Ctr Syst Biol, Suzhou 215006, Jiangsu, Peoples R China
[2] Soochow Univ, Sch Med, Lab Anim Res Ctr, Suzhou 215006, Jiangsu, Peoples R China
[3] Suzhou Univ Sci & Technol, Dept Chem & Biol Engn, Suzhou 215011, Jiangsu, Peoples R China
基金
中国国家自然科学基金; 国家高技术研究发展计划(863计划); 高等学校博士学科点专项科研基金;
关键词
Clustering coefficient; Long-range link percentage; Network diameter; Protein evolutionary rate; Protein secondary structure density; GENE-EXPRESSION; REGRESSION; DYNAMICS; RATES;
D O I
10.1016/j.jtbi.2014.03.032
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
One of the most challenging tasks in structural proteomics is to understand the relationship between protein structure, biological function, and evolution. An understanding of amino acid networks based on protein topology has an important role in the study of this relationship; however, the relationship between network parameters underlying protein topology with structural properties or evolutionary rate is still unknown. To investigate this further, we modeled the three dimensional structure of proteins as amino acid contact energy networks (AACENs) with nodes represented as amino acid residues and edges established according to environment-dependent residue-residue contact energies. Five other types of networks were also constructed to investigate their topological parameters and compare their effect on protein structure and evolution: (1) a random contact network (RCN), (2) a rewiring network with the same degree of distribution as AACEN (RNDD), (3) long-range contact energy networks with and without the backbone connectivity (LCEN_BBs and LCENs), and (4) short range contact energy networks (SCENs). The results indicated that the long-range link percentage and the network clustering coefficient showed a significantly positive and negative correlation, respectively, with protein secondary structure density. In addition, the long-range link percentage and network diameter had a significantly positive and negative correlation, respectively, with evolutionary rate. According to our knowledge, this is the first study to identify the potential role of long-range links and network diameter in protein evolution. (C) 2014 Elsevier Ltd. All rights reserved.
引用
收藏
页码:95 / 104
页数:10
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