Computational protocol: Unusual architecture of the p7 channel from hepatitis C virus

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Protocol publication

[…] Structures were calculated using the program XPLOR-NIH. The monomer structures (mainly the secondary structures) were first calculated using intramonomer NOE-derived distance restraints, backbone dihedral restraints derived from chemical shifts using the TALOS program, and RDC restraints. A total of 10 monomer structures were calculated using a standard simulated annealing (SA) protocol. Six copies of the lowest-energy monomer structure were used to construct an initial model of the hexamer using intermonomer NOE restraints collected from the mixed-labeled sample for the H1 and H2 helical segments. For each intermonomer restraint between two adjacent monomers, six identical distance restraints were assigned respectively to all pairs of neighboring monomers to satisfy the condition of C6 rotational symmetry (as indicated by the EM data). The assembled hexamer was then subject to refinement against RDCs to accurately orient the three helical segments. Finally, using the SA protocol, the hexamer was refined against the complete set of NOE restraints (including intramonomer and intermonomer distance restraints), dihedral restraints, and RDC restraints. A total of 60 hexamer structures were calculated and 15 low energy structures were selected as the structural ensemble. Ramachandran plot statistics for the structure ensemble, calculated using PROCHECK, are as follows: most favored (96.6%), additionally allowed (2.8%), generously allowed (0.6%) and disallowed (0.0%). […]

Pipeline specifications

Software tools Xplor-NIH, PROCHECK
Applications NMR-based proteomics analysis, Protein structure analysis
Organisms Hepacivirus C
Diseases Hepatitis C, Infection
Chemicals Adamantane, Amantadine, Rimantadine