Cargando…

Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain

To ascertain the role of Zn(II) as an allosteric modulator on P2X4R, QM/MM molecular dynamic simulations were performed on the WT and two P2X4R mutants suggested by previous electrophysiological data to affect Zn(II) binding. The Gibbs free energy for the reduction of the putative P2X4R Zn(II) bindi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Peralta, Francisco Andrés, Huidobro-Toro, J. Pablo, Mera-Adasme, Raúl
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8303255/ https://www.ncbi.nlm.nih.gov/pubmed/34298909 http://dx.doi.org/10.3390/ijms22147288

Ejemplares similares

QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases
por: Escorcia, Andrés M., et al.
Publicado: (2018)

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
por: Misini Ignjatović, Majda, et al.
Publicado: (2016)

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

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)

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)

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

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

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)

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

Distinct Roles of Catalytic Cysteine and Histidine in the Protease and Ligase Mechanisms of Human Legumain As Revealed by DFT-Based QM/MM Simulations
por: Elsässer, Brigitta, et al.
Publicado: (2017)

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)

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

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)

QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase
por: Grigorenko, Bella, et al.
Publicado: (2023)

Insight into the reaction mechanism of lipoyl synthase: a QM/MM study
por: Dong, Geng, et al.
Publicado: (2017)

A QM/MM Derived Polarizable Water Model for Molecular Simulation
por: Visscher, Koen M., et al.
Publicado: (2018)

QM/MM Studies of Contemporary and Novel Membrane Raft Fluorescent Probes
por: Blake, Hannah L., et al.
Publicado: (2014)

Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics
por: Macaluso, Veronica, et al.
Publicado: (2021)

Spectral Features of Canthaxanthin in HCP2. A QM/MM Approach
por: Clark, Kevin, et al.
Publicado: (2021)

Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin
por: Schulz, Christine E., et al.
Publicado: (2021)

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease
por: Saito, Toru, et al.
Publicado: (2022)

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach
por: López, Roberto, et al.
Publicado: (2022)

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation
por: Bondanza, Mattia, et al.
Publicado: (2022)

Dopamine-Decorated TiO(2) Nanoparticles in Water: A QM/MM vs an MM Description
por: Siani, Paulo, et al.
Publicado: (2020)

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method
por: Chen, Cheng Giuseppe, et al.
Publicado: (2022)

New Insights of the Zn(II)-Induced P2 × 4R Positive Allosteric Modulation: Role of Head Receptor Domain SS2/SS3, E160 and D170
por: Peralta, Francisco Andrés, et al.
Publicado: (2020)

Exploring the RING-Catalyzed Ubiquitin Transfer Mechanism by MD and QM/MM Calculations
por: Zhen, Yunmei, et al.
Publicado: (2014)

Hybrid QM/MM study of FMO complex with polarized protein-specific charge
por: Jia, Xiangyu, et al.
Publicado: (2015)

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

Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data
por: Salvadori, Andrea, et al.
Publicado: (2016)

New Insights into the Catalytic Mechanism of Aldose Reductase: A QM/MM Study
por: Dréanic, Marie-Pierre, et al.
Publicado: (2017)

An MM and QM Study of Biomimetic Catalysis of Diels-Alder Reactions Using Cyclodextrins
por: Chen, Wei, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_crmg7uoefv5b9lsvq228ciea9g