Factors that determine the variation of equilibrium and kinetic properties of QM/MM enzyme simulations: QM region, conformation, and boundary condition
D Demapan, J Kussmann… - Journal of chemical …, 2022 - ACS Publications
To analyze the impact of various technical details on the results of quantum mechanical
(QM)/molecular mechanical (MM) enzyme simulations, including the QM region size …
(QM)/molecular mechanical (MM) enzyme simulations, including the QM region size …
Quantum mechanical description of electrostatics provides a unified picture of catalytic action across methyltransferases
Methyl transferases (MTases) are a well-studied class of enzymes for which competing
enzymatic enhancement mechanisms have been suggested, ranging from structural methyl …
enzymatic enhancement mechanisms have been suggested, ranging from structural methyl …
Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study
To accurately simulate the inner workings of an enzyme active site with quantum mechanics
(QM), not only must the reactive species be included in the model but also important …
(QM), not only must the reactive species be included in the model but also important …
Covalent Adduct Formation as a Strategy for Efficient CO2 Fixation in Crotonyl-CoA Carboxylases/Reductases
Increasing levels of CO2 in the atmosphere have led to a growing interest into the various
ways nature transforms this greenhouse gas into valuable organic compounds. Crotonyl …
ways nature transforms this greenhouse gas into valuable organic compounds. Crotonyl …
Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol O-methyltransferase reaction
Human catechol O-methyltransferase (COMT) has emerged as a model for understanding
enzyme-catalyzed methyl transfer from S-adenosylmethionine (AdoMet) to small-molecule …
enzyme-catalyzed methyl transfer from S-adenosylmethionine (AdoMet) to small-molecule …
How a Second Mg2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study
Mg2+ ions are essential for the proper functioning of protein kinases, and their roles in
kinase activity have been studied for years. However, recent investigations have shed light …
kinase activity have been studied for years. However, recent investigations have shed light …
Examining the origin of catalytic power of catechol O-methyltransferase
X Chen, SD Schwartz - ACS catalysis, 2019 - ACS Publications
For decades, there has been debate regarding the origin of the catalytic power of enzymes.
In this work, we use the approach of computational chemistry to study the enzyme catechol …
In this work, we use the approach of computational chemistry to study the enzyme catechol …
Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most
abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is …
abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is …
[图书][B] The Design and Application of Enzyme Inter-residue Interaction Networks Towards Quantum Mechanical Modeling
TJ Summers - 2021 - search.proquest.com
In order to accurately simulate the inner workings of an enzyme active site with quantum
mechanics (QM), not only must the reactive species be included in the model, but also any …
mechanics (QM), not only must the reactive species be included in the model, but also any …
Towards a cheminformatic design for quantum mechanical enzyme models: the case of catechol-O-methyltransferase
The efficiency, accuracy, and replicability of enzyme simulations is often hampered by ad
hoc model design. To address this problem, we have developed the Residue Interaction …
hoc model design. To address this problem, we have developed the Residue Interaction …