Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

MW van der Kamp, AJ Mulholland - Biochemistry, 2013 - ACS Publications
Computational enzymology is a rapidly maturing field that is increasingly integral to
understanding mechanisms of enzyme-catalyzed reactions and their practical applications …

Recent advances in food biopeptides: Production, biological functionalities and therapeutic applications

S Saadi, N Saari, F Anwar, AA Hamid… - Biotechnology advances, 2015 - Elsevier
The growing momentum of several common life-style diseases such as myocardial
infarction, cardiovascular disorders, stroke, hypertension, diabetes, and atherosclerosis has …

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 …

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 …

Molecular Dynamics of Iron Porphyrin-Catalyzed C–H Hydroxylation of Ethylbenzene

Y Zhang, C Cao, Y She, YF Yang… - Journal of the American …, 2023 - ACS Publications
Quasi-classical molecular dynamics (MD) simulations were carried out to study the
mechanism of iron porphyrin-catalyzed hydroxylation of ethylbenzene. The hydrogen atom …

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

LYP Luk, J Javier Ruiz-Pernia… - Proceedings of the …, 2013 - National Acad Sciences
Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis,
but identification and analysis of dynamical effects in enzyme-catalyzed reactions have …

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 …

Protein dynamics and enzyme catalysis: insights from simulations

JD McGeagh, KE Ranaghan, AJ Mulholland - Biochimica et Biophysica …, 2011 - Elsevier
The role of protein dynamics in enzyme catalysis is one of the most active and controversial
areas in enzymology today. Some researchers claim that protein dynamics are at the heart …

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

JN Bandaria, S Dutta, MW Nydegger… - Proceedings of the …, 2010 - National Acad Sciences
The potential for femtosecond to picosecond time-scale motions to influence the rate of the
intrinsic chemical step in enzyme-catalyzed reactions is a source of significant controversy …

Temperature dependence of the kinetic isotope effects in thymidylate synthase. A theoretical study

N Kanaan, S Ferrer, S Marti… - Journal of the …, 2011 - ACS Publications
In recent years, the temperature dependence of primary kinetic isotope effects (KIE) has
been used as indicator for the physical nature of enzyme-catalyzed H-transfer reactions. An …