Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step

(2015) Iñaki Tuñón et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness

(2015) Arren Bar-Even et al.   BIOCHEMISTRY

Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

(2015) Moshe Ben-David et al.   JOURNAL OF MOLECULAR BIOLOGY

Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition

(2015) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily

(2015) Alexandre Barrozo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mediation of donor–acceptor distance in an enzymatic methyl transfer reaction

(2015) Jianyu Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The entropic contributions in vitamin B12enzymes still reflect the electrostatic paradigm

(2015) Patrick Schopf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

(2015) Jeronimo Lameira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Network of Remote and Local Protein Dynamics in Dihydrofolate Reductase Catalysis

(2015) Priyanka Singh et al.   ACS Catalysis

Role of Dynamics in Enzyme Catalysis: Substantial versus Semantic Controversies

(2014) Amnon Kohen   ACCOUNTS OF CHEMICAL RESEARCH

Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)

(2014) Arieh Warshel   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Maintenance of Native-like Protein Dynamics May Not Be Required for Engineering Functional Proteins

(2014) Sophie M.C. Gobeil et al.   CHEMISTRY & BIOLOGY

Enzyme Dynamics and Engineering: One Step at a Time

(2014) Nobuhiko Tokuriki et al.   CHEMISTRY & BIOLOGY

Computer aided enzyme design and catalytic concepts

(2014) Maria P Frushicheva et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2014) Stephen D. Fried et al.   SCIENCE

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

(2014) Geir Villy Isaksen et al.   PLoS Computational Biology

Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis

(2013) Judith P. Klinman et al.   Annual Review of Biochemistry

Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase

(2013) Yao Fan et al.   BIOCHEMISTRY

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

(2013) Rafael García-Meseguer et al.   Nature Chemistry

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

(2013) L. Y. P. Luk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling

(2012) Nikolay V. Plotnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evidence that a ‘dynamic knockout’ in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis

(2012) E. Joel Loveridge et al.   Nature Chemistry

Good vibrations in enzyme-catalysed reactions

(2012) Sam Hay et al.   Nature Chemistry

Taking Ockham's razor to enzyme dynamics and catalysis

(2012) David R. Glowacki et al.   Nature Chemistry

Resolving the complex role of enzyme conformational dynamics in catalytic function

(2012) U. Doshi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

(2012) B. Ram Prasad et al.   THEORETICAL CHEMISTRY ACCOUNTS

Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

Enzymatic Methyl Transfer: Role of an Active Site Residue in Generating Active Site Compaction That Correlates with Catalytic Efficiency

(2011) Jianyu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiscale modeling of biological functions

(2011) Shina Caroline Lynn Kamerlin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Olfaction is a chemical sense, not a spectral sense

(2011) T. P. Hettinger   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular vibration-sensing component inDrosophila melanogasterolfaction

(2011) Maria Isabel Franco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

(2011) A. J. Adamczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics and dissipation in enzyme catalysis

(2011) N. Boekelheide et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prechemistry versus preorganization in DNA replication fidelity

(2011) B. Ram Prasad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

Barrier Compression and Its Contribution to Both Classical and Quantum Mechanical Aspects of Enzyme Catalysis

(2010) Sam Hay et al.   BIOPHYSICAL JOURNAL

ENZYMES’ MANY MOVEMENTS

(2010) CELIA HENRY ARNAUD   CHEMICAL & ENGINEERING NEWS

Choreographing an enzyme's dance

(2010) Janice Villali et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Conformational diversity and computational enzyme design

(2010) Jonathan K Lassila   CURRENT OPINION IN CHEMICAL BIOLOGY

Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues

(2010) Shina Caroline Lynn Kamerlin et al.   FEBS LETTERS

Transition-State Theory, Dynamics, and Narrow Time Scale Separation in the Rate-Promoting Vibrations Model of Enzyme Catalysis

(2010) Baron Peters   Journal of Chemical Theory and Computation

An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunneling

(2010) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL ORGANIC CHEMISTRY

Dynamics connect substrate recognition to catalysis in protein kinase A

(2010) Larry R Masterson et al.   Nature Chemical Biology

Reply to Karplus: Conformational dynamics have no role in the chemical step

(2010) Shina C. L. Kamerlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) M. P. Frushicheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

An integrated model for enzyme catalysis emerges from studies of hydrogen tunneling

(2009) Judith P. Klinman   CHEMICAL PHYSICS LETTERS

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

(2009) Shina C. L. Kamerlin et al.   FARADAY DISCUSSIONS

A 21st century revisionist's view at a turning point in enzymology

(2009) Zachary D Nagel et al.   Nature Chemical Biology

Enzyme millisecond conformational dynamics do not catalyze the chemical step

(2009) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

(2009) D. T. Major et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

(2009) Shina C. L. Kamerlin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Free-Energy Landscape of Enzyme Catalysis†

(2008) Stephen J. Benkovic et al.   BIOCHEMISTRY

Remote Mutations and Active Site Dynamics Correlate with Catalytic Properties of Purine Nucleoside Phosphorylase

(2008) Suwipa Saen-Oon et al.   BIOPHYSICAL JOURNAL

Molecular simulations of protein dynamics: new windows on mechanisms in biology

(2008) Guy G Dodson et al.   EMBO REPORTS

Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method

(2008) Masahiro Higashi et al.   Journal of Chemical Theory and Computation

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Experimental Evidence for Hydrogen Tunneling when the Isotopic Arrhenius Prefactor (AH/AD) is Unity

(2008) Sudhir C. Sharma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex

(2008) S. Kale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the relationship between folding and chemical landscapes in enzyme catalysis

(2008) M. Roca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction:  Effects of Protein Conformational Dynamics on Enzyme Catalysis†

(2007) Wei Min et al.   JOURNAL OF PHYSICAL CHEMISTRY B