{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T20:29:49Z","timestamp":1758400189683,"version":"3.40.5"},"reference-count":55,"publisher":"Elsevier BV","issue":"40","license":[{"start":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T00:00:00Z","timestamp":1601510400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T00:00:00Z","timestamp":1606348800000},"content-version":"vor","delay-in-days":56,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CEF-MC"],"award-info":[{"award-number":["CEF-MC"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CRC 807"],"award-info":[{"award-number":["CRC 807"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SPP 1623"],"award-info":[{"award-number":["SPP 1623"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["RTG 1986"],"award-info":[{"award-number":["RTG 1986"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CIPSM"],"award-info":[{"award-number":["CIPSM"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 749\/C8"],"award-info":[{"award-number":["SFB 749\/C8"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1035"],"award-info":[{"award-number":["SFB 1035"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["WE 4388\/6-1"],"award-info":[{"award-number":["WE 4388\/6-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["IGSSE Graduate School"],"award-info":[{"award-number":["IGSSE Graduate School"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"MEXT | Japan Society for the Promotion of Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001655","name":"Deutscher Akademischer Austauschdienst","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001655","id-type":"DOI","asserted-by":"publisher"}]},{"name":"TMP"},{"name":"DRUID"},{"DOI":"10.13039\/501100003042","name":"Else Kr\u00f6ner-Fresenius-Stiftung","doi-asserted-by":"publisher","award":["TRIP"],"award-info":[{"award-number":["TRIP"]}],"id":[{"id":"10.13039\/501100003042","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["jbc.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biological Chemistry"],"published-print":{"date-parts":[[2020,10]]},"DOI":"10.1074\/jbc.ra120.013898","type":"journal-article","created":{"date-parts":[[2020,8,3]],"date-time":"2020-08-03T21:45:16Z","timestamp":1596491116000},"page":"13862-13874","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":13,"title":["Extended interaction networks with HCV protease NS3-4A substrates explain the lack of adaptive capability against protease inhibitors"],"prefix":"10.1016","volume":"295","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0775-0907","authenticated-orcid":false,"given":"Georg","family":"Dultz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tetsuro","family":"Shimakami","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuhisa","family":"Murai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Yamane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8266-8957","authenticated-orcid":false,"given":"Antoine","family":"Marion","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias M.","family":"Zeitler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia","family":"Stross","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Grimm","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3831-7666","authenticated-orcid":false,"given":"Rebecca M.","family":"Richter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrin","family":"B\u00e4umer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5978-2452","authenticated-orcid":false,"given":"MinKyung","family":"Yi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8873-7167","authenticated-orcid":false,"given":"Ricardo M.","family":"Biondi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Zeuzem","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0403-2160","authenticated-orcid":false,"given":"Robert","family":"Tamp\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iris","family":"Antes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian M.","family":"Lange","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1823-4863","authenticated-orcid":false,"given":"Christoph","family":"Welsch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1074\/jbc.RA120.013898_bib1","doi-asserted-by":"crossref","first-page":"12098","DOI":"10.1128\/JVI.01860-14","article-title":"Increased