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Network analysis of protein dynamics
Author(s) -
Böde Csaba,
Kovács István A.,
Szalay Máté S.,
Palotai Robin,
Korcsmáros Tamás,
Csermely Péter
Publication year - 2007
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2007.05.021
Subject(s) - allosteric regulation , centrality , protein dynamics , computer science , modularity (biology) , network dynamics , representation (politics) , folding (dsp implementation) , topology (electrical circuits) , modular design , protein folding , network topology , computational biology , molecular dynamics , physics , biology , chemistry , mathematics , computational chemistry , engineering , computer network , discrete mathematics , law , enzyme , operating system , political science , combinatorics , politics , electrical engineering , genetics , nuclear magnetic resonance
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here, we review the results of the topological analysis of protein structures as molecular networks describing their small‐world character, and the role of hubs and central network elements in governing enzyme activity, allosteric regulation, protein motor function, signal transduction and protein stability. We summarize available data how central network elements are enriched in active centers and ligand binding sites directing the dynamics of the entire protein. We assess the feasibility of conformational and energy networks to simplify the vast complexity of rugged energy landscapes and to predict protein folding and dynamics. Finally, we suggest that modular analysis, novel centrality measures, hierarchical representation of networks and the analysis of network dynamics will soon lead to an expansion of this field.