A generative model for protein contact networks

TL;DR

This paper introduces a new generative model for protein contact networks that better captures their spectral and topological properties, with improvements achieved through a targeted edge reconfiguration process.

Contribution

The paper proposes a novel generative model for protein contact networks and demonstrates its superiority in spectral and topological similarity over existing models, including a reconfiguration step.

Findings

The model improves approximation of diffusion properties.

Reconfiguration enhances shortest path structure.

Modularity is an emergent property, not a defining feature.

Abstract

In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement the analysis, we study also classical topological descriptors, such as statistics of the shortest paths and the important feature of modularity. Our experiments show that the proposed model results in a considerable improvement with respect to two suitably chosen generative mechanisms, mimicking with better approximation real protein contact networks in terms of diffusion properties elaborated from the Laplacian spectra. However, as well as the other considered models, it does not reproduce with sufficient accuracy the shortest paths structure. To compensate this drawback, we designed a second step involving a targeted edge reconfiguration process. The ensemble of reconfigured networks denotes improvements that are statistically significant. As a byproduct of our study, we demonstrate that modularity, a well-known property of proteins, does not entirely explain the actual network architecture characterizing protein contact networks. In fact, we conclude that modularity, intended as a quantification of an underlying community structure, should be considered as an emergent property of the structural organization of proteins. Interestingly, such a property is suitably optimized in protein contact networks together with the feature of path efficiency.