(Q43537248)

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On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

scientific article published on 29 February 2008

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scholarly article

1 reference

Europe PubMed Central

24 November 2017

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution (English)

1 reference

Europe PubMed Central

24 November 2017

Shina Caroline Lynn Kamerlin

2

1 reference

Europe PubMed Central

24 November 2017

object named as

Edina Rosta

1

0 references

3

object named as

Arieh Warshel

1 reference

Europe PubMed Central

24 November 2017

language of work or name

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publication date

29 February 2008

1 reference

Europe PubMed Central

24 November 2017

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Europe PubMed Central

24 November 2017

47

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Europe PubMed Central

24 November 2017

12

1 reference

Europe PubMed Central

24 November 2017

3725-3735

1 reference

Europe PubMed Central

24 November 2017

Why does the Ras switch "break" by oncogenic mutations?

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A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases

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The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors

1 reference

11 October 2022

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Mechanistic analysis of the observed linear free energy relationships in p21ras and related systems.

1 reference

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Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes

1 reference

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

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Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP

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A primer for the Bema Hapothle. An empirical approach to the characterization of changing transition-state structures

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Energy analysis of chemistry for correct insertion by DNA polymerase beta

1 reference

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Probing the structure and mechanism of Ras protein with an expanded genetic code

1 reference

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Examination of P-OR bridging bond orders in phosphate monoesters using (18)O isotope shifts in 31P NMR.

1 reference

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Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

1 reference

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Structural and catalytic similarities between nucleotide pyrophosphatases/phosphodiesterases and alkaline phosphatases

1 reference

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Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?

1 reference

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On the mechanism of guanosine triphosphate hydrolysis in ras p21 proteins

1 reference

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Linear free energy relationships in the intrinsic and GTPase activating protein-stimulated guanosine 5'-triphosphate hydrolysis of p21ras.

1 reference

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

1 reference

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Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

1 reference

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

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11 October 2022

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Transition State Analogues for Nucleotidyl Transfer Reactions: Structure and Stability of Pentavalent Vanadate and Phosphate Ester Dianions

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How important are entropic contributions to enzyme catalysis?

1 reference

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Structural analysis of inositol monophosphatase complexes with substrates

1 reference

11 October 2022

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Enzymatic mechanisms of phosphate and sulfate transfer.

1 reference

11 October 2022

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Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis

1 reference

11 October 2022

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Supermolecule density functional calculations suggest a key role for solvent in alkaline hydrolysis of p-nitrophenyl phosphate.

1 reference

11 October 2022

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The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level

1 reference

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Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases

1 reference

11 October 2022

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Parameters for the Description of Transition States

1 reference

11 October 2022

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Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase

1 reference

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Conserved core structure and active site residues in alkaline phosphatase superfamily enzymes

1 reference

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Monoalkyl sulfates as alkylating agents in water, alkylsulfatase rate enhancements, and the "energy-rich" nature of sulfate half-esters

1 reference

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A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

1 reference

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

1 reference

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Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta

1 reference

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

1 reference

11 October 2022

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Theoretical studies of the hydroxide-catalyzed P-O cleavage reactions of neutral phosphate triesters and diesters in aqueous solution: examination of the changes induced by H/Me substitution

1 reference

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Ras-catalyzed hydrolysis of GTP: a new perspective from model studies

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Eukaryotic DNA Polymerases

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

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

1 reference

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Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

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

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Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-.

1 reference

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Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis

1 reference

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The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphorothioates by alkaline phosphatase

1 reference

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Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins.

1 reference

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Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis

1 reference

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On the calculation of absolute macromolecular binding free energies

1 reference

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New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution

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Why have mutagenesis studies not located the general base in ras p21.

1 reference

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1 reference

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Structure and mechanism of alkaline phosphatase

1 reference

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Theoretical evaluation of the substrate-assisted catalysis mechanism for the hydrolysis of phosphate monoester dianions

1 reference

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The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA

1 reference

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Reactivity of Phosphate Diesters Doubly Coordinated to a Dinuclear Cobalt(III) Complex: Dependence of the Reactivity on the Basicity of the Leaving Group

1 reference

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The role of metal ions in phosphate ester hydrolysis.

1 reference

11 October 2022

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Mutation of Arg-166 of Alkaline Phosphatase Alters the Thio Effect but Not the Transition State for Phosphoryl Transfer. Implications for the Interpretation of Thio Effects in Reactions of Phosphatases†

1 reference

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The Protein Data Bank

1 reference

11 October 2022

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Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: evidence for a loose transition state

1 reference

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

1 reference

11 October 2022

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Identifiers

10.1021/BI702106M

1 reference

Europe PubMed Central

24 November 2017

1 reference

Europe PubMed Central

24 November 2017

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