Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein
| Autor: | Stephen Griffin, Monoj Mon Kalita, James J. Chou, Wolfgang B. Fischer |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Models
Molecular Molecular model Genotype In silico Genotypes Molecular Sequence Data Biophysics Hepacivirus Biology Random hexamer Biochemistry Article Permeability Turn (biochemistry) Viral Proteins Molecular dynamics simulation Computer Simulation Amino Acid Sequence Amino Acids Lipid bilayer chemistry.chemical_classification p7 of HCV Water Cell Biology Amino acid Protein Structure Tertiary Membrane protein chemistry Helix NMR structure Protons Viral channel protein Channel gating Sequence Alignment |
| Zdroj: | Biochimica et Biophysica Acta. Biomembranes |
| ISSN: | 1879-2642 0005-2736 |
| Popis: | 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. Graphical abstract Highlights • Genotype specific structural features of hexameric bundles of p7 of HCV • In silico built models of genotype 1a bundle compared with models of genotypes 1b and 5a from NMR • Genotype 1a and 1b channels are gated via movement of the parallel aligned helices. • Complex scenario for genotype 5a bundle model • All bundles show pulsatile dynamics. |
| Databáze: | OpenAIRE |
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