ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?

(2015) M. Krepl et al.   Journal of Chemical Theory and Computation

Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+through the SOMA string method

(2015) Davide Branduardi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

pH-Dependent Conformational Changes in the HCV NS3 Protein Modulate Its ATPase and Helicase Activities

(2015) Gustavo Tavares Ventura et al.   PLoS One

Accurate Multiple Time Step in Biased Molecular Simulations

(2014) Marco Jacopo Ferrarotti et al.   Journal of Chemical Theory and Computation

The role of nucleobase interactions in RNA structure and dynamics

(2014) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

(2013) John D. Chodera et al.   Annual Review of Biophysics

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

(2013) Christoph Dellago et al.   Entropy

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

RNA/Peptide Binding Driven by Electrostatics—Insight from Bidirectional Pulling Simulations

(2013) Trang N. Do et al.   Journal of Chemical Theory and Computation

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations

(2013) Matthew J. McGrath et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB

(2013) Yan Zhou et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

(2013) Paul C. Whitford et al.   PLoS Computational Biology

Structure-Based Simulations of the Translocation Mechanism of the Hepatitis C Virus NS3 Helicase along Single-Stranded Nucleic Acid

(2012) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

(2012) Olof Allnér et al.   Journal of Chemical Theory and Computation

RNA Unwinding from Reweighted Pulling Simulations

(2012) Francesco Colizzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Mechanism of ATP Hydrolysis in F1-ATPase Revealed by Molecular Simulations and Single-Molecule Observations

(2012) Shigehiko Hayashi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification and analysis of hepatitis C virus NS3 helicase inhibitors using nucleic acid binding assays

(2012) Sourav Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Path Finding on High-Dimensional Free Energy Landscapes

(2012) Grisell Díaz Leines et al.   PHYSICAL REVIEW LETTERS

Forcing a connection: Impacts of single-molecule force spectroscopy on in vivo tension sensing

(2011) Michael D. Brenner et al.   BIOPOLYMERS

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Single-Base Pair Unwinding and Asynchronous RNA Release by the Hepatitis C Virus NS3 Helicase

(2011) W. Cheng et al.   SCIENCE

Stepwise translocation of nucleic acid motors

(2010) Sua Myong et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Protease Domain Increases the Translocation Stepping Efficiency of the Hepatitis C Virus NS3-4A Helicase

(2010) Vaishnavi Rajagopal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Hepatitis C Virus Non-structural Protein 3 (HCV NS3): A Multifunctional Antiviral Target

(2010) Kevin D. Raney et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV

(2010) Todd C. Appleby et al.   JOURNAL OF MOLECULAR BIOLOGY

Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism

(2010) M. Gu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations

(2010) H. Flechsig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA helicases at work: binding and rearranging

(2010) Eckhard Jankowsky   TRENDS IN BIOCHEMICAL SCIENCES

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA Unwinding by NS3 Helicase: A Statistical Approach

(2009) Srikesh G. Arunajadai   PLoS One

Translocation and Unwinding Mechanisms of RNA and DNA Helicases

(2008) Anna Marie Pyle   Annual Review of Biophysics

MESPEUS: a database of the geometry of metal sites in proteins

(2008) K. Hsin et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Hepatitis C Virus NS3 Helicase Forms Oligomeric Structures That Exhibit Optimal DNA Unwinding Activityin Vitro

(2008) Bartek Sikora et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

NS3 Helicase from the Hepatitis C Virus Can Function as a Monomer or Oligomer Depending on Enzyme and Substrate Concentrations

(2008) Thomas A. Jennings et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation