Structural transitions in the RNA 7SK 5′ hairpin and their effect on HEXIM binding

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Energy Landscapes of Mini-Dumbbell DNA Octanucleotides

(2018) James S. Klimavicz et al.   Journal of Chemical Theory and Computation

Evolved Minimal Frustration in Multifunctional Biomolecules

(2018) Konstantin Röder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7

(2018) Catherine D. Eichhorn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the Ub to Ub-CR transition in ubiquitin

(2018) Konstantin Röder et al.   BIOCHEMISTRY

HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry

(2018) Vincent V. Pham et al.   Nature Communications

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

(2017) Tristan Cragnolini et al.   JOURNAL OF CHEMICAL PHYSICS

Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations

(2017) Konstantin Röder et al.   Journal of Chemical Theory and Computation

Energy Landscape and Pathways for Transitions between Watson–Crick and Hoogsteen Base Pairing in DNA

(2017) Debayan Chakraborty et al.   Journal of Physical Chemistry Letters

Reconstitution of a functional 7SK snRNP

(2017) John E. Brogie et al.   NUCLEIC ACIDS RESEARCH

Probing helical transitions in a DNA duplex

(2017) Debayan Chakraborty et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On the representability problem and the physical meaning of coarse-grained models

(2016) Jacob W. Wagner et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes

(2016) Petr Stadlbauer et al.   Journal of Chemical Theory and Computation

Solution structure of the 5′-terminal hairpin of the 7SK small nuclear RNA

(2016) Sarah Bourbigot et al.   RNA

Intermolecular recognition of the non-coding RNA 7SK and HEXIM protein in perspective

(2015) Denise Martinez-Zapien et al.   BIOCHIMIE

Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent

(2015) Guillaume Stirnemann et al.   Journal of Chemical Theory and Computation

Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7

(2015) Emiko Uchikawa et al.   NUCLEIC ACIDS RESEARCH

Intrinsically Disordered Energy Landscapes

(2015) Yassmine Chebaro et al.   Scientific Reports

Design and application of implicit solvent models in biomolecular simulations

(2014) Jens Kleinjung et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins

(2014) Debayan Chakraborty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hamiltonian replica exchange in GROMACS: a flexible implementation

(2013) Giovanni Bussi   MOLECULAR PHYSICS

RNA elements directing in vivo assembly of the 7SK/MePCE/Larp7 transcriptional regulatory snRNP

(2013) L. Muniz et al.   NUCLEIC ACIDS RESEARCH

Studying “Invisible” Excited Protein States in Slow Exchange with a Major State Conformation

(2012) Pramodh Vallurupalli et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

(2011) Phillip J. Stansfeld et al.   Journal of Chemical Theory and Computation

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription

(2011) B. Matija Peterlin et al.   Wiley Interdisciplinary Reviews-RNA

Energy landscapes: some new horizons

(2010) David J Wales   CURRENT OPINION IN STRUCTURAL BIOLOGY

HEXIM1 targets a repeated GAUC motif in the riboregulator of transcription 7SK and promotes base pair rearrangements

(2010) Isabelle Lebars et al.   NUCLEIC ACIDS RESEARCH

7SK RNA, a non-coding RNA regulating P-TEFb, a general transcription factor

(2010) Gaelle Diribarne et al.   RNA Biology

Controlling Cellular P-TEFb Activity by the HIV-1 Transcriptional Transactivator Tat

(2010) Lisa Muniz et al.   PLoS Pathogens

U30 of 7SK RNA Forms a Specific Photo-cross-link with Hexim1 in the Context of Both a Minimal RNA-binding site and a Fully Reconstituted 7SK/Hexim1/P-TEFb Ribonucleoprotein Complex

(2009) François Bélanger et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolution of 7SK RNA and Its Protein Partners in Metazoa

(2009) M. Marz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Non-coding RNAs regulating the transcriptional machinery

(2008) Charlotte Barrandon et al.   BIOLOGY OF THE CELL

Transition networks for modeling the kinetics of conformational change in macromolecules

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

Invertebrate 7SK snRNAs

(2008) Andreas R. Gruber et al.   JOURNAL OF MOLECULAR EVOLUTION

A La-Related Protein Modulates 7SK snRNP Integrity to Suppress P-TEFb-Dependent Transcriptional Elongation and Tumorigenesis

(2008) Nanhai He et al.   MOLECULAR CELL

LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated

(2008) B. J. Krueger et al.   NUCLEIC ACIDS RESEARCH