Redesigning the substrate specificity of the hepatitis C virus NS3 protease

Dougherty, 1993, Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes, Microbiol. Rev, 57, 781, 10.1128/MMBR.57.4.781-822.1993 Kuo, 1989, An assay for circulating antibodies to a major etiologic virus of human non-A non-B hepatitis, Science, 244, 362, 10.1126/science.2496467 Choo, 1989, Isolation of a cDNA clone derived from a blood-borne non-A non-B viral hepatitis genome, Science, 244, 359, 10.1126/science.2523562 Chien, 1992, Diagnosis of hepatitis C virus (HCV) infection using an immunodominant chimeric polyprotein to capture circulating antibodies: reevaluation of the role of HCV in liver disease, Proc. Natl. Acad. Sci. USA, 89, 10011, 10.1073/pnas.89.21.10011 Choo, 1991, Genetic organization and diversity of the hepatitis C virus, Proc. Natl. Acad. Sci. USA, 88, 2451, 10.1073/pnas.88.6.2451 Kato, 1990, Molecular cloning of human hepatitis C virus genome from Japanese patients with non-A non-B hepatitis, Proc. Natl. Acad. Sci. USA, 87, 9524, 10.1073/pnas.87.24.9524 Takamizawa, 1991, Structure and organization of the hepatitis C virus genome isolated from human carriers, J. Virol, 65, 1105, 10.1128/JVI.65.3.1105-1113.1991 Hijikata, 1993, Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus, J. Virol, 67, 4665, 10.1128/JVI.67.8.4665-4675.1993 Grakoui, 1993, A second hepatitis C virus-encoded proteinase, Proc. Natl. Acad. Sci. USA, 90, 10583, 10.1073/pnas.90.22.10583 Bartenschlager, 1993, Nonstructural protein 3 of the hepatitis C virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions, J. Virol, 67, 3835, 10.1128/JVI.67.7.3835-3844.1993 Eckart, 1993, The hepatitis C virus encodes a serine protease involved in processing of the putative nonstructural proteins from the viral polyprotein precursor, Biochem. Biophys. Res. Commun, 192, 399, 10.1006/bbrc.1993.1429 Grakoui, 1993, Expression and identification of hepatitis C virus polyprotein cleavage products, J. Virol, 67, 1385, 10.1128/JVI.67.3.1385-1395.1993 Tomei, 1993, NS3 is a serine protease required for processing of hepatitis C virus polyprotein, J. Virol, 67, 4017, 10.1128/JVI.67.7.4017-4026.1993 Manabe, 1994, Production of nonstructural proteins of hepatitis C virus requires a putative viral protease encoded by NS3, Virology, 198, 636, 10.1006/viro.1994.1075 Bartenschlager, 1994, Kinetic and structural analysis of hepatitis C virus polyprotein processing, J. Virol, 68, 5045, 10.1128/JVI.68.8.5045-5055.1994 Failla, 1994, Both NS3 and NS4A are required for processing of hepatitis C virus polyprotein, J. Virol, 68, 3753, 10.1128/JVI.68.6.3753-3760.1994 Lin, 1994, Hepatitis C virus NS3 serine proteinase:trans-cleavage requirements and processing kinetics, J. Virol, 68, 8147, 10.1128/JVI.68.12.8147-8157.1994 Tanji, 1994, Identification of the domain required fortrans-cleavage activity of hepatitis C viral serine protease, Gene, 145, 215, 10.1016/0378-1119(94)90008-6 Grakoui, 1993, Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites, J. Virol, 67, 2832, 10.1128/JVI.67.5.2832-2843.1993 Pizzi, 1993, Molecular model of the specificity pocket of the hepatitis c virus protease: implications for substrate recognition, Proc. Natl. Acad. Sci. USA, 91, 888, 10.1073/pnas.91.3.888 Read, 1983, Structure of the complex ofStreptomyces griseus protease B, a serine protease, with the third domain of the ovomucoid inhibitor at 1.8 å resolution, Biochemistry, 22, 4420, 10.1021/bi00288a012 Hedstrom, 1992, Converting trypsin to chymotrypsin: the role of surface loops, Science, 255, 1249, 10.1126/science.1546324 Bone, 1989, Structural plasticity broadens the specificity of an engineered protease, Nature, 339, 191, 10.1038/339191a0 Abrahnsen, 1991, Engineering subtilisin and its substrates for efficient ligation of peptide bonds in aqueous solution, Biochemistry, 30, 4151, 10.1021/bi00231a007 Caputo, 1994, Conversion of the substrate specificity of mouse proteinase granzyme B, Nature Struct. Biol, 6, 364, 10.1038/nsb0694-364 Kolykhalov, 1994, Specificity of the hepatitis C virus NS3 serine protease: effects of substitutions at the 3/4A, 4A/4B, 4B/5A and 5A/5B cleavage sites on polyprotein processing, J. Virol, 68, 7525, 10.1128/JVI.68.11.7525-7533.1994 Komoda, 1994, Substrate requirements of hepatitis C virus serine proteinase for intermolecular polypeptide cleavage inEscherichia coli, J. Virol, 68, 7351, 10.1128/JVI.68.11.7351-7357.1994 Murzin, 1995, Scop: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol, 27, 536, 10.1016/S0022-2836(05)80134-2 Holm, 1994, The FSSP database of structurally aligned protein fold families, Nucleic Acids Res, 22, 3600 Simons, 1995, Identification of two flavivirus-like genomes in the GB hepatitis agent, Proc. Natl. Acad. Sci. USA, 92, 3401, 10.1073/pnas.92.8.3401 Rost, 1993, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol, 232, 584, 10.1006/jmbi.1993.1413 Bauer, 1978, Active centers ofStreptomyces griseus protease 1, Streptomyces griseus protease 3 and alpha-chymotrypsin: enzyme–substrate interactions, Biochemistry, 17, 375, 10.1021/bi00595a028 Tomei, 1996, A central hydrophobic domain of the hepatitis C virus NS4A protein is necessary and sufficient for the activation of the NS3 protease, J. Gen. Virol, 10.1099/0022-1317-77-5-1065 Fuerst, 1986, Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase, Proc. Natl. Acad. Sci. USA, 83, 8122, 10.1073/pnas.83.21.8122 Elroy-Stein, 1989, Cap-independent translation of mRNA conferred by encephalomyocarditis virus 5′ sequence improves the performance of the vaccinia/bacteriophage T7 hybrid expression system, Proc. Natl. Acad. Sci. USA, 86, 6126, 10.1073/pnas.86.16.6126 Jang, 1889, Initiation of protein synthesis by internal entry of ribosomes into the 5′ nontranslated region of encephalomyocarditis virus RNAin vivo, J. Virol, 63, 1651, 10.1128/JVI.63.4.1651-1660.1989 Sambrook, 1989 Higuchi, 1988, A general method ofin vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions, Nucleic Acids Res, 16, 7351, 10.1093/nar/16.15.7351 Dayringer, 1986, Interactive program for visualization and modeling of proteins, nucleic acids and small molecules, J. Mol. Graphics, 4, 82, 10.1016/0263-7855(86)80002-9 Kraulis, 1991, MOLSCRIPT. A program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr, 24, 946, 10.1107/S0021889891004399 Bernstein, 1977, The Protein Data Bank: a computer based archival file for macromolecular structures, J. Mol. Biol, 112, 532, 10.1016/S0022-2836(77)80200-3