Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.
- 1Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States.
Abstract
SARS-CoV-2 nonstructural protein 13 (nsp13) is a highly conserved helicase that couples ATP hydrolysis to RNA translocation through long-range allosteric communication between its ATPase and RNA-binding domains. In prior work, we identified L405 as a key regulator of interdomain motions and proposed that the L405D mutation would disrupt this coupling by perturbing conformational transitions required for translocation [J. Phys. Chem. B2024, v128, 492-503. ]. Subsequent experiments confirmed that L405D attenuates helicase activity and ATPase activity, implicating the potential formation of a new salt bridge, D405-R560, for both effects [ J. Biol. Chem.2026, v302, 111198.]. Here, we provide a data-driven explanation for both effects by combining Gaussian accelerated molecular dynamics (GaMD) simulations with Shape-GMM clustering and linear discriminant analysis. Whereas wild-type nsp13 exhibits both conformational selection and induction, L405D collapses the conformational landscape to operate predominantly through selection, with ATP-induced structural transitions observed in the wild-type ensemble no longer sampled by the mutant. This loss of induction likely impairs ATP turnover while simultaneously disrupting coordinated motif-RNA interactions required for inchworm translocation. These findings demonstrate how mutation-induced reshaping of conformational ensembles can modulate access to reaction-competent states, providing a general framework for understanding how targeted mutations disrupt catalytic function through allosteric ensemble remodeling in motor proteins.
Related
- RipplePLM: Structural and Property Decoupling for Protein Mutation Effect Generation
- Tafazzin catalyzes transacylation and hydrolysis with inverse acyl specificities
- Snapshots of ATP-driven substrate translocation by the mitochondrial AAA+ protease AFG3L2
- Synergistic Alcalase-papain hydrolysis of egg white protein: enhancing structural unfolding, antioxidant activity, and gastrointestinal stability.
- A Saliva-Inspired Model of Enzymatic Starch Hydrolysis by Alpha Amylase
BibTeX
@article{fazelpour2026mechanochemical,
title = {{Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.}},
author = {Elham Fazelpour and Priti Roy and Kole J Frederick and Martin McCullagh},
journal = {The journal of physical chemistry. B},
year = {2026},
month = sep,
doi = {10.1021/acs.jpcb.6c03935},
url = {https://europepmc.org/article/MED/42917542},
note = {CC BY},
}
RIS
TY - JOUR
TI - Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.
AU - Elham Fazelpour
AU - Priti Roy
AU - Kole J Frederick
AU - Martin McCullagh
PY - 2026
DA - 2026/09/01
JO - The journal of physical chemistry. B
DO - 10.1021/acs.jpcb.6c03935
UR - https://europepmc.org/article/MED/42917542
AB - SARS-CoV-2 nonstructural protein 13 (nsp13) is a highly conserved helicase that couples ATP hydrolysis to RNA translocation through long-range allosteric communication between its ATPase and RNA-binding domains. In prior work, we identified L405 as a key regulator of interdomain motions and proposed that the L405D mutation would disrupt this coupling by perturbing conformational transitions required for translocation [J. Phys. Chem. B2024, v128, 492-503. ]. Subsequent experiments confirmed that L405D attenuates helicase activity and ATPase activity, implicating the potential formation of a new salt bridge, D405-R560, for both effects [ J. Biol. Chem.2026, v302, 111198.]. Here, we provide a data-driven explanation for both effects by combining Gaussian accelerated molecular dynamics (GaMD) simulations with Shape-GMM clustering and linear discriminant analysis. Whereas wild-type nsp13 exhibits both conformational selection and induction, L405D collapses the conformational landscape to operate predominantly through selection, with ATP-induced structural transitions observed in the wild-type ensemble no longer sampled by the mutant. This loss of induction likely impairs ATP turnover while simultaneously disrupting coordinated motif-RNA interactions required for inchworm translocation. These findings demonstrate how mutation-induced reshaping of conformational ensembles can modulate access to reaction-competent states, providing a general framework for understanding how targeted mutations disrupt catalytic function through allosteric ensemble remodeling in motor proteins.
SN - 1520-6106
SN - 1520-5207
ER -