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

SCL Kamerlin, A Warshel - Proteins: Structure, Function, and …, 2010 - Wiley Online Library
Enzymes play a key role in almost all biological processes, accelerating a variety of
metabolic reactions as well as controlling energy transduction, the transcription, and …

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 …

An NMR perspective on enzyme dynamics

DD Boehr, HJ Dyson, PE Wright - Chemical reviews, 2006 - ACS Publications
Enzyme catalysis is an inherently dynamic process. Binding and release of ligands is often
accompanied by conformational changes, both subtle and dramatic (reviewed more …

Good vibrations in enzyme-catalysed reactions

S Hay, NS Scrutton - Nature chemistry, 2012 - nature.com
Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-
catalysed reactions have ignited considerable interest in recent years. Their influence on …

QM/MM methods for biological systems

HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …

Site-specific solvation of the photoexcited protochlorophyllide a in methanol: formation of the hydrogen-bonded intermediate state induced by hydrogen-bond …

GJ Zhao, KL Han - Biophysical journal, 2008 - cell.com
The site-specific solvation of the photoexcited protochlorophyllide a (Pchlide a) in methanol
solvent was investigated using the time-dependent density functional theory method for the …

Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions

J Pu, J Gao, DG Truhlar - Chemical reviews, 2006 - ACS Publications
Although many aspects of enzyme catalysis have been constructively analyzed, 1-52 there
are still many aspects that are imperfectly understood. Of particular interest in this regard are …

Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis

MHM Olsson, WW Parson, A Warshel - Chemical Reviews, 2006 - ACS Publications
Enzymes play fundamental roles in almost all life processes. They accelerate a great variety
of metabolic reactions and they control signaling, energy transduction, and transcription and …

Enzymatic transition states and dynamic motion in barrier crossing

SD Schwartz, VL Schramm - Nature chemical biology, 2009 - nature.com
What are the atomic motions at enzymatic catalytic sites on the timescale of chemical
change? Combined experimental and computational chemistry approaches take advantage …

Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity

E Karvelis, C Swanson, B Tidor - ACS catalysis, 2024 - ACS Publications
The task of adapting enzymes for specific applications is often hampered by our incomplete
ability to tune and tailor catalytic functions, particularly when seeking increased activity …