replicative fitness can lead to decreased drug sensitivity of hepatitis C virus","volume":"88","author":"Sheldon","year":"2014","journal-title":"J. Virol"},{"key":"10.1074\/jbc.RA120.013898_bib2","doi-asserted-by":"crossref","first-page":"2354","DOI":"10.1016\/j.jmb.2019.04.034","article-title":"Near-neighbor interactions in the NS3-4A protease of HCV impact replicative fitness of drug-resistant viral variants","volume":"431","author":"Doncheva","year":"2019","journal-title":"J. Mol. Biol"},{"key":"10.1074\/jbc.RA120.013898_bib3","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1128\/MMBR.05023-11","article-title":"Viral quasispecies evolution","volume":"76","author":"Domingo","year":"2012","journal-title":"Microbiol. Mol. Biol. Rev"},{"key":"10.1074\/jbc.RA120.013898_bib4","doi-asserted-by":"crossref","first-page":"30ra32","DOI":"10.1126\/scitranslmed.3000544","article-title":"Rapid emergence of protease inhibitor resistance in hepatitis C virus","volume":"2","author":"Rong","year":"2010","journal-title":"Sci. Transl. Med"},{"key":"10.1074\/jbc.RA120.013898_bib5","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1053\/j.gastro.2016.04.003","article-title":"Hepatitis C virus resistance to direct-acting antiviral drugs in interferon-free regimens","volume":"151","author":"Pawlotsky","year":"2016","journal-title":"Gastroenterology"},{"key":"10.1074\/jbc.RA120.013898_bib6","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.jtbi.2010.08.036","article-title":"Understanding hepatitis C viral dynamics with direct-acting antiviral agents due to the interplay between intracellular replication and cellular infection dynamics","volume":"267","author":"Guedj","year":"2010","journal-title":"J. Theor. Biol"},{"key":"10.1074\/jbc.RA120.013898_bib7","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1053\/j.gastro.2010.10.056","article-title":"Protease inhibitor-resistant hepatitis C virus mutants with reduced fitness from impaired production of infectious virus","volume":"140","author":"Shimakami","year":"2011","journal-title":"Gastroenterology"},{"year":"2017","series-title":"Handbook of Antimicrobial Resistance","author":"G\u00f6tte","key":"10.1074\/jbc.RA120.013898_bib8"},{"key":"10.1074\/jbc.RA120.013898_bib9","first-page":"20160984","article-title":"Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations","volume":"283","author":"Cervera","year":"2016","journal-title":"Proc. Biol. Sci"},{"key":"10.1074\/jbc.RA120.013898_bib10","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/nature12861","article-title":"Mutational and fitness landscapes of an RNA virus revealed through population sequencing","volume":"505","author":"Acevedo","year":"2014","journal-title":"Nature"},{"key":"10.1074\/jbc.RA120.013898_bib11","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/nrmicro3046","article-title":"The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection","volume":"11","author":"Bartenschlager","year":"2013","journal-title":"Nat. Rev. Microbiol"},{"key":"10.1074\/jbc.RA120.013898_bib12","doi-asserted-by":"crossref","first-page":"7624","DOI":"10.1128\/JVI.00724-08","article-title":"NS3 helicase domains involved in infectious intracellular hepatitis C virus particle assembly","volume":"82","author":"Ma","year":"2008","journal-title":"J. Virol"},{"key":"10.1074\/jbc.RA120.013898_bib13","doi-asserted-by":"crossref","first-page":"5362","DOI":"10.1128\/JVI.03188-14","article-title":"Protease inhibitors block multiple functions of the NS3\/4A protease-helicase during the hepatitis C virus life cycle","volume":"89","author":"McGivern","year":"2015","journal-title":"J. Virol"},{"key":"10.1074\/jbc.RA120.013898_bib14","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1038\/nature04193","article-title":"Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus","volume":"437","author":"Meylan","year":"2005","journal-title":"Nature"},{"key":"10.1074\/jbc.RA120.013898_bib15","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.molcel.2005.08.014","article-title":"VISA is an adapter protein required for virus-triggered IFN-\u03b2 