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Dynamic proteomics in modeling of the living cell. Protein-protein interactions

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Abstract

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.

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Abbreviations

AFP:

alpha-fetoprotein

CDK:

cyclin-dependent kinase

CKI:

cyclin-dependent kinase inhibitor

EGF:

epidermal growth factor

FLIM:

fluorescence lifetime imaging microscopy

FRET:

fluorescence resonance energy transfer

MALDI-TOF:

matrix-assisted laser desorption/ionization-time of flight

MAPK:

mitogen-activated protein kinase

MD:

molecular dynamics

NF-κB:

nuclear factor κB

OASS:

O-acetylserine sulfohydrolase

PTB:

phosphotyrosine binding

SAT:

serine acetyl transferase

SELDI:

surface enhanced laser desorption/ionization

SH:

Src homology (homolog of the chicken sarcoma oncogene product)

TAP-MS:

tandem affinity purification-mass spectrometry

TNF-α:

tumor necrosis factor α

Y2H:

yeast two-hybrid assay

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Authors and Affiliations

  1. Russian State Medical University, ul. Ostrovityanova 1, 117997, Moscow, Russia

    A. A. Terentiev & N. T. Moldogazieva

  2. Biological Faculty, Lomonosov Moscow State University, 119191, Moscow, Russia

    K. V. Shaitan

Authors
  1. A. A. Terentiev
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  2. N. T. Moldogazieva
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  3. K. V. Shaitan
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Corresponding authors

Correspondence to A. A. Terentiev or N. T. Moldogazieva.

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Original Russian Text © A. A. Terentiev, N. T. Moldogazieva, K. V. Shaitan, 2009, published in Uspekhi Biologicheskoi Khimii, 2009, Vol. 49, pp. 429–480.

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Terentiev, A.A., Moldogazieva, N.T. & Shaitan, K.V. Dynamic proteomics in modeling of the living cell. Protein-protein interactions. Biochemistry Moscow 74, 1586–1607 (2009). https://doi.org/10.1134/S0006297909130112

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  • DOI: https://doi.org/10.1134/S0006297909130112

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