Abstract

Using 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. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.