Primary Citation PubMed: 23023261
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Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function.
(2012) Nat Chem Biol 8
PubMed: 23023261 | PubMedCentral: PMC3480716 | DOI: 10.1038/nchembio.1081
The pdb accession codes for the complex structures are 4b6e, 4b6f, 4b76, 4b71,4b73 and 4b74 for compounds 1-6 in the wildtype enzyme respectively, and 4b75 for compound 5 in the Val630Leu mutant enzym... .
Publication Year: 2012
Computational study on the inhibitor binding mode and allosteric regulation mechanism in hepatitis C virus NS3/4A protein.
(2014) PLoS One 9
PubMed: 24586263 | PubMedCentral: PMC3934852 | DOI: 10.1371/journal.pone.0087077
systems simulation time starting structure apo protein 100 ns X-ray structure of HCV NS3/4A protein (PDB ID code 1CU1) inhibitor bound protein 100 ns X-ray structure of HCV NS3/4A protein complexed wi... h inhibitor (PDB ID code 4B73) apo protein (truncated) 100 ns removal of the six C-terminal residues from apo protein inhibitor bound protein(truncated) 100 ns removal of the six C-terminal residues from protein complexed with inhibitor All the structures were then modeled by using the program LEaP embedded in AMBER10  with the standard AMBER03 force field  for protein, including adding all missing hydrogen atoms of the protein.
The simulations of the X-ray crystal structure of 1CU1  and 4B73  were designed to prove the importance of the stability of an autoinhibited form of HCV NS3/4A protein by a small molecular binding at the novel allosteric site.
As shown in Table 1 , the truncated forms of HCV NS3/4A protein models were created by in silico removing the six C-terminal residues coordinates starting from above structures 1CU1 and 4B73.
Publication Year: 2014
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