Propagation of large concentration changes in reversible protein binding networks

TL;DR

This study investigates how large changes in protein concentrations affect the dynamics of reversible protein binding networks in yeast, revealing that effects are generally localized but can propagate over distances under certain conditions.

Contribution

It provides a quantitative analysis of how perturbations propagate in protein networks, highlighting factors influencing localization and conditions for long-range effects.

Findings

Perturbations mostly decay exponentially with network distance.

Functional modules operate independently despite network connectivity.

Long-range propagation occurs under specific concentration conditions.

Abstract

We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound concentrations of their immediate and more distant neighbors in the network is influenced by such factors as the network topology, the distribution of protein concentrations among its nodes, and the average binding strength. Our primary conclusion is that, on average, the effects of a perturbation are strongly localized and exponentially decay with the network distance away from the perturbed node, which explains why, despite globally connected topology, individual functional modules in such networks are able to operate fairly independently. We also found that under specific favorable conditions, realized in a significant number of paths in the yeast 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.