Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Hydrogen tunneling links protein dynamics to enzyme catalysis

JP Klinman, A Kohen - Annual review of biochemistry, 2013 - annualreviews.org
The relationship between protein dynamics and function is a subject of considerable
contemporary interest. Although protein motions are frequently observed during ligand …

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 …

Protein dynamics and enzymatic catalysis

SD Schwartz - The Journal of Physical Chemistry B, 2023 - ACS Publications
This Perspective presents a review of our work and that of others in the highly controversial
topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in …

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

ZD Nagel, JP Klinman - Nature chemical biology, 2009 - nature.com
Despite the fact that the number of publications associated with the keyword'enzyme'
increases every year, the precise origin of enzyme catalysis has remained unresolved …

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 …

Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes

VL Schramm - Annual review of biochemistry, 2011 - annualreviews.org
Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects
(KIEs) to report on bonding and geometry differences between reactants and the transition …

Enzyme dynamics point to stepwise conformational selection in catalysis

B Ma, R Nussinov - Current opinion in chemical biology, 2010 - Elsevier
Recent data increasingly reveal that conformational dynamics are indispensable to enzyme
function throughout the catalytic cycle, in substrate recruiting, chemical transformation, and …

Transition states, analogues, and drug development

VL Schramm - ACS chemical biology, 2013 - ACS Publications
Enzymes achieve their transition states by dynamic conformational searches on the
femtosecond to picosecond time scale. Mimics of reactants at enzymatic transition states …

Dynamics and dissipation in enzyme catalysis

N Boekelheide, R Salomón-Ferrer… - Proceedings of the …, 2011 - National Acad Sciences
We use quantized molecular dynamics simulations to characterize the role of enzyme
vibrations in facilitating dihydrofolate reductase hydride transfer. By sampling the full …