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Dultz G, Srikakulam SK, Konetschnik M, Shimakami T, Doncheva NT, Dietz J, Sarrazin C, Biondi RM, Zeuzem S, Tampé R, Kalinina OV, Welsch C. Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability. J Biol Chem 2021; 297:101031. [PMID: 34339738 PMCID: PMC8405986 DOI: 10.1016/j.jbc.2021.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022] Open
Abstract
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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Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sanjay K Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Graduate School of Computer Science, Saarland University, Saarbrücken, Germany; Interdisciplinary Graduate School of Natural Product Research, Saarland University, Saarbrücken, Germany
| | - Michael Konetschnik
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Julia Dietz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ricardo M Biondi
- Molecular Targeting, Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Medical Faculty, Saarland University, Homburg, Germany; Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany.
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