Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures

Fernando Hinostroza,Vanessa Marabolí,Alan Neely,Ana M Cárdenas,Fernando D González-Nilo,Ingrid Araya-Duran,Jonathan Canan,Ramón Latorre,Maximiliano Rojas,Daniel Aguayo

doi:10.1038/s41598-020-75216-0

Abstract

High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases. Dynamin-2 is one of such protein forming helical oligomers that catalyze membrane fission. Mutations in this protein, where R465W is the most frequent, cause dominant centronuclear myopathy, but the molecular mechanisms underpinning the functional modifications remain to be investigated. To unveil the structural impact of this mutation in dynamin-2, we used full-atom molecular dynamics simulations and coarse-grained models and built dimers and helices of wild-type (WT) monomers, mutant monomers, or both WT and mutant monomers combined. Our results show that the mutation R465W causes changes in the interactions with neighbor amino acids that propagate through the oligomer. These new interactions perturb the contact between monomers and favor an extended conformation of the bundle signaling element (BSE), a dynamin region that transmits the conformational changes from the GTPase domain to the rest of the protein. This extended configuration of the BSE that is only relevant in the helices illustrates how a small change in the microenvironment surrounding a single residue can propagate through the oligomer structures of dynamin explaining how dominance emerges in large protein complexes.

Highlights

High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases
They all share a common structure consisting of five domains: an N-terminal G domain that hydrolyzes GTP when it interacts with other G domains, a middle and a GTPase effector domains that compose the “stalk region” involved in oligomerization, a bundle signaling element (BSE) that connects the G-domain with the stalk, a pleckstrin homology domain (PH) that binds inositol phospholipids, and a C-terminal proline and arginine-rich domain (PRD) that mediates the interaction with SH3-domain-containing proteins[3] (Fig. 1A,B)
Our analyses reveal that the substitution of arginine by tryptophan at position 465 of dyn-2 modifies the interactions of this residue with other amino acids in both HT and R465W dimers and helix models

Summary

Introduction

High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases. We found that the exchange of the arginine by a tryptophan at this position impairs the interaction zones between dyn-2 monomers and favors an extended BSE conformation that impacts the helix structure and dynamics. We should bear in mind that these are dimers and we focused on whether this mutation impacts the interaction between monomers involving alpha-helices αs[2] to αs[4] (Fig. 3A), described as interface-2 by Faelber et al.[24].

Results

Conclusion