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 …

Enzyme-mediated oxidations for the chemist

F Hollmann, IWCE Arends, K Buehler, A Schallmey… - Green …, 2011 - pubs.rsc.org
Biocatalysis is an enabling technology adding to organic oxidation chemistry. Especially the
high selectivity of enzymatic oxidation coevally operating under mild conditions and not …

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 …

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 …

Molecular dynamics explorations of active site structure in designed and evolved enzymes

S Osuna, G Jimenez-Oses, EL Noey… - Accounts of chemical …, 2015 - ACS Publications
Conspectus This Account describes the use of molecular dynamics (MD) simulations to
reveal how mutations alter the structure and organization of enzyme active sites. As …

Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii

Q Guo, L Gakhar, K Wickersham, K Francis… - Biochemistry, 2016 - ACS Publications
The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic
and practical interests. First, this enzyme represents a unique model system for studies on …

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 …

Shuffling active site substate populations affects catalytic activity: the case of glucose oxidase

D Petrović, D Frank, SCL Kamerlin, K Hoffmann… - ACS …, 2017 - ACS Publications
Glucose oxidase has wide applications in the pharmaceutical, chemical, and food industries.
Many recent studies have enhanced key properties of this enzyme using directed evolution …

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 …

Increased Dynamic Effects in a Catalytically Compromised Variant of Escherichia coli Dihydrofolate Reductase

JJ Ruiz-Pernia, LYP Luk… - Journal of the …, 2013 - ACS Publications
Isotopic substitution (15N, 13C, 2H) of a catalytically compromised variant of Escherichia coli
dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of …