title: Asymmetric dynamics of ion channel forming proteins - Hepatitis C virus (HCV) p7 bundles.
abstract: Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400 ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected.
authors.affiliation: Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
authors.forename: Monoj Mon
authors.initials: MM
authors.lastname: Kalita
authors.affiliation: Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC. Electronic address: wfischer@ym.edu.tw.
authors.forename: Wolfgang B
authors.initials: WB
authors.lastname: Fischer
mesh_terms: D000595:Amino Acid Sequence; D002118:Calcium / Q000737:chemistry; D002413:Cations, Divalent; D005838:Genotype; D016174:Hepacivirus / Q000737:chemistry*; D007473:Ion Channels / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D010713:Phosphatidylcholines / Q000737:chemistry*; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011522:Protons; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry*; D000086082:Viroporin Proteins
chemical_list: D002118:Calcium; D002413:Cations, Divalent; D007473:Ion Channels; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D011522:Protons; D014764:Viral Proteins; C088369:p7 protein, Hepatitis C virus; D000086082:Viroporin Proteins; C028694:1-palmitoyl-2-oleoylphosphatidylcholine
keywords: Genotypes; Molecular dynamics simulations; NMR structure; Protein mechanics; Viral channel protein; p7 of HCV