Sergei Maslov et al 2007 New J. Phys. 9 273 doi:10.1088/1367-2630/9/8/273
Sergei Maslov1, Kim Sneppen2 and I Ispolatov3,4
Show affiliationsUsing an example of physical interactions between proteins, we study how a perturbation propagates in the equilibrium of a network of reversible reactions governed by the law of mass action. We introduce a matrix formalism to describe the linear response of all equilibrium concentrations to shifts in total abundances of individual reactants, and reveal its heuristic analogy to the flow of electric current in a network of resistors. Our main conclusion is that, on average, the induced changes in equilibrium concentrations decay exponentially as a function of network distance from the source of perturbation. We analyze how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. We find that the minimal branching of the network, small values of dissociation constants, and low equilibrium free (unbound) concentrations of reacting substances all decrease the decay constant and thus increase the range of propagation. Exact analytic expressions for the decay constant are obtained for the case of equally strong interactions and uniform as well as oscillating concentrations on the Bethe lattice. Our general findings are illustrated using a real network of protein–protein interactions in baker's yeast with experimentally determined protein concentrations.
87.15.K- Molecular interactions; membrane-protein interactions
Issue 8 (August 2007)
Received 2 May 2007
Published 17 August 2007
Sergei Maslov et al 2007 New J. Phys. 9 273
Cliff P. Burgess et al JHEP10(2002)028
Shamit Kachru et al JCAP10(2003)013
Chiang-Mei Chen et al JHEP11(2006)044
Chiang-Mei Chen et al JHEP10(2003)058
Alex Buchel and Johannes Walcher JHEP05(2003)069
Clifford P. Burgess et al JHEP03(2003)050
Shinji Tsujikawa and M Sami JCAP01(2007)006
Ben M Leith and Ishwaree P Neupane JCAP05(2007)019
S. Roeser et al. 2010 The Astronomical Journal 139 2440