Computational Study of the Ground State of Thermophilic Indole Glycerol Phosphate Synthase:  Structural Alterations at the Active Site with Temperature

2004 ◽  
Vol 126 (19) ◽  
pp. 5936-5937 ◽  
Author(s):  
Devleena Mazumder-Shivakumar ◽  
Kalju Kahn ◽  
Thomas C. Bruice
Keyword(s):  
Ground State ◽  
Active Site ◽  
