The G\=oMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes

TL;DR

This paper reviews contact map methods for modeling protein interactions, introduces the GoMartini approach for protein complexes, and discusses its extension and validation within the Martini force field.

Contribution

It revisits contact map concepts, introduces an extended GoMartini model for protein-sugar complexes, and discusses its application and validation in Martini 3.

Findings

GoMartini is a gold-standard for protein conformational studies.

Contact maps are sensitive to parameters and may neglect key interactions.

The extended GoMartini approach supports protein-sugar complex modeling.

Abstract

We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g. distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust G\=oMartini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based G\=o-like approach for the study of protein-sugar complexes, and also limitations of this approach are discussed. The G\=oMartini approach was first introduced by Poma et al. J. Chem. Theory Comput. 2017, 13(3), 1366-1374 in Martini 2 force field and recently, it has gained the status of gold-standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support to this approach in the context of the biophysical community.