Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein

Abstract

The 63 amino acid polytopic membrane protein, p7, encoded by hepatitis C virus (HCV) is involved in the modulation of electrochemical gradients across membranes within infected cells. Structural information relating to p7 from multiple genotypes has been generated in silico (e.g. genotype (GT) 1a), as well as obtained from experiments in form of monomeric and hexameric structures (GTs 1b and 5a, respectively). However, sequence diversity and structural differences mean that comparison of their channel gating behaviour has not thus far been simulated. Here, a molecular model of the monomeric GT 1a protein is optimized and assembled into a hexameric bundle for comparison with both the 5a hexamer structure and another hexameric bundle generated using the GT 1b monomer structure. All bundles tend to turn into a compact structure during molecular dynamics (MD) simulations (Gromos96 (ffG45a3)) in hydrated lipid bilayers, as well as when simulated at 'low pH', which may trigger channel opening according to some functional studies. Both GT 1a and 1b channel models are gated via movement of the parallel aligned helices, yet the scenario for the GT 5a protein is more complex, with a short N-terminal helix being involved. However, all bundles display pulsatile dynamics identified by monitoring water dynamics within the pore.

Viral channel forming proteins — How to assemble and depolarize lipid membranes in silico

“…In the case of p7 of HCV, the idea of a titrable histidine within TMD1 of the protein facing a putative pore can still be validated with models of monomers derived from experiments which are assembled into a bundle. Protein p7 in a parallel aligned arrangement of the two membrane spanning segments is extensively simulated [87,88]. Analysis of the TMDs using RMSF data allows us to support the experimental findings [47] that both of the TMDs are literally separated into two 'sub-helical' segments with alternate dynamics.…”

“…In a consecutive step, the polytopic monomer then needs to be docked to form the respective oligomer. [87,88] as well as models of 3a of SARS-CoV which contains three TMDs per monomer [77] have been generated.…”

Interaction of antivirals with a heptameric bundle model of the p7 protein of hepatitis C virus

“…The monomer was adopted from the work of Kalita et al . In brief, the two predicted TMDs of p7 were aligned antiparallel and screened using a 2D docking program written with the scripting language ‘scientific vector language’ of MOE (v2012.10, Molecular Operation Environment, http://www.chemcomp.com).…”

All-atom virus simulations

“…All-atom simulations were also applied to develop a model for the Paramecium bursaria chlorella virus type 1 (PBCV-1) Kcv potassium channel to probe structure-function relationships [97, 98] and elucidate its mechanism of ion transport [99]. More recently, all-atom simulations were employed to determine the structure of the hepatitis C virus (HCV) p7 viroporin monomer [100] and to model various channel oligomer states, enabling characterization of their dynamics and conductance properties [101, 102, 103, 104, 105]. …”