Modeling Protein Contact Networks

TL;DR

This paper investigates protein structures using complex network analysis, modeling them as Protein Contact Networks and Long-range Interaction Networks, revealing their small-world and assortative properties, which are uncommon in other complex networks.

Contribution

The study introduces a network theoretical approach to protein structures, identifying their unique small-world and assortative properties, and determining topological factors influencing assortativity.

Findings

Proteins are characterized as small-world networks.

Proteins exhibit assortativity, unlike most other complex networks.

Identified topological determinants of protein network assortativity.

Abstract

Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a network theoretical approach. While doing so we used a coarse-grained method, viz., complex network analysis. We model protein structures at two length scales as Protein Contact Networks (PCN) and as Long-range Interaction Networks (LINs). We found that proteins by virtue of being characterised by high amount of clustering, are small-world networks. Apart from the small-world nature, we found that proteins have another general property, viz., assortativity. This is an interesting and exceptional finding as all other complex networks (except for social networks) are known to be disassortative. Importantly, we could identify one of the major topological determinant of assortativity by building appropriate controls.