Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

K Nam, Y Shao, DT Major, M Wolf-Watz - ACS omega, 2024 - ACS Publications
Understanding enzyme mechanisms is essential for unraveling the complex molecular
machinery of life. In this review, we survey the field of computational enzymology …

Simple SPR-based colorimetric sensor to differentiate Mg2+ and Ca2+ in aqueous solutions

A Amirjani, K Salehi, SK Sadrnezhaad - Spectrochimica Acta Part A …, 2022 - Elsevier
L-tryptophan functionalized AgNPs were successfully fabricated using a one-pot synthesis
method and assessed as a colorimetric probe for rapid and accurate determination of Mg 2+ …

On the origins of enzymes: Phosphate-binding polypeptides mediate phosphoryl transfer to synthesize adenosine triphosphate

P Vyas, S Malitsky, M Itkin… - Journal of the American …, 2023 - ACS Publications
Reactions involving the transfer of a phosphoryl (− PO32–) group are fundamental to cellular
metabolism. These reactions are catalyzed by enzymes, often large and complex, belonging …

Simulation toolkits at the molecular scale for trans-scale thermal signaling

I Kurisaki, M Suzuki - Computational and Structural Biotechnology Journal, 2023 - Elsevier
Thermogenesis is a physiological activity of releasing heat that originates from intracellular
biochemical reactions. Recent experimental studies discovered that externally applied heat …

Covalent Adduct Formation as a Strategy for Efficient CO2 Fixation in Crotonyl-CoA Carboxylases/Reductases

R Recabarren, M Tinzl, DA Saez, A Gomez, TJ Erb… - ACS …, 2023 - ACS Publications
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 …

Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ

ST Nicolaou, S Kannan, J Warwicker… - Proteins: Structure …, 2022 - Wiley Online Library
The N‐terminal transactivation domain (TAD) of p53 is a disordered region with multiple
phosphorylation sites. Phosphorylation at Thr18 is crucial for the release of p53 from its …

Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation

A Gomez, TJ Erb, H Grubmüller… - Journal of Chemical …, 2023 - ACS Publications
Crotonyl-CoA carboxylase/reductase (Ccr) is one of the fastest CO2 fixing enzymes and has
become part of efficient artificial CO2-fixation pathways in vitro, paving the way for future …

Mechanism of triphosphate hydrolysis by human MAT2A at 1.07 Å resolution

A Ghosh, CN Niland, SM Cahill… - Journal of the …, 2021 - ACS Publications
Human methionine adenosyltransferase MAT2A provides S-adenosyl-l-methionine
(AdoMet) for methyl-transfer reactions. Epigenetic methylations influence expression …

Simultaneous formation of P–C/P–O-cage phosphoranes in the reaction of 2-[(2-methylcarbonyl) phenyloxy]-4, 4, 5, 5-tetramethyl-1, 3, 2-dioxaphospholane with …

VF Mironov, MN Dimukhametov, IA Litvinov… - Mendeleev …, 2022 - Elsevier
Abstract Reaction of 2-[(2-methylcarbonyl) phenyloxy]-4, 4, 5, 5-tetra-methyl-1, 3, 2-
dioxaphospholane with hexafluoroacetone leads to the simultaneous formation of two P …

Developing Computational Methods to Understand the Biology of Charge Interactions in Intrinsically Disordered Proteins

ST Nicolaou - 2023 - search.proquest.com
Intrinsically disordered proteins (IDPs) are proteins that lack well-defined three-dimensional
structures and instead exist as dynamic ensembles of conformations. Post-translational …