Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

Structure of transcribing mammalian RNA polymerase II

(2016) Carrie Bernecky et al.   NATURE

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

(2015) Christopher O. Barnes et al.   MOLECULAR CELL

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Allostery through the computational microscope: cAMP activation of a canonical signalling domain

(2015) Robert D. Malmstrom et al.   Nature Communications

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis

(2014) Liang Xu et al.   DNA REPAIR

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states

(2014) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

(2014) Robert D. Malmstrom et al.   Journal of Chemical Theory and Computation

Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

(2014) Om P Choudhary et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement

(2014) Pyae P Hein et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details

(2014) Beibei Wang et al.   NUCLEIC ACIDS RESEARCH

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

(2014) D.-A. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration

(2014) Sung-Hoon Jun et al.   Nature Communications

Energetic and Structural Details of the Trigger-Loop Closing Transition in RNA Polymerase II

(2013) Beibei Wang et al.   BIOPHYSICAL JOURNAL

Structural Basis of Transcriptional Pausing in Bacteria

(2013) Albert Weixlbaumer et al.   CELL

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation

(2013) Qin Qiao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

(2013) Manchuta Dangkulwanich et al.   eLife

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intrinsic Translocation Barrier as an Initial Step in Pausing by RNA Polymerase II

(2012) Masahiko Imashimizu et al.   JOURNAL OF MOLECULAR BIOLOGY

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription

(2012) Matthew W Kellinger et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Active site opening and closure control translocation of multisubunit RNA polymerase

(2012) Anssi M. Malinen et al.   NUCLEIC ACIDS RESEARCH

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase

(2012) Maria L Kireeva et al.   BMC Biophysics

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

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

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II

(2011) Lin-Tai Da et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

(2011) Jan-Hendrik Prinz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation

(2010) Michael Feig et al.   BIOPHYSICAL JOURNAL

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

(2010) Ilyas Yildirim et al.   Journal of Chemical Theory and Computation

Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

(2010) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evidence that Transcript Cleavage Is Essential for RNA Polymerase II Transcription and Cell Viability

(2010) Stefan Sigurdsson et al.   MOLECULAR CELL

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

(2010) Jing Jin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

(2010) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Polymerase Active Center: The Molecular Engine of Transcription

(2009) Evgeny Nudler   Annual Review of Biochemistry

RNA polymerase fidelity and transcriptional proofreading

(2009) Jasmin F Sydow et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNA

(2009) Jasmin F. Sydow et al.   MOLECULAR CELL

Role of the RNA polymerase trigger loop in catalysis and pausing

(2009) Jinwei Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional pausing without backtracking

(2009) R. Landick   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

(2009) D. Wang et al.   SCIENCE

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

Can Morphing Methods Predict Intermediate Structures?

(2008) Dahlia R. Weiss et al.   JOURNAL OF MOLECULAR BIOLOGY

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The X-ray crystal structure of RNA polymerase from Archaea

(2008) Akira Hirata et al.   NATURE