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Electrostatic basis for enzyme catalysis

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title

Electrostatic basis for enzyme catalysis (English)

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1

Arieh Warshel

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author name string

Pankaz K Sharma

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2

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Mitsunori Kato

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3

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Yun Xiang

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4

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Hanbin Liu

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5

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Mats H M Olsson

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6

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language of work or name

English

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publication date

August 2006

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published in

Chemical Reviews

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volume

106

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page(s)

3210-35

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issue

8

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Enzymes do what is expected (chalcone isomerase versus chorismate mutase).

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Direct observation of substrate distortion by triosephosphate isomerase using Fourier transform infrared spectroscopy

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Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

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A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme

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Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase

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

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Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates

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A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase

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Insights into enzyme function from studies on mutants of dihydrofolate reductase

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Conformational substates modulate hydride transfer in dihydrofolate reductase.

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Theoretical Perspectives on the Reaction Mechanism of Serine Proteases: The Reaction Free Energy Profiles of the Acylation Process

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Mechanism of peptide bond synthesis on the ribosome

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Low-barrier hydrogen bonds and enzymic catalysis

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Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution

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11 October 2022

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Collective protein dynamics in relation to function

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Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

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Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.

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Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases

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Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization

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The burden borne by urease.

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Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study

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Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds

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11 October 2022

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Role of enzyme-ribofuranosyl contacts in the ground state and transition state for orotidine 5'-phosphate decarboxylase: a role for substrate destabilization?

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Enzyme dynamics during catalysis

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The low barrier hydrogen bond in enzymatic catalysis.

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Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase

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11 October 2022

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Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase

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The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis

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Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction

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Quantum mechanical methods for enzyme kinetics

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11 October 2022

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Combined effects of two mutations of catalytic residues on the ketosteroid isomerase reaction

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Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis

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

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Evidence that cobalt-carbon bond homolysis is coupled to hydrogen atom abstraction from substrate in methylmalonyl-CoA mutase

1 reference

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Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.

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What are the dielectric "constants" of proteins and how to validate electrostatic models?

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Enzymatic H-transfer requires vibration-driven extreme tunneling

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Intrinsic dynamics of an enzyme underlies catalysis

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11 October 2022

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Site-directed mutagenesis shows that tyrosine 248 of carboxypeptidase A does not play a crucial role in catalysis

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11 October 2022

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Calculations of electrostatic interactions in biological systems and in solutions

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Structural bases of stability-function tradeoffs in enzymes

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Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes.

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A new concept for the mechanism of action of chymotrypsin: the role of the low-barrier hydrogen bond

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Binding Energy and Catalysis: The Implications for Transition-State Analogs and Catalytic Antibodies.

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Evaluation of catalytic free energies in genetically modified proteins

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11 October 2022

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Engineering subtilisin BPN' for site-specific proteolysis.

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Separation of factors responsible for lysozyme catalysis

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Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion

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The depth of chemical time and the power of enzymes as catalysts.

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11 October 2022

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Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

1 reference

11 October 2022

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Enzymatic transition states: thermodynamics, dynamics and analogue design

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11 October 2022

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Crystallographic studies of the activity of hen egg-white lysozyme

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Evaluation of the internal equilibrium constant for 3-oxo-delta 5-steroid isomerase using the D38E and D38N mutants: the energetic basis for catalysis

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1 reference

11 October 2022

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Critical analysis of antibody catalysis.

1 reference

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Quantum Dynamics of Hydride Transfer in Enzyme Catalysis

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11 October 2022

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Selective chemical catalysis by an antibody

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11 October 2022

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1 reference

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The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases

1 reference

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A QM/MM Exploration of the Potential Energy Surface of Pyruvate to Lactate Transformation Catalyzed by LDH. Improving the Accuracy of Semiempirical Descriptions

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

1 reference

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A relationship between protein stability and protein function

1 reference

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Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor"

1 reference

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Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction

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Dynamics of proteins: elements and function

1 reference

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Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin

1 reference

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Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect

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Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase.

1 reference

11 October 2022

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How much do enzymes really gain by restraining their reacting fragments?

1 reference

11 October 2022

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Effect of mutation on enzyme motion in dihydrofolate reductase

1 reference

11 October 2022

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Catalytic acceleration of reactions by enzymes. Effect of screening of a polar medium by a protein globule

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Quantum chemical studies of radical-containing enzymes

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11 October 2022

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Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant

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11 October 2022

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Hydrophobic interactions via mutants of Escherichia coli dihydrofolate reductase: separation of binding and catalysis.

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11 October 2022

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NMR chemical shifts in the low-pH form of a-chymotrypsin. A QM/MM and ONIOM-NMR study

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11 October 2022

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Serine Proteases: Structure and Mechanism of Catalysis

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11 October 2022

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Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway

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What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations

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Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Solvation, reorganization energy, and biological catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Energetics of nucleophile activation in a protein tyrosine phosphatase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Prediction of functionally important residues based solely on the computed energetics of protein structure.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

A mechanism for rotamase catalysis by the FK506 binding protein (FKBP)

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Dynamics of biochemical and biophysical reactions: insight from computer simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Electrostatic control of GTP and GDP binding in the oncoprotein p21ras

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Catalytic proficiency: the unusual case of OMP decarboxylase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

A low-barrier hydrogen bond in the catalytic triad of serine proteases

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Computational modeling of the catalytic reaction in triosephosphate isomerase.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Combinedab initioand Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Characterization of Low-Barrier Hydrogen Bonds. 5. Microsolvation of Enol-Enolate. An ab Initio and DFT Investigation

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Synthesis and evaluation of a model for the so-called "charge-relay" system of the serine esterases

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Structure, dynamics, and catalytic function of dihydrofolate reductase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Network of coupled promoting motions in enzyme catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

Hydrogen tunneling in biology

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/CR0503106

(Q28256502)

Electrostatic basis for enzyme catalysis

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