title: Communities in the iron superoxide dismutase amino acid network.
abstract: Amino acid networks (AANs) analysis is a new way to reveal the relationship between protein structure and function. We constructed six different types of AANs based on iron superoxide dismutase (Fe-SOD) three-dimensional structure information. These Fe-SOD AANs have clear community structures when they were modularized by different methods. Especially, detected communities are related to Fe-SOD secondary structures. Regular structures show better correlations with detected communities than irregular structures, and loops weaken these correlations, which suggest that secondary structure is the unit element in Fe-SOD folding process. In addition, a comparative analysis of mesophilic and thermophilic Fe-SOD AANs' communities revealed that thermostable Fe-SOD AANs had more highly associated community structures than mesophilic one. Thermophilic Fe-SOD AANs also had more high similarity between communities and secondary structures than mesophilic Fe-SOD AANs. The communities in Fe-SOD AANs show that dense interactions in modules can help to stabilize thermophilic Fe-SOD.
authors.affiliation: School of Digital Media, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China; Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China. Electronic address: yr_ding@jiangnan.edu.cn.
authors.forename: Yanrui
authors.initials: Y
authors.lastname: Ding
authors.affiliation: School of Digital Media, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
authors.forename: Xueqin
authors.initials: X
authors.lastname: Wang
authors.affiliation: School of Digital Media, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
authors.forename: Zhaolin
authors.initials: Z
authors.lastname: Mou
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D030562:Databases, Protein; D004795:Enzyme Stability; D017433:Protein Structure, Secondary; D013482:Superoxide Dismutase / Q000737:chemistry*; D013696:Temperature
chemical_list: D000596:Amino Acids; D013482:Superoxide Dismutase
keywords: Amino acid network; Community; Fe-SOD; Thermostability