Characterization of graphs for protein structure modeling and recognition of solubility

TL;DR

This study models E.Coli proteins as graphs based on their 3D structures to analyze their topological features and predict solubility using pattern recognition techniques, revealing size as a key factor.

Contribution

It introduces a graph-based structural representation of proteins combined with a novel classifier to predict protein solubility, advancing understanding of protein properties.

Findings

Protein size is the main discriminator of solubility.

Graph topological features correlate with protein architectural principles.

Pattern recognition techniques effectively classify protein solubility.

Abstract

This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented according to its known folded 3D shape. This step consists in representing the available E.Coli proteins in terms of graphs. We first analyze those graphs by considering pure topological characterizations, i.e., by analyzing the mass fractal dimension and the distribution underlying both shortest paths and vertex degrees. Results confirm the general architectural principles of proteins. Successively, we focus on the statistical properties of a representation of such graphs in terms of vectors composed of several numerical features, which we extracted from their structural representation. We found that protein size is the main discriminator for the solubility, while however there are other factors that help explaining the solubility degree. We finally analyze such data through a novel one-class classifier, with the aim of discriminating among very and poorly soluble proteins. Results are encouraging and consolidate the potential of pattern recognition techniques when employed to describe complex biological systems.