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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase. Nucleic Acids Res 2024:gkae500. [PMID: 38884215 DOI: 10.1093/nar/gkae500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/11/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The Orthoflavivirus NS3 helicase (NS3h) is crucial in virus replication, representing a potential drug target for pathogenesis. NS3h utilizes nucleotide triphosphate (ATP) for hydrolysis energy to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. Intermediate states along the ATP hydrolysis cycle and conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. Extensive molecular dynamics simulations of West Nile virus NS3h+ssRNA in the apo, ATP, ADP+Pi and ADP bound states were used to model the conformational ensembles along this cycle. Energetic and structural clustering analyses depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). Based on these results, MVIL mutants (D471L, D471N and D471E) were found to have a substantial reduction in ATPase activity and RNA replication compared to the wild-type. Simulations of the mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
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Roy P, Walter Z, Berish L, Ramage H, McCullagh M. Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569434. [PMID: 38077049 PMCID: PMC10705498 DOI: 10.1101/2023.11.30.569434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The flavivirus NS3 helicase (NS3h), a highly conserved protein, plays a pivotal role in virus replication and thus represents a potential drug target for flavivirus pathogenesis. NS3h utilizes nucleotide triphosphate, such as ATP, for hydrolysis energy (ATPase) to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. The intermediate states along the ATP binding and hydrolysis cycle, as well as the conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. We use extensive molecular dynamics simulations of apo, ATP, ADP+Pi, and ADP bound to WNV NS3h+ssRNA to model the conformational ensembles along this cycle. Energetic and structural clustering analyses on these trajectories depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). These findings were experimentally corroborated using viral replicons encoding three mutations at the D471 position. Replication assays using these mutants demonstrated a substantial reduction in viral replication compared to the wild-type. Molecular simulations of the D471 mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.
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Affiliation(s)
- Priti Roy
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
| | - Zachary Walter
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Lauren Berish
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Holly Ramage
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA, 19107
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA, 74078
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Caldwell HS, Kuo L, Pata JD, Dupuis AP, Arnold JJ, Yeager C, Stout J, Koetzner CA, Payne AF, Bialosuknia SM, Banker EM, Nolen TA, Cameron CE, Ciota AT. Maintenance of a host-specific minority mutation in the West Nile virus NS3. iScience 2023; 26:107468. [PMID: 37593454 PMCID: PMC10428113 DOI: 10.1016/j.isci.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
West Nile virus (WNV), the most prevalent arthropod-borne virus (arbovirus) in the United States, is maintained in a cycle between Culex spp. mosquitoes and birds. Arboviruses exist within hosts and vectors as a diverse set of closely related genotypes. In theory, this genetic diversity can facilitate adaptation to distinct environments during host cycling, yet host-specific fitness of minority genotypes has not been assessed. Utilizing WNV deep-sequencing data, we previously identified a naturally occurring, mosquito-biased substitution, NS3 P319L. Using both cell culture and experimental infection in natural hosts, we demonstrated that this substitution confers attenuation in vertebrate hosts and increased transmissibility by mosquitoes. Biochemical assays demonstrated temperature-sensitive ATPase activity consistent with host-specific phenotypes. Together these data confirm the maintenance of host-specific minority variants in arbovirus mutant swarms, suggest a unique role for NS3 in viral fitness, and demonstrate that intrahost sequence data can inform mechanisms of host-specific adaptation.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
| | - Lili Kuo
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alan P. Dupuis
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Calvin Yeager
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jessica Stout
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Cheri A. Koetzner
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Anne F. Payne
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Sean M. Bialosuknia
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Elyse M. Banker
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Taylor A. Nolen
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA
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Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1688. [PMID: 34472205 PMCID: PMC8888775 DOI: 10.1002/wrna.1688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Flaviviruses are a major health concern because over half of the world population is at risk of infection and there are very few antiviral therapeutics to treat diseases resulting from infection. Replication is an essential part of the flavivirus survival. One of the viral proteins, NS3 helicase, is critical for unwinding the double stranded RNA intermediate during flaviviral replication. The helicase performs the unwinding of the viral RNA intermediate structure in an ATP-dependent manner. NS3 helicase is a member of the Viral/DEAH-like subfamily of the superfamily 2 helicase containing eight highly conserved structural motifs (I, Ia, II, III, IV, IVa, V, and VI) localized between the ATP-binding and RNA-binding pockets. Of these structural motifs only three are well characterized for function in flaviviruses (I, II, and VI). The roles of the other structural motifs are not well understood for NS3 helicase function, but comparison of NS3 with other superfamily 2 helicases within the viral/DEAH-like, DEAH/RHA, and DEAD-box subfamilies can be used to elucidate the roles of these structural motifs in the flavivirus NS3 helicase. This review aims to summarize the role of each conserved structural motif within flavivirus NS3 in RNA helicase function. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
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