Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction.

Ennys Gheyouche,Stéphane Téletchéa,Gervaise Loirand,Bernard Offmann,Matthias Bagueneau

doi:10.3389/fmolb.2021.643728

Abstract

The interaction between two proteins may involve local movements, such as small side-chains re-positioning or more global allosteric movements, such as domain rearrangement. We studied how one can build a precise and detailed protein-protein interface using existing protein-protein docking methods, and how it can be possible to enhance the initial structures using molecular dynamics simulations and data-driven human inspection. We present how this strategy was applied to the modeling of RHOA-ARHGEF1 interaction using similar complexes of RHOA bound to other members of the Rho guanine nucleotide exchange factor family for comparative assessment. In parallel, a more crude approach based on structural superimposition and molecular replacement was also assessed. Both models were then successfully refined using molecular dynamics simulations leading to protein structures where the major data from scientific literature could be recovered. We expect that the detailed strategy used in this work will prove useful for other protein-protein interface design. The RHOA-ARHGEF1 interface modeled here will be extremely useful for the design of inhibitors targeting this protein-protein interaction (PPI).

Highlights

Precise interactions between proteins allow a tight control on many functions and pathways, eventually leading to gene expression or silencing, to protein release or degradation, and even to cell death
In order to determine which docking method was the best for our specific needs, we have evaluated their performance (i) on recovering existing crystallographic structures of RHOA bound to a guanine exchange factors (GEFs), a process called re-docking, and (ii) on assembling the bound RHOA from a given crystallographic with a GEF from another crystallographic structure, this process being known as cross-docking
Assessment of Webserver Performance in Re-docking Experiments We evaluated the performance of each software according to its ability to recover the existing structure of bound RHOA and ARHGEFs

Summary

Introduction

Precise interactions between proteins allow a tight control on many functions and pathways, eventually leading to gene expression or silencing, to protein release or degradation, and even to cell death. There are between 130,000 and up to 650,000 protein-protein interactions (PPIs) described (Ottmann, 2015), but only a fraction of PPIs is validated experimentally, ranging from 14,000 (Rolland et al, 2014) to 125,000 PPIs (http://interactome3d.irbbarcelona.org/, Mosca et al, 2013). This structural gap comes from the difficulties of obtaining experimentally fulllength interacting proteins and to resolving their structures using crystallography, NMR, or electron microscopy (EM). When no protein-protein structure is available, one has to perform protein-protein docking predictions

Methods

Results

Discussion

Conclusion