signaling","volume":"19","author":"Xu","year":"2005","journal-title":"Mol. Cell"},{"key":"10.1074\/jbc.RA120.013898_bib16","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1038\/ni1243","article-title":"IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction","volume":"6","author":"Kawai","year":"2005","journal-title":"Nat. Immunol"},{"key":"10.1074\/jbc.RA120.013898_bib17","doi-asserted-by":"crossref","first-page":"1973","DOI":"10.1056\/NEJMoa1402869","article-title":"ABT-450\/r-ombitasvir and dasabuvir with ribavirin for hepatitis C with cirrhosis","volume":"370","author":"Poordad","year":"2014","journal-title":"N. Engl. J. Med"},{"key":"10.1074\/jbc.RA120.013898_bib18","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.jhep.2014.11.009","article-title":"Hepatitis C virus variants resistant to macrocyclic NS3-4A inhibitors subvert IFN-\u03b2 induction by efficient MAVS cleavage","volume":"62","author":"Welsch","year":"2015","journal-title":"J. Hepatol"},{"key":"10.1074\/jbc.RA120.013898_bib19","doi-asserted-by":"crossref","first-page":"6236","DOI":"10.1128\/AAC.01578-13","article-title":"In vitro phenotypic characterization of hepatitis C virus NS3 protease variants observed in clinical studies of telaprevir","volume":"57","author":"Jiang","year":"2013","journal-title":"Antimicrob. Agents Chemother"},{"key":"10.1074\/jbc.RA120.013898_bib20","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.2147\/IDR.S218584","article-title":"Computational analysis of naturally occurring resistance-associated substitutions in genes NS3, NS5A, and NS5B among 86 subtypes of hepatitis C virus worldwide","volume":"12","author":"Wu","year":"2019","journal-title":"Infect. Drug Resist"},{"key":"10.1074\/jbc.RA120.013898_bib21","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1073\/pnas.0510727103","article-title":"Production of infectious genotype 1a hepatitis C virus (Hutchinson strain) in cultured human hepatoma cells","volume":"103","author":"Yi","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"10.1074\/jbc.RA120.013898_bib22","doi-asserted-by":"crossref","first-page":"S500","DOI":"10.1016\/S0168-8278(17)31399-5","article-title":"Pooled resistance analysis in HCV genotype 1\u20136-infected patients treated with glecaprevir\/pibrentasvir in phase 2 and 3 clinical trials","volume":"66","author":"Krishnan","year":"2017","journal-title":"J. Hepatol"},{"key":"10.1074\/jbc.RA120.013898_bib23","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.jhep.2017.03.014","article-title":"Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses","volume":"67","author":"Welzel","year":"2017","journal-title":"J. Hepatol"},{"key":"10.1074\/jbc.RA120.013898_bib24","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1016\/j.cell.2005.08.012","article-title":"Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-\u03baB and IRF 3","volume":"122","author":"Seth","year":"2005","journal-title":"Cell"},{"key":"10.1074\/jbc.RA120.013898_bib25","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/s41467-017-02624-8","article-title":"Human cytomegalovirus-encoded US9 targets MAVS and STING signaling to evade type I interferon immune responses","volume":"9","author":"Choi","year":"2018","journal-title":"Nat. Commun"},{"key":"10.1074\/jbc.RA120.013898_bib26","doi-asserted-by":"crossref","first-page":"e1003231","DOI":"10.1371\/journal.ppat.1003231","article-title":"Enterovirus 71 protease 2Apro targets MAVS to inhibit anti-viral type I interferon responses","volume":"9","author":"Wang","year":"2013","journal-title":"PLoS Pathog"},{"key":"10.1074\/jbc.RA120.013898_bib27","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.jhep.2019.02.020","article-title":"Hepatovirus 3ABC proteases and evolution of mitochondrial antiviral signaling protein (MAVS)","volume":"71","author":"Feng","year":"2019","journal-title":"J. Hepatol"},{"key":"10.1074\/jbc.RA120.013898_bib28","doi-asserted-by":"crossref","first-page":"e1001282","DOI":"10.1371\/journal.pbio.1001282","article-title":"Convergent evolution of escape from hepaciviral antagonism in primates","volume":"10","author":"Patel","year":"2012","journal-title":"PLos