Simulating enzyme reactions: challenges and perspectives (Q40650848)

22 September 2017

Simulating enzyme reactions: challenges and perspectives (English)

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22 September 2017

Martin J Field

1

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22 September 2017

1 January 2002

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Journal of Computational Chemistry

22 September 2017

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22 September 2017

23

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22 September 2017

48-58

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22 September 2017

1

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So do we understand how enzymes work?

22 September 2017

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Chemical basis for enzyme catalysis

21 January 2018

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Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions

21 January 2018

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The low barrier hydrogen bond in enzymatic catalysis.

21 January 2018

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

21 January 2018

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Computer simulations of enzyme catalysis: finding out what has been optimized by evolution.

21 January 2018

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A perspective on biological catalysis

21 January 2018

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

21 January 2018

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How important are entropic contributions to enzyme catalysis?

21 January 2018

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A relationship between protein stability and protein function

21 January 2018

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Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

21 January 2018

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Ground states of molecules. 38. The MNDO method. Approximations and parameters

21 January 2018

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Optimization of parameters for semiempirical methods I. Method

21 January 2018

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Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

21 January 2018

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Macromolecular electrostatics: continuum models and their growing pains

21 January 2018

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

21 January 2018

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

21 January 2018

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A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

21 January 2018

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Calculations of electrostatic interactions in biological systems and in solutions

21 January 2018

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Reaction coordinates of biomolecular isomerization

21 January 2018

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21 January 2018

Computational enzymology

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Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities

21 January 2018

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Theozymes and compuzymes: theoretical models for biological catalysis

21 January 2018

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QM−FE and Molecular Dynamics Calculations on CatecholO-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction

21 January 2018

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A hybrid potential reaction path and free energy study of the chorismate mutase reaction

21 January 2018

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The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

21 January 2018

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Active site dynamics of the HhaI methyltransferase: insights from computer simulation

21 January 2018

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

21 January 2018

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

21 January 2018

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Computational modeling of the rate limiting step in low molecular weight protein tyrosine phosphatase.

21 January 2018

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

21 January 2018

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

21 January 2018

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Design of fast enzymes by optimizing interaction potential in active site.

21 January 2018

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21 January 2018

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The structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase

21 January 2018

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On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions

21 January 2018

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On low-barrier hydrogen bonds and enzyme catalysis.

21 January 2018

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

21 January 2018

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Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution

21 January 2018

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Density functional theory of biologically relevant metal centers.

21 January 2018

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Enzyme catalysis: over-the-barrier or through-the-barrier?

21 January 2018

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New insights into enzyme catalysis. Ground state tunnelling driven by protein dynamics

21 January 2018

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Hydrogen tunneling in biology

21 January 2018

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Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids

21 January 2018

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Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).

21 January 2018

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Recent advances in structure-based rational drug design.

21 January 2018

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Tailoring new enzyme functions by rational redesign

21 January 2018

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Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results

21 January 2018

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Beyond the MNDO model: Methodical considerations and numerical results

21 January 2018

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Orthogonalization corrections for semiempirical methods

21 January 2018

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Parameterization of NDDO wavefunctions using genetic algorithms. An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic reactions

21 January 2018

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Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions

21 January 2018

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Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods

21 January 2018

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Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

21 January 2018

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Solvent Dynamics and Mechanism of Proton Transfer in Human Carbonic Anhydrase II

21 January 2018

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Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction

21 January 2018

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Quantum Dynamics of Hydride Transfer in Enzyme Catalysis

21 January 2018

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Molecular Dynamics Simulations of Ground and Transition States for the Hydride Transfer from Formate to NAD+in the Active Site of Formate Dehydrogenase

21 January 2018

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Characterization of the Short Strong Hydrogen Bond in Benzoylacetone by ab Initio Calculations and Accurate Diffraction Experiments. Implications for the Electronic Nature of Low-Barrier Hydrogen Bonds in Enzymatic Reactions

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/JCC.1156

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22 September 2017

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DBLP Dataset 2021-01-02

28 January 2021

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PubMed ID

11913389