title: Substrate specificity of the hepatitis C virus serine protease NS3.
abstract: The substrate specificity of a purified protein encompassing the hepatitis C virus NS3 serine protease domain was investigated by introducing systematic modifications, including non-natural amino acids, into substrate peptides derived from the NS4A/NS4B cleavage site. Kinetic parameters were determined in the absence and presence of a peptide mimicking the protease co-factor NS4A (Pep4A). Based on this study we draw the following conclusions: (i) the NS3 protease domain has an absolute requirement for a small residue in the P1 position of substrates, thereby confirming previous modelling predictions. (ii) Optimization of the P1 binding site occupancy primarily influences transition state binding, whereas the occupancy of distal binding sites is a determinant for both ground state and transition state binding. (iii) Optimized contacts at distal binding sites may contribute synergistically to cleavage efficiency.
authors.affiliation: Istituto di Ricerche di Biologia Molecolare (IRBM) P. Angeletti, Pomezia, Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Urbani
authors.forename: E
authors.initials: E
authors.lastname: Bianchi
authors.forename: F
authors.initials: F
authors.lastname: Narjes
authors.forename: A
authors.initials: A
authors.lastname: Tramontano
authors.forename: R
authors.initials: R
authors.lastname: De Francesco
authors.forename: C
authors.initials: C
authors.lastname: Steinkühler
authors.forename: A
authors.initials: A
authors.lastname: Pessi
mesh_terms: D000409:Alanine; D001665:Binding Sites; D002851:Chromatography, High Pressure Liquid; D007700:Kinetics; D008958:Models, Molecular; D012697:Serine Endopeptidases / Q000378:metabolism*; D013379:Substrate Specificity; D017361:Viral Nonstructural Proteins / Q000378:metabolism*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000409:Alanine; D012697:Serine Endopeptidases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases