Small-world communication of residues and significance for protein dynamics

TL;DR

This study demonstrates that protein residue interactions form a small-world network, linking residue arrangement to protein dynamics and stability, with implications for understanding protein function.

Contribution

It reveals that protein residue networks exhibit small-world properties, connecting local packing to long-range interactions and correlating network topology with residue fluctuations.

Findings

Residue interactions form small-world networks.

Core residues have consistent local packing across proteins.

Average shortest path lengths correlate with residue fluctuations.

Abstract

It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that regular packing is preserved in short-range interactions, but short average path lengths are achieved through some long-range contacts. Thus, lying between the two extremes of regularity and randomness, residues in folded proteins are distributed according to a "small-world" topology. Using this topology, we show that the core residues have the same local packing arrangements irrespective of protein size. Furthermore, we find that the average shortest path lengths are highly correlated with residue fluctuations, providing a link between the spatial arrangement of the residues and protein dynamics.