Dynamics and asymmetry in the dimer of the norovirus major capsid protein

PLoS One. 2017 Jul 27;12(7):e0182056. doi: 10.1371/journal.pone.0182056. eCollection 2017.

Abstract

Noroviruses are the major cause of non-bacterial acute gastroenteritis in humans and livestock worldwide, despite being physically among the simplest animal viruses. The icosahedral capsid encasing the norovirus RNA genome is made of 90 dimers of a single ca 60-kDa polypeptide chain, VP1, arranged with T = 3 icosahedral symmetry. Here we study the conformational dynamics of this main building block of the norovirus capsid. We use molecular modeling and all-atom molecular dynamics simulations of the VP1 dimer for two genogroups with 50% sequence identity. We focus on the two points of flexibility in VP1 known from the crystal structure of the genogroup I (GI, human) capsid and from subsequent cryo-electron microscopy work on the GII capsid (also human). First, with a homology model of the GIII (bovine) VP1 dimer subjected to simulated annealing then classical molecular dynamics simulations, we show that the N-terminal arm conformation seen in the GI crystal structure is also favored in GIII VP1 but depends on the protonation state of critical residues. Second, simulations of the GI dimer show that the VP1 spike domain will not keep the position found in the GII electron microscopy work. Our main finding is a consistent propensity of the VP1 dimer to assume prominently asymmetric conformations. In order to probe this result, we obtain new SAXS data on GI VP1 dimers. These data are not interpretable as a population of symmetric dimers, but readily modeled by a highly asymmetric dimer. We go on to discuss possible implications of spontaneously asymmetric conformations in the successive steps of norovirus capsid assembly. Our work brings new lights on the surprising conformational range encoded in the norovirus major capsid protein.

MeSH terms

  • Amino Acid Sequence
  • Capsid Proteins / chemistry*
  • Cluster Analysis
  • Conserved Sequence
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Molecular Dynamics Simulation
  • Norovirus / chemistry*
  • Protein Conformation
  • Protein Domains
  • Protein Multimerization*
  • Protons
  • Scattering, Small Angle
  • Solutions
  • Structural Homology, Protein

Substances

  • Capsid Proteins
  • Protons
  • Solutions

Grants and funding

This work was supported by a grant from Région Ile-de-France to S.B. including predoctoral funding for T.T. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.