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REVIEW: Dynamic Proteomics in Modeling of the Living Cell. Protein–Protein Interactions

A. A. Terentiev1*, N. T. Moldogazieva1*, and K. V. Shaitan2

1Russian State Medical University, ul. Ostrovityanova 1, 117997 Moscow, Russia; E-mail: aaterent@mtu-net.ru; nmoldogazieva@mail.ru

2Biological Faculty, Lomonosov Moscow State University, 119191 Moscow, Russia; E-mail: shaitan@moldyn.org

* To whom correspondence should be addressed.

Received March 23, 2009; Revision received June 26, 2009
This review is devoted to describing, summarizing, and analyzing of dynamic proteomics data obtained over the last few years and concerning the role of protein–protein interactions in modeling of the living cell. Principles of modern high-throughput experimental methods for investigation of protein–protein interactions are described. Systems biology approaches based on integrative view on cellular processes are used to analyze organization of protein interaction networks. It is proposed that finding of some proteins in different protein complexes can be explained by their multi-modular and polyfunctional properties; the different protein modules can be located in the nodes of protein interaction networks. Mathematical and computational approaches to modeling of the living cell with emphasis on molecular dynamics simulation are provided. The role of the network analysis in fundamental medicine is also briefly reviewed.
KEY WORDS: systems biology, modeling of living cells, dynamic proteomics, interactomes, protein interaction networks, structural and functional mapping of proteins, molecular dynamics, fundamental medicine

DOI: 10.1134/S0006297909130112