ArticleNucleic acids research2015
ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 36 citations in OpenAlex.
- Allosteric Regulation of RNA Affinity by Motif V-VI Coupling in West Nile Virus NS3 Helicase.Proteins · 2026Article
- Improving the potency prediction for chemically modified siRNAs through insights from molecular modeling of individual sequence positions.Molecular therapy. Nucleic acids · 2025Article
- Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase.Nucleic acids research · 2024Article
- Sustained antiviral insulin signaling during West Nile virus infection results in viral mutations.Frontiers in cellular and infection microbiology · 2024Article
- The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase.Nucleic acids research · 2023Article
- Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations.Chemical science · 2021Article
- A Hyperactive Kunjin Virus NS3 Helicase Mutant Demonstrates Increased Dissemination and Mortality in Mosquitoes.Journal of virology · 2020Article
- Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft.The Journal of biological chemistry · 2020Article
- Screening of Duck Tembusu Virus NS3 Interacting Host Proteins and Identification of Its Specific Interplay Domains.Viruses · 2019Article
- Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.International journal of molecular sciences · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations.PLoS computational biology · 2018Article
- Cefminox, a Dual Agonist of Prostacyclin Receptor and Peroxisome Proliferator-Activated Receptor-Gamma Identified by Virtual Screening, Has Therapeutic Efficacy against Hypoxia-Induced Pulmonary Hypertension in Rats.Frontiers in pharmacology · 2018Article
- Unraveling MgRNA (New York, N.Y.) · 2017Article
- RNA folding pathways in stop motion.Nucleic acids research · 2016Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures. We also construct and simulate putative intermediates for the translocation process, and we perform non-equilibrium targeted simulations to estimate their relative stability. For each of the simulated structures we carefully characterize the available conformational space, the ligand binding pocket, and the RNA binding cleft. The analysis of the hydrogen bond network and of the non-equilibrium trajectories indicates an ATP-dependent stabilization of one of the protein conformers. Additionally, enthalpy calculations suggest that entropic effects might be crucial for the stabilization of the experimentally observed structures.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.