Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability

  • The Q80K polymorphism in the NS3-4A protease of the hepatitis C virus is associated with treatment failure of direct-acting antiviral agents. This polymorphism is highly prevalent in genotype 1a infections and stably transmitted between hosts. Here, we investigated the underlying molecular mechanisms of evolutionarily conserved coevolving amino acids in NS3-Q80K and revealed potential implications of epistatic interactions in immune escape and variants persistence. Using purified protein, we characterized the impact of epistatic amino acid substitutions on the physicochemical properties and peptide cleavage kinetics of the NS3-Q80K protease. We found that Q80K destabilized the protease protein fold (p < 0.0001). Although NS3-Q80K showed reduced peptide substrate turnover (p < 0.0002), replicative fitness in an H77S.3 cell culture model of infection was not significantly inferior to the WT virus. Epistatic substitutions at residues 91 and 174 in NS3-Q80K stabilized the protein fold (p < 0.0001) and leveraged the WT protease stability. However, changes in protease stability inversely correlated with enzymatic activity. In infectious cell culture, these secondary substitutions were not associated with a gain of replicative fitness in NS3-Q80K variants. Using molecular dynamics, we observed that the total number of residue contacts in NS3-Q80K mutants correlated with protein folding stability. Changes in the number of contacts reflected the compensatory effect on protein folding instability by epistatic substitutions. In summary, epistatic substitutions in NS3-Q80K contribute to viral fitness by mechanisms not directly related to RNA replication. By compensating for protein-folding instability, epistatic interactions likely protect NS3-Q80K variants from immune cell recognition.

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Author:Georg DultzORCiDGND, Sanjay K. SrikakulamORCiD, Michael KonetschnikGND, Tetsuro Shimakami, Nadezhda T. DonchevaORCiD, Julia DietzORCiDGND, Christoph SarrazinGND, Ricardo M. BiondiORCiDGND, Stefan ZeuzemORCiDGND, Robert TampéORCiDGND, Olga V. KalininaORCiD, Christoph WelschORCiDGND
URN:urn:nbn:de:hebis:30:3-779744
DOI:https://doi.org/10.1016/j.jbc.2021.101031
ISSN:0021-9258
Parent Title (English):Journal of biological chemistry
Publisher:American Society for Biochemistry and Molecular Biology Publications
Place of publication:Bethesda, Md
Document Type:Article
Language:English
Date of Publication (online):2021/08/25
Date of first Publication:2021/07/31
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2024/04/22
Tag:hepatitis C virus; immune escape; protein evolution; protein folding; resistance mutation; serine protease (NS3-4A); viral fitness
Volume:297.2021
Issue:3, art. 101031
Article Number:101031
Page Number:12
Institutes:Medizin
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - CC BY - Namensnennung 4.0 International