Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping (Q42682544)

4 November 2017

Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping (English)

1 reference

4 November 2017

3

Arieh Warshel

1 reference

4 November 2017

B Ram Prasad

1

1 reference

4 November 2017

Nikolay V Plotnikov

series ordinal

2

1 reference

4 November 2017

language of work or name

English

0 references

publication date

28 December 2012

1 reference

Journal of Physical Chemistry B

4 November 2017

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4 November 2017

117

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4 November 2017

1

1 reference

4 November 2017

153-163

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Why nature really chose phosphate

4 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Quantum and classical dynamics simulations of ATP hydrolysis in solution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Exploring, refining, and validating the paradynamics QM/MM sampling

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

The Role of Gln61 in HRas GTP hydrolysis: a quantum mechanics/molecular mechanics study.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

The Mechanism for Activation of GTP Hydrolysis on the Ribosome

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

What recent ribosome structures have revealed about the mechanism of translation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

The Crystal Structure of the Ribosome Bound to EF-Tu and Aminoacyl-tRNA

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

GTPase activation of elongation factor EF-Tu by the ribosome during decoding

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Enzymatic mechanisms of phosphate and sulfate transfer.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Transition state differences in hydrolysis reactions of alkyl versus aryl phosphate monoester monoanions.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Isotope effects in the study of phosphoryl and sulfuryl transfer reactions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

The Role of Metals in Enzyme-Catalyzed Substitutions at each of the Phosphorus Atoms of ATP

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

What we have learned from ribosome structures.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Mechanism of triphosphate hydrolysis in aqueous solution: QM/MM simulations in water clusters

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer?

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Theoretical Studies on the Hydrolysis of Mono-Phosphate and Tri-Phosphate in Gas Phase and Aqueous Solution

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Substitution of histidine-84 and the GTPase mechanism of elongation factor Tu.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Methyl Phosphate Dianion Hydrolysis in Solution Characterized by Path Collective Variables Coupled with DFT-Based Enhanced Sampling Simulations

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Density Functionals with Broad Applicability in Chemistry

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3542406

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

1 December 2018

1 reference

12 December 2020

Relevance of histidine-84 in the elongation factor Tu GTPase activity and in poly(Phe) synthesis: its substitution by glutamine and alanine

1 reference

12 December 2020

Minimum energy reaction profiles for ATP hydrolysis in myosin

1 reference

12 December 2020

Mechanistic insights into the hydrolysis of a nucleoside triphosphate model in neutral and acidic solution

1 reference

12 December 2020

The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA

1 reference

12 December 2020

Theoretical study of the importance of the spectator groups on the hydrolysis of phosphate triesters

1 reference

12 December 2020

Methyl Phosphate Dianion Hydrolysis in Solution Characterized by Path Collective Variables Coupled with DFT-Based Enhanced Sampling Simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP309778N

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP309778N

Density-functional thermochemistry. III. The role of exact exchange

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP309778N

Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP309778N

Identifiers

DOI

10.1021/JP309778N

1 reference

4 November 2017

1 reference

4 November 2017

PubMed publication ID

23198768

1 reference