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

A Warshel, RP Bora - The Journal of chemical physics, 2016 - pubs.aip.org
Enzymes control chemical reactions that are key to life processes, and allow them to take
place on the time scale needed for synchronization between the relevant reaction cycles. In …

Promoting vibrations and the function of enzymes. Emerging theoretical and experimental convergence

VL Schramm, SD Schwartz - Biochemistry, 2018 - ACS Publications
A complete understanding of enzyme catalysis requires knowledge of both transition state
features and the detailed motions of atoms that cause reactant molecules to form and …

Chemical kinetics and mechanisms of complex systems: A perspective on recent theoretical advances

SJ Klippenstein, VS Pande… - Journal of the American …, 2014 - ACS Publications
This Perspective presents a personal overview of the current status of the theory of chemical
kinetics and mechanisms for complex processes. We attempt to assess the status of the field …

The role of dimer asymmetry and protomer dynamics in enzyme catalysis

TH Kim, P Mehrabi, Z Ren, A Sljoka, C Ing, A Bezginov… - Science, 2017 - science.org
INTRODUCTION Enzymes greatly accelerate biochemical reactions by providing a scaffold
to bind and recognize substrate, position catalytic units, and facilitate the formation of …

Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase

CT Liu, JP Layfield, RJ Stewart III… - Journal of the …, 2014 - ACS Publications
Electrostatic interactions play an important role in enzyme catalysis by guiding ligand
binding and facilitating chemical reactions. These electrostatic interactions are modulated by …

Transition state theory for enzyme kinetics

DG Truhlar - Archives of biochemistry and biophysics, 2015 - Elsevier
This article is an essay that discusses the concepts underlying the application of modern
transition state theory to reactions in enzymes. Issues covered include the potential of mean …

Understanding DNA under oxidative stress and sensitization: The role of molecular modeling

E Dumont, A Monari - Frontiers in chemistry, 2015 - frontiersin.org
DNA is constantly exposed to damaging threats coming from oxidative stress, ie, from the
presence of free radicals and reactive oxygen species. Sensitization from exogenous and …

Influence of monomer structures for polymeric multivalent ligands: consideration of the molecular mobility of glycopolymers

M Nagao, M Kichize, Y Hoshino, Y Miura - Biomacromolecules, 2021 - ACS Publications
Molecular mobility is important for interactions of biofunctional polymers with target
molecules. Monomer structures for synthetic biofunctional polymers are usually selected …

[HTML][HTML] Challenges in computational studies of enzyme structure, function and dynamics

ATP Carvalho, A Barrozo, D Doron, AV Kilshtain… - Journal of Molecular …, 2014 - Elsevier
In this review we give an overview of the field of Computational enzymology. We start by
describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel …

The importance of ensemble averaging in enzyme kinetics

L Masgrau, DG Truhlar - Accounts of chemical research, 2015 - ACS Publications
Conspectus The active site of an enzyme is surrounded by a fluctuating environment of
protein and solvent conformational states, and a realistic calculation of chemical reaction …