Network analysis of protein dynamics

Böde, Csaba; Kovács, István A.; Szalay, Máté S.; Palotai, Robin; Korcsmáros, Tamás; Csermely, Péter

doi:10.1016/j.febslet.2007.05.021

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Volume 581, Issue 15 , Pages 2776-2782, 19 June 2007

Network analysis of protein dynamics

Edited by Horst Feldmann

Csaba Böde
- Department of Biophysics and Radiation Biology, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary
- Started their research as members of the Hungarian Research Student Association (www.kutdiak.hu), which provides research opportunities for talented high school students since 1996.
István A. Kovács
- Department of Medical Chemistry, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary
- Started their research as members of the Hungarian Research Student Association (www.kutdiak.hu), which provides research opportunities for talented high school students since 1996.
Máté S. Szalay
- Department of Medical Chemistry, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary
- Started their research as members of the Hungarian Research Student Association (www.kutdiak.hu), which provides research opportunities for talented high school students since 1996.
Robin Palotai
- Department of Medical Chemistry, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary
- Started their research as members of the Hungarian Research Student Association (www.kutdiak.hu), which provides research opportunities for talented high school students since 1996.
Tamás Korcsmáros
- Department of Medical Chemistry, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary
- Started their research as members of the Hungarian Research Student Association (www.kutdiak.hu), which provides research opportunities for talented high school students since 1996.
Péter Csermely
- Department of Medical Chemistry, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary
- Corresponding author. Fax: +361 266 6550.

Received 11 March 2007; received in revised form 30 April 2007; accepted 8 May 2007. published online 18 May 2007.

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.

Keywords: Allosteric regulation, Disordered proteins, Enzyme catalysis, Molecular machines, Motions, Network topology, Protein structure, Signal transduction, Small-world, Water