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Topological and Dynamical Properties of Protein Interaction Networks

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Book cover Protein-protein Interactions and Networks

Part of the book series: Computational Biology ((COBO,volume 9))

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Abstract

This chapter reviews some of the recent research on topological and dynamical properties of Protein-protein Interaction (PPI) networks. In its first part we describe the set of numerical algorithms aimed at: 1) constructing a null-model random network with a desired set of low-level topological properties; 2) detection of over- or under-represented topological patterns such as degree-degree correlations between interacting nodes. In the second part of the chapter we describe a recently developed set of computational tools and analytical methods which allow one to go beyond purely topological studies of PPI networks and efficiently calculate the mass-action equilibrium of protein concentrations and its response to systematic perturbations. In particular, we explore how large (several-fold) changes in total abundance of a small number of proteins shift the equilibrium between free and bound concentrations of proteins throughout the PPI network. Our primary conclusion is that, on average, the effects of such perturbations exponentially decay with the network distance away from the perturbed node. This explains why, despite globally connected topology, individual functional modules in such networks are able to operate fairly independently. Under specific favorable conditions, realized in a significant number of paths in the yeast PPI network, concentration perturbations can selectively propagate over considerable network distances (up to four steps). Such “action-at-a-distance” requires high concentrations of heterodimers along the path as well as low free (unbound) concentration of intermediate proteins.

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Authors and Affiliations

  1. Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York, USA

    Sergei Maslov

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  1. Sergei Maslov
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Correspondence to Sergei Maslov .

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Editors and Affiliations

  1. National Institutes of Health, Bethesda, Maryland, USA

    Anna Panchenko  & Teresa Przytycka  & 

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© 2008 Springer-Verlag London Limited

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Maslov, S. (2008). Topological and Dynamical Properties of Protein Interaction Networks. In: Panchenko, A., Przytycka, T. (eds) Protein-protein Interactions and Networks. Computational Biology, vol 9. Springer, London. https://doi.org/10.1007/978-1-84800-125-1_7

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  • DOI: https://doi.org/10.1007/978-1-84800-125-1_7

  • Publisher Name: Springer, London

  • Print ISBN: 978-1-84800-124-4

  • Online ISBN: 978-1-84800-125-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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