Biol"},{"key":"10.1074\/jbc.RA120.013898_bib29","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.1128\/JVI.79.5.2689-2699.2005","article-title":"Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I","volume":"79","author":"Sumpter","year":"2005","journal-title":"J. Virol"},{"key":"10.1074\/jbc.RA120.013898_bib30","doi-asserted-by":"crossref","first-page":"3678","DOI":"10.1128\/JVI.03540-13","article-title":"Evolution of a cell culture-derived genotype 1a hepatitis C virus (H77S.2) during persistent infection with chronic hepatitis in a chimpanzee","volume":"88","author":"Yi","year":"2014","journal-title":"J. Virol"},{"key":"10.1074\/jbc.RA120.013898_bib31","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1126\/science.277.5325.570","article-title":"Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA","volume":"277","author":"Kolykhalov","year":"1997","journal-title":"Science"},{"key":"10.1074\/jbc.RA120.013898_bib32","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1006\/viro.1998.9092","article-title":"Transcripts of a chimeric cDNA clone of hepatitis C virus genotype 1b are infectious in vivo","volume":"244","author":"Yanagi","year":"1998","journal-title":"Virology"},{"key":"10.1074\/jbc.RA120.013898_bib33","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1093\/embo-reports\/kvf236","article-title":"RIP4 (DIK\/PKK), a novel member of the RIP kinase family, activates NF-\u03ba B and is processed during apoptosis","volume":"3","author":"Meylan","year":"2002","journal-title":"EMBO Rep"},{"key":"10.1074\/jbc.RA120.013898_bib34","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1002\/pro.5560071011","article-title":"Construction, expression, and characterization of a novel fully activated recombinant single-chain hepatitis C virus protease","volume":"7","author":"Taremi","year":"1998","journal-title":"Protein Sci"},{"key":"10.1074\/jbc.RA120.013898_bib35","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1038\/nprot.2007.321","article-title":"The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability","volume":"2","author":"Niesen","year":"2007","journal-title":"Nat. Protoc"},{"year":"2013","series-title":"Evaluation of enzyme inhibitors in drug discovery: A guide for medicinal chemists and pharmacologists","author":"Copeland","key":"10.1074\/jbc.RA120.013898_bib36"},{"key":"10.1074\/jbc.RA120.013898_bib37","doi-asserted-by":"crossref","first-page":"29929","DOI":"10.1074\/jbc.M804065200","article-title":"Hepatitis C viral NS3-4A protease activity is enhanced by the NS3 helicase","volume":"283","author":"Beran","year":"2008","journal-title":"J. Biol. Chem"},{"key":"10.1074\/jbc.RA120.013898_bib38","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1111\/jcmm.12801","article-title":"Hepatitis C virus NS3-4A inhibits the peroxisomal MAVS-dependent antiviral signalling response","volume":"20","author":"Ferreira","year":"2016","journal-title":"J. Cell. Mol. Med"},{"key":"10.1074\/jbc.RA120.013898_bib39","doi-asserted-by":"crossref","first-page":"6106","DOI":"10.1128\/JVI.00377-11","article-title":"Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3\/4A protease","volume":"85","author":"Romano","year":"2011","journal-title":"J. Virol"},{"key":"10.1074\/jbc.RA120.013898_bib40","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/0022-2836(92)91029-O","article-title":"Crystal and molecular structure of the bovine \u03b1-chymotrypsin-eglin c complex at 2.0 A resolution","volume":"225","author":"Frigerio","year":"1992","journal-title":"J. Mol. Biol"},{"key":"10.1074\/jbc.RA120.013898_bib41","doi-asserted-by":"crossref","first-page":"12909","DOI":"10.1021\/jp0743469","article-title":"Comparison of different quantum mechanical\/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A\/5B substrate","volume":"111","author":"Rodr\u00edguez","year":"2007","journal-title":"J. Phys. Chem. B"},{"year":"2015","series-title":"Amber 2015","author":"Case","key":"10.1074\/jbc.RA120.013898_bib42"},{"key":"10.1074\/jbc.RA120.013898_bib43","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1021\/j100308a038","article-title":"The missing term in effective pair potentials","volume":"91","author":"Berendsen","year":"1987","journal-title":"J. Phys. Chem"},{"key":"10.1074\/jbc.RA120.013898_bib44","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","article-title":"A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations","volume":"24","author":"Duan","year":"2003","journal-title":"J. Comput. Chem"},{"key":"10.1074\/jbc.RA120.013898_bib45","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1021\/acschembio.5b00905","article-title":"Sequential inactivation of gliotoxin by the S-methyltransferase TmtA","volume":"11","author":"Duell","year":"2016","journal-title":"ACS Chem. Biol"},{"key":"10.1074\/jbc.RA120.013898_bib46","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1074\/jbc.RA120.013898_bib47","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory. Comput"},{"key":"10.1074\/jbc.RA120.013898_bib48","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA.py: An Efficient Program for End-State Free Energy Calculations","volume":"8","author":"Miller","year":"2012","journal-title":"J. Chem. Theory. Comput"},{"key":"10.1074\/jbc.RA120.013898_bib49","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S1574-1400(09)00502-7","article-title":"Quantifying uncertainty and sampling quality in biomolecular simulations","volume":"5","author":"Grossfield","year":"2009","journal-title":"Annu. Rep. Comput. Chem"},{"key":"10.1074\/jbc.RA120.013898_bib50","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1021\/jm060173k","volume":"50","author":"Prongay","year":"2007","journal-title":"J. Med. Chem"},{"key":"10.1074\/jbc.RA120.013898_bib51","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/j.bbrc.2012.08.015","article-title":"Reprint of \u201cOn the size of the active site in proteases. I. Papain. 1967.\u201d","volume":"425","author":"Schechter","year":"2012","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"10.1074\/jbc.RA120.013898_bib52","doi-asserted-by":"crossref","first-page":"2992","DOI":"10.1073\/pnas.0408824102","article-title":"Immune evasion by hepatitis C virus NS3\/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF","volume":"102","author":"Li","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"10.1074\/jbc.RA120.013898_bib53","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.1002\/hep.22857","article-title":"Nonstructural 3\/4A protease of hepatitis C virus activates epithelial growth factor-induced signal transduction by cleavage of the T-cell protein tyrosine phosphatase","volume":"49","author":"Brennd\u00f6rfer","year":"2009","journal-title":"Hepatology"},{"key":"10.1074\/jbc.RA120.013898_bib54","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1002\/hep.26671","article-title":"Quantitative proteomics identifies the membrane-associated peroxidase GPx8 as a cellular substrate of the hepatitis C virus NS3-4A protease","volume":"59","author":"Morikawa","year":"2014","journal-title":"Hepatology"},{"key":"10.1074\/jbc.RA120.013898_bib55","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.virol.2012.10.025","article-title":"DDB1 is a cellular substrate of NS3\/4A protease and required for hepatitis C virus replication","volume":"435","author":"Kang","year":"2013","journal-title":"Virology"}],"container-title":["Journal of Biological Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925817498346?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925817498346?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1074\/jbc.RA120.013898","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,31]],"date-time":"2021-12-31T16:43:26Z","timestamp":1640969006000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0021925817498346"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,10]]},"references-count":55,"journal-issue":{"issue":"40","published-print":{"date-parts":[[2020,10]]}},"alternative-id":["S0021925817498346"],"URL":"https:\/\/doi.org\/10.1074\/jbc.ra120.013898","relation":{},"ISSN":["0021-9258"],"issn-type":[{"type":"print","value":"0021-9258"}],"subject":[],"published":{"date-parts":[[2020,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Extended interaction networks with HCV protease NS3-4A substrates explain the lack of adaptive capability against protease inhibitors","name":"articletitle","label":"Article Title"},{"value":"Journal of Biological Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1074\/jbc.RA120.013898","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Dultz et al.","name":"copyright","label":"Copyright"}]}}