Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase

Authors

Priti Roy
Zachary Walter, Thomas Jefferson UniversityFollow
Lauren Berish, Thomas Jefferson UniversityFollow
Holly Ramage, Thomas Jefferson UniversityFollow
Martin McCullagh

Document Type

Article

Publication Date

7-22-2024

Comments

This article is the author's final published version in Nucleic acids research, Volume 52, Issue 13, July 2024, Pages 7447 - 7464.

The published version is available at https://doi.org/10.1093/nar/gkae500.

Copyright © The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Recommended Citation

Roy, Priti; Walter, Zachary; Berish, Lauren; Ramage, Holly; and McCullagh, Martin, "Motif-VI Loop Acts as a Nucleotide Valve in the West Nile Virus NS3 Helicase" (2024). Department of Microbiology and Immunology Faculty Papers. Paper 187.
https://jdc.jefferson.edu/mifp/187

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

PubMed ID

38884215

Language

English