Computational protocol: NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities

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Protocol publication

[…] N- and C-terminal boundaries of NS2 and NS3N domains from RHV, BHV, GHV and NPHV were predicted by determining signal peptidase cleavage sites using the SignalP 4.0 server ( and examining sequence homology with HCV and GBV-B polyproteins. Protein sequence analyses were performed by using the Mobyle portal for bioinformatics analyses ( []. Multiple sequence alignments were performed with the T-coffee multiple sequence alignment program [] using the corresponding web server facility ( and aa identity or similarity percentages were calculated according to CLUSTAL W conventions. Phylogenetic trees were constructed using the neighbor joining method under the Jones-Thornton-Taylor model of aa substitution implemented in the MEGA6 program [] and bootstrap resampling from 2,000 replicates was performed. [...] Three-dimensional homology models of NS2 and NS3 proteases were constructed by the Swiss-Model automated protein structure homology modeling server [] ( by using the crystal structures of HCV NS2 protease domain and NS3 as templates (PDB entries: 2HD0 [] and 1CU1[], respectively). Figures were generated from structure coordinates by using VMD [] ( and rendered with POV-Ray ( […]

Pipeline specifications

Software tools SignalP, Galaxy@Pasteur, T-Coffee, Clustal W, MEGA, SWISS-MODEL, VMD
Databases ExPASy
Applications Phylogenetics, Protein structure analysis
Organisms Homo sapiens, Equus caballus, Rattus norvegicus, Hepatitis GB virus B, Viruses
Diseases Hepatitis C
Chemicals Cysteine