Cargando…

Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields

Ion–ion interactions (salt bridges) between favorable pairs of charged residues are important for the conformational stability of proteins. Molecular dynamic (MD) simulations are useful for elucidating the interactions among charged residues fluctuating in solution. However, the quality of MD result...

Descripción completa

Detalles Bibliográficos
Autores principales:	Matsuura, Yoshinori, Joti, Yasumasa, Bagautdinov, Bagautdin, Yutani, Katsuhide
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	John Wiley and Sons Inc. 2019
Materias:	Research Articles
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6823277/ https://www.ncbi.nlm.nih.gov/pubmed/31509647 http://dx.doi.org/10.1002/2211-5463.12731

Ejemplares similares

Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations
por: Yutani, Katsuhide, et al.
Publicado: (2019)

Ion–ion interactions in the denatured state contribute to the stabilization of CutA1 proteins
por: Yutani, Katsuhide, et al.
Publicado: (2018)

Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues
por: Matsuura, Yoshinori, et al.
Publicado: (2015)

Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine
por: Malik, Deepshikha, et al.
Publicado: (2020)

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields
por: Debiec, Karl T., et al.
Publicado: (2014)

How well do force fields capture the strength of salt bridges in proteins?
por: Ahmed, Mustapha Carab, et al.
Publicado: (2018)

Correction to “Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields”
por: Debiec, Karl T., et al.
Publicado: (2019)

Crystal structure of stable protein CutA1 from psychrotrophic bacterium Shewanella sp. SIB1
por: Sato, Aya, et al.
Publicado: (2011)

Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology
por: Mietzsch, Mario, et al.
Publicado: (2020)

La zona arqueológica de "Cuta", Zapotitlán, Salinas, Puebla, México /
por: Cossío, José L. (José Lorenzo), 1864-1941
Publicado: (1940)

Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3′-terminal positions of synthesized tails
por: Kobyłecki, Kamil, et al.
Publicado: (2017)

Hydration Effect on Low-Frequency Protein Dynamics Observed in Simulated Neutron Scattering Spectra
por: Joti, Yasumasa, et al.
Publicado: (2008)

Synthesis and characterization of visible-light-driven novel CuTa(2)O(6) as a promising practical photocatalyst
por: Alageshwaramoorthy, Krishnaprasanth, et al.
Publicado: (2023)

Effect of Heavy Atoms on the Thermal Stability of α-Amylase from Aspergillus oryzae
por: Sugahara, Michihiro, et al.
Publicado: (2013)

Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra
por: Joti, Yasumasa, et al.
Publicado: (2019)

An Analytical and Experimental Study on Cutting Characteristics and Transient Cutting Force Modeling in Feed Directional Ultrasonic Vibration-Assisted Cutting of High Strength Alloys
por: Chen, Xuelin, et al.
Publicado: (2022)

Parameterization and optimization of the menthol force field for molecular dynamics simulations
por: Jasik, Mateusz, et al.
Publicado: (2016)

Molecular dynamics simulation of reversible electroporation with Martini force field
por: Zhou, Cheng, et al.
Publicado: (2019)

Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes
por: Li, Na, et al.
Publicado: (2021)

SALT BRIDGES AND NEGATIVE VARIATIONS
por: Osterhout, W. J. V., et al.
Publicado: (1930)

Commentary: Strength at the cutting edge
por: Wan, Song, et al.
Publicado: (2020)

A Novel and Safe Approach to Simulate Cutting Movements Using Ground Reaction Forces
por: Lanier, Amelia S., et al.
Publicado: (2018)

Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
por: Pabis, Anna, et al.
Publicado: (2014)

Towards exact molecular dynamics simulations with machine-learned force fields
por: Chmiela, Stefan, et al.
Publicado: (2018)

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants
por: Ewen, James P., et al.
Publicado: (2016)

Research on the Method of Reducing Dynamic Cutting Force in Aspheric Machining
por: Zhuang, Guilin, et al.
Publicado: (2023)

Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters
por: Průša, Jiří, et al.
Publicado: (2020)

Effects of Knee Flexion Angles on the Joint Force and Muscle Force during Bridging Exercise: A Musculoskeletal Model Simulation
por: Takeshita, Yasufumi, et al.
Publicado: (2022)

Experimental Study and Artificial Neural Network Simulation of Cutting Forces and Delamination Analysis in GFRP Drilling
por: Biruk-Urban, Katarzyna, et al.
Publicado: (2022)

Salt-Bridge Energetics in Halophilic Proteins
por: Nayek, Arnab, et al.
Publicado: (2014)

The importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation
por: Dehghan-Shasaltaneh, Marzieh, et al.
Publicado: (2018)

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation
por: Gu, Junfeng, et al.
Publicado: (2012)

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
por: Bedrov, Dmitry, et al.
Publicado: (2019)

Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations
por: Kitjanon, Jiramate, et al.
Publicado: (2021)

Experimental Study on a “Snake-Type” Vibration Cutting Method for Cutting Force and Cutting Heat Reductions
por: Zhang, Xiangyu, et al.
Publicado: (2019)

Foot force models of crowd dynamics on a wobbly bridge
por: Belykh, Igor, et al.
Publicado: (2017)

Simulating Polymerization by Boltzmann Inversion Force Field Approach and Dynamical Nonequilibrium Reactive Molecular Dynamics
por: Monteferrante, Michele, et al.
Publicado: (2022)

Upgraded Kalman Filtering of Cutting Forces in Milling
por: Totis, Giovanni, et al.
Publicado: (2020)

Cutting Forces in Peripheral Up-Milling of Particleboard
por: Pałubicki, Bartosz
Publicado: (2021)

Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics
por: Choi, Minseo, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_bmkhr195io2n7muuisfe9tm6q8