Data Driven Charge Transfer Atlas Provides Topological View of Electronic Structure Properties for Arbitrary Proteins Complexes

TL;DR

This paper introduces a data-driven charge transfer atlas and network analysis method to efficiently analyze electronic structure properties and identify critical residues in arbitrary protein complexes, aiding proteomics research.

Contribution

It presents a novel charge transfer database and the D2Net analysis approach for topological electronic structure analysis in proteins, with minimal computational costs.

Findings

Identified critical residues with large node degrees as network hubs.

Demonstrated the method on two proteins, highlighting key residues.

Provided a computational protocol for electronic structure analysis in proteomics.

Abstract

Due to the highly complex chemical structure of biomolecules, the extensive understanding of the electronic information for proteomics can be challenging. Here, we constructed a charge transfer database at residue level derived from millions of electronic structure calculations among 20x20 possible amino acid side-chains combinations, which were extracted from available high-quality structures of thousands of protein complexes. Then, the data driven network (D2Net) analysis was proposed to quickly identify the critical residue or residue groups for any possible protein complex. As an initial evaluation, we applied this model to scrutinize the charge transfer networks for two randomly selected proteins, which highlighted the most critical residues with large node degrees as network hubs. This work may provide us a promising computional protocol for topologically understanding the electronic structure information in the growing number of high-quality experimental proteins structures, with minor computational costs.