Cargando…

Exploring the RING-Catalyzed Ubiquitin Transfer Mechanism by MD and QM/MM Calculations

Ubiquitylation is a universal mechanism for controlling cellular functions. A large family of ubiquitin E3 ligases (E3) mediates Ubiquitin (Ub) modification. To facilitate Ub transfer, RING E3 ligases bind both the substrate and ubiquitin E2 conjugating enzyme (E2) linked to Ub via a thioester bond...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zhen, Yunmei, Qin, Guangrong, Luo, Cheng, Jiang, Hualiang, Yu, Kunqian, Chen, Guanghui
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2014
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086935/ https://www.ncbi.nlm.nih.gov/pubmed/25003393 http://dx.doi.org/10.1371/journal.pone.0101663

Ejemplares similares

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region
por: Jindal, Garima, et al.
Publicado: (2016)

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations
por: Reiter, Sebastian, et al.
Publicado: (2023)

On the Difference Between Additive and Subtractive QM/MM Calculations
por: Cao, Lili, et al.
Publicado: (2018)

QM/MM Calculations with deMon2k
por: Salahub, Dennis R., et al.
Publicado: (2015)

Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study
por: Romero-Téllez, Sonia, et al.
Publicado: (2019)

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase
por: Kulik, Heather J., et al.
Publicado: (2016)

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions
por: Mulholland, Adrian J
Publicado: (2007)

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations
por: Fang, Dong, et al.
Publicado: (2014)

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations
por: Pan, Xiaoliang, et al.
Publicado: (2018)

Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study
por: Suenaga, Shunya, et al.
Publicado: (2023)

Solvent Organization and Rate Regulation of a Menshutkin Reaction by Oriented External Electric Fields are Revealed by Combined MD and QM/MM Calculations
por: Dutta Dubey, Kshatresh, et al.
Publicado: (2020)

Recent advances in QM/MM free energy calculations using reference potentials()
por: Duarte, Fernanda, et al.
Publicado: (2015)

Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 through QM/MM MD and Free Energy Simulations
por: Yue, Yufei, et al.
Publicado: (2015)

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations
por: Liu, Fei, et al.
Publicado: (2015)

The Binding Mode of the Sonic Hedgehog Inhibitor Robotnikinin, a Combined Docking and QM/MM MD Study
por: Hitzenberger, Manuel, et al.
Publicado: (2017)

The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study
por: Landi, Alessandro, et al.
Publicado: (2021)

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems
por: Berraud-Pache, Romain, et al.
Publicado: (2018)

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes
por: Jin, Xinsheng, et al.
Publicado: (2018)

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations
por: Voice, Angus T., et al.
Publicado: (2021)

Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations
por: Moriwaki, Yoshitaka, et al.
Publicado: (2015)

Insights into the Interaction between Polyphenols and β-Lactoglobulin through Molecular Docking, MD Simulation, and QM/MM Approaches
por: Baruah, Indrani, et al.
Publicado: (2022)

On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis
por: Alvarado, Raúl, et al.
Publicado: (2022)

Review on the QM/MM Methodologies and Their Application to Metalloproteins
por: Tzeliou, Christina Eleftheria, et al.
Publicado: (2022)

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase
por: Prejanò, Mario, et al.
Publicado: (2018)

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods
por: Yildiz, Ibrahim, et al.
Publicado: (2018)

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
por: König, Gerhard, et al.
Publicado: (2014)

Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis
por: Pérez-Barcia, Álvaro, et al.
Publicado: (2023)

Structure–Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations
por: Schulz, Christine E., et al.
Publicado: (2021)

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations
por: Korlyukov, Alexander A., et al.
Publicado: (2023)

Exploration of the Activation Mechanism of the Epigenetic Regulator MLL3: A QM/MM Study
por: Miranda-Rojas, Sebastián, et al.
Publicado: (2021)

MD simulations and QM/MM calculations reveal the key mechanistic elements which are responsible for the efficient C–H amination reaction performed by a bioengineered P450 enzyme
por: Kalita, Surajit, et al.
Publicado: (2021)

QM/MM study of the reaction mechanism of sulfite oxidase
por: Caldararu, Octav, et al.
Publicado: (2018)

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies
por: Elsässer, Brigitta, et al.
Publicado: (2021)

Mechanism of Chiral-Selective Aminoacylation of an RNA Minihelix Explored by QM/MM Free-Energy Simulations
por: Ando, Tadashi, et al.
Publicado: (2023)

QM/MM Molecular Dynamics Studies of Metal Binding Proteins
por: Vidossich, Pietro, et al.
Publicado: (2014)

Projected Hybrid Orbitals: A General QM/MM Method
por: Wang, Yingjie, et al.
Publicado: (2014)

Robotic QM/MM-driven maturation of antibody combining sites
por: Smirnov, Ivan V., et al.
Publicado: (2016)

NAMD goes quantum: An integrative suite for QM/MM simulations
por: Melo, Marcelo C. R., et al.
Publicado: (2018)

A QM/MM study of the nature of the entatic state in plastocyanin
por: Hurd, Catherine A., et al.
Publicado: (2016)

QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate
por: Boneta, Sergio, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_2di5kqb0h6vkip6ni4nqqtddhg