title: Network analysis of protein dynamics.
abstract: 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.
authors.affiliation: Department of Biophysics and Radiation Biology, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary. csabi@puskin.sote.hu
authors.forename: Csaba
authors.initials: C
authors.lastname: Böde
authors.forename: István A
authors.initials: IA
authors.lastname: Kovács
authors.forename: Máté S
authors.initials: MS
authors.lastname: Szalay
authors.forename: Robin
authors.initials: R
authors.lastname: Palotai
authors.forename: Tamás
authors.initials: T
authors.lastname: Korcsmáros
authors.forename: Péter
authors.initials: P
authors.lastname: Csermely
mesh_terms: D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D011506:Proteins; D014867:Water