Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
Quantum mechanics/molecular mechanics (QM/MM) methods offer a very appealing option
for the computational study of enzymatic reaction mechanisms, by separating the problem …
for the computational study of enzymatic reaction mechanisms, by separating the problem …
Modelling enzymatic mechanisms with QM/MM approaches: current status and future challenges
RP Magalhães, HS Fernandes… - Israel Journal of …, 2020 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐
established alternative for the study of enzymatic reaction mechanisms. They enable the …
established alternative for the study of enzymatic reaction mechanisms. They enable the …
Infrared spectroscopy of phenylalanine Ag (I) and Zn (II) complexes in the gas phase
Infrared multiple-photon dissociation (IR-MPD) spectroscopy has been applied to singly-
charged complexes involving the transition metals Ag+ and Zn2+ with the aromatic amino …
charged complexes involving the transition metals Ag+ and Zn2+ with the aromatic amino …
Computational enzymatic catalysis
Computational methodologies are playing increasingly important roles in elucidating and
presenting the complete and detailed mechanisms of enzymatic reactions because of their …
presenting the complete and detailed mechanisms of enzymatic reactions because of their …
A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions
R Wu, S Wang, N Zhou, Z Cao… - Journal of the American …, 2010 - ACS Publications
Zinc-dependent histone deacetylase 8 (HDAC8) catalyzes the removal of acetyl moieties
from histone tails, and is critically involved in regulating chromatin structure and gene …
from histone tails, and is critically involved in regulating chromatin structure and gene …
The carboxylate shift in zinc enzymes: A computational study
Zinc is the second most abundant transition element in biology and the only metal known to
be represented in enzymes from each one of the six classes established by the International …
be represented in enzymes from each one of the six classes established by the International …
Farnesyltransferase inhibitors: a detailed chemical view on an elusive biological problem
Farnesyltransferase (FTase) is a zinc enzyme that has been the subject of particular
attention in anti-cancer research. This enzyme promotes the addition of a farnesyl group …
attention in anti-cancer research. This enzyme promotes the addition of a farnesyl group …
Systematic derivation of AMBER force field parameters applicable to zinc-containing systems
F Lin, R Wang - Journal of chemical theory and computation, 2010 - ACS Publications
Metal ions are indispensable for maintaining the structural stability and catalytic activity of
metalloproteins. Molecular modeling studies of such proteins with force fields, however, are …
metalloproteins. Molecular modeling studies of such proteins with force fields, however, are …
Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel
It is of significant biological interest and medical importance to develop class-and isoform-
selective histone deacetylase (HDAC) modulators. The impact of the linker component on …
selective histone deacetylase (HDAC) modulators. The impact of the linker component on …
Intracellular zinc elevation measured with a “calcium-specific” indicator during ischemia and reperfusion in rat hippocampus: a question on calcium overload
CJ Stork, YV Li - Journal of Neuroscience, 2006 - Soc Neuroscience
Much of our current evidence concerning of the role of calcium (Ca2+) as a second
messenger comes from its interaction with fluorescent probes; however, many Ca2+ probes …
messenger comes from its interaction with fluorescent probes; however, many Ca2+ probes …