A conserved asparagine in a ubiquitin‐conjugating enzyme positions the substrate for nucleophilic attack

Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2-25K

(2018) Manoj K. Rout et al.   Scientific Reports

Structural Evidence for Dimer-Interface-Driven Regulation of the Type II Cysteine Desulfurase, SufS

(2018) Jack A. Dunkle et al.   BIOCHEMISTRY

Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme

(2017) R. Hunter Wilson et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase

(2017) Yashraj S. Kulkarni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment

(2016) Curtis D. Hodge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer

(2016) Jamie M. Schiffer et al.   STRUCTURE

Chemical shift assignments for S. cerevisiae Ubc13

(2015) D. Reid Putney et al.   Biomolecular NMR Assignments

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains

(2015) Emma Branigan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Distinct activation of an E2 ubiquitin-conjugating enzyme by its cognate E3 ligases

(2015) Itamar Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains

(2015) Emma Branigan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Confidence limits, error bars and method comparison in molecular modeling. Part 1: The calculation of confidence intervals

(2014) A. Nicholls   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Stochastic Gate Dynamics Regulate the Catalytic Activity of Ubiquitination Enzymes

(2014) Manoj K. Rout et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New insights into ubiquitin E3 ligase mechanism

(2014) Christopher E Berndsen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

A conserved asparagine has a structural role in ubiquitin-conjugating enzymes

(2013) Christopher E Berndsen et al.   Nature Chemical Biology

Architecture of the catalytic HPN motif is conserved in all E2 conjugating enzymes

(2012) Benjamin W. Cook et al.   BIOCHEMICAL JOURNAL

Structural Insights into the Conformation and Oligomerization of E2∼Ubiquitin Conjugates

(2012) Richard C. Page et al.   BIOCHEMISTRY

Structure of an E3:E2∼Ub Complex Reveals an Allosteric Mechanism Shared among RING/U-box Ligases

(2012) Jonathan N. Pruneda et al.   MOLECULAR CELL

Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis

(2012) Anna Plechanovová et al.   NATURE

BIRC7–E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer

(2012) Hao Dou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme∼Ubiquitin Conjugate

(2011) Jonathan N. Pruneda et al.   BIOCHEMISTRY

Hydrogen-bond stabilization in oxyanion holes: grand jeté to three dimensions

(2011) Luis Simón et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors

(2011) Z. D. Nagel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ONIOM method: its foundation and applications to metalloenzymes and photobiology

(2011) Lung Wa Chung et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

E2s: structurally economical and functionally replete

(2010) Dawn M. Wenzel et al.   BIOCHEMICAL JOURNAL

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)

(2010) Tsutomu Kawatsu et al.   Journal of Chemical Theory and Computation

On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models

(2010) Shina C. L. Kamerlin et al.   JOURNAL OF ORGANIC CHEMISTRY

Matrix Metalloproteinase 2 Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of (4-Phenoxyphenylsulfonyl)methylthiirane and Its Oxirane Analogue

(2009) Peng Tao et al.   BIOCHEMISTRY

Implementation and benchmark tests of the DFTB method and its application in the ONIOM method

(2009) Guishan Zheng et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes

(2009) Luis Simón et al.   JOURNAL OF ORGANIC CHEMISTRY

A 21st century revisionist's view at a turning point in enzymology

(2009) Zachary D Nagel et al.   Nature Chemical Biology