(Q48046709)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

title

Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

5

1 reference

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3 April 2020

author name string

Xiya Lu

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Victor Ovchinnikov

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Darren Demapan

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Daniel Roston

4

1 reference

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3 April 2020

language of work or name

English

0 references

publication date

1 March 2017

1 reference

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3 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

volume

56

1 reference

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3 April 2020

issue

10

1 reference

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3 April 2020

page(s)

1482-1497

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

Perspective: Quantum mechanical methods in biochemistry and biophysics

3 April 2020

cites work

1 reference

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Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

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Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily

27 July 2018

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The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations

27 July 2018

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Parametrization and Benchmark of DFTB3 for Organic Molecules

27 July 2018

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BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase".

27 July 2018

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Advances in quantum simulations of ATPase catalysis in the myosin motor.

27 July 2018

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Computational enzyme design

27 July 2018

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Automated discovery of chemically reasonable elementary reaction steps

27 July 2018

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Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations

27 July 2018

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Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and oxidation free energy in proteins

27 July 2018

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Catalytic mechanism of a mammalian Rab⋅RabGAP complex in atomic detail

27 July 2018

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DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).

27 July 2018

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Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations

27 July 2018

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Biomolecular dynamics: order-disorder transitions and energy landscapes

27 July 2018

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Iterative approach to computational enzyme design

27 July 2018

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A conformational transition in the myosin VI converter contributes to the variable step size

27 July 2018

1 reference

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Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

27 July 2018

1 reference

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Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

27 July 2018

1 reference

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Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

27 July 2018

1 reference

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Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

27 July 2018

1 reference

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Emerging complex pathways of the actomyosin powerstroke.

27 July 2018

1 reference

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Origins of catalysis by computationally designed retroaldolase enzymes

27 July 2018

1 reference

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Structural and functional insights into the Myosin motor mechanism

27 July 2018

1 reference

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Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations.

27 July 2018

1 reference

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The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state

27 July 2018

1 reference

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CHARMM: the biomolecular simulation program

27 July 2018

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Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol

27 July 2018

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Directed enzyme evolution: climbing fitness peaks one amino acid at a time

27 July 2018

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Allosteric regulation and catalysis emerge via a common route.

27 July 2018

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Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.

27 July 2018

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Protein Design by Directed Evolution

27 July 2018

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Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods

27 July 2018

1 reference

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Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

27 July 2018

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Cellular senescence: when bad things happen to good cells

27 July 2018

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Mechanism of the myosin catalyzed hydrolysis of ATP as rationalized by molecular modeling

27 July 2018

1 reference

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Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations

27 July 2018

1 reference

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Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

27 July 2018

1 reference

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A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase

27 July 2018

1 reference

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The molecular mechanism of muscle contraction.

27 July 2018

1 reference

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Structural mechanism of the recovery stroke in the myosin molecular motor

27 July 2018

1 reference

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Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths, and bond angles of the GTP ligand induced by the Ras-protein

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

27 July 2018

1 reference

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Early stages of energy transduction by myosin: roles of Arg in switch I, of Glu in switch II, and of the salt-bridge between them

27 July 2018

1 reference

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Escaping free-energy minima

27 July 2018

1 reference

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Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center

27 July 2018

1 reference

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Functional transitions in myosin: formation of a critical salt-bridge and transmission of effect to the sensitive tryptophan.

27 July 2018

1 reference

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The ATP synthase--a splendid molecular machine

27 July 2018

1 reference

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The structural basis of the myosin ATPase activity

27 July 2018

1 reference

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X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution

27 July 2018

1 reference

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

27 July 2018

1 reference

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Kinetic Analysis of ATPase Mechanisms

27 July 2018

1 reference

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Oxygen exchange in the gamma-phosphoryl group of protein-bound ATP during Mg2+-dependent adenosine triphosphatase activity of myosin

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Comparing the catalytic strategy of ATP hydrolysis in biomolecular motors.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase".

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Destruction of chemical warfare agents using metal-organic frameworks.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Comparative laboratory evolution of ordered and disordered enzymes.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Extreme electric fields power catalysis in the active site of ketosteroid isomerase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Unraveling the mystery of ATP hydrolysis in actin filaments

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

What vibrations tell us about GTPases

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Catalytic strategy used by the myosin motor to hydrolyze ATP.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency?

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

All-atom empirical potential for molecular modeling and dynamics studies of proteins

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Density functional tight binding: values of semi-empirical methods in an ab initio era.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Computer aided enzyme design and catalytic concepts

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Proton-coupled electron transfer in molecular electrocatalysis: theoretical methods and design principles

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Quantitative exploration of the molecular origin of the activation of GTPase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Stabilization of the ADP/metaphosphate intermediate during ATP hydrolysis in pre-power stroke myosin: quantitative anatomy of an enzyme

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Phosphate release coupled to rotary motion of F1-ATPase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Design of protein catalysts

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single-molecule observations.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

High-speed atomic force microscopy reveals rotary catalysis of rotorless F₁-ATPase.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Enzyme promiscuity: evolutionary and mechanistic aspects.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Enzymatic mechanisms of phosphate and sulfate transfer.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

String method in collective variables: minimum free energy paths and isocommittor surfaces.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Biomolecular motors: the F1-ATPase paradigm

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

On the Mechanism of ATP Hydrolysis in F1-ATPase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Kinetic resolution of a conformational transition and the ATP hydrolysis step using relaxation methods with a Dictyostelium myosin II mutant containing a single tryptophan residue

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

The physics of molecular motors

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

A myosin II mutation uncouples ATPase activity from motility and shortens step size.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

The rotary machine in the cell, ATP synthase

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Dynamically controlled protein tunneling paths in photosynthetic reaction centers

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

X-ray structures of the apo and MgATP-bound states of Dictyostelium discoideum myosin motor domain

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

How does GAP catalyze the GTPase reaction of Ras? A computer simulation study

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Structural mechanism of muscle contraction.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Catalytic promiscuity and the evolution of new enzymatic activities

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

The proton inventory technique.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

Mechanism of adenosine triphosphate hydrolysis by actomyosin

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5705175

A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method

14 August 2018

1 reference

12 December 2020

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme

1 reference

12 December 2020

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

1 reference

12 December 2020

pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications

1 reference

12 December 2020

Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke

1 reference

12 December 2020

Muscle contraction and free energy transduction in biological systems

1 reference

12 December 2020

Electronic design criteria for O-O bond formation via metal-oxo complexes

1 reference

12 December 2020

The hydrolysis of gamma-phenylpropyl di- and triphosphates

1 reference

12 December 2020

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

1 reference

12 December 2020

The mechanism of ATP hydrolysis catalyzed by myosin and actomyosin, using rapid reaction techniques to study oxygen exchange

1 reference

12 December 2020

10.1021/ACS.BIOCHEM.7B00016

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28225609%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

PubMed publication ID

28225609

1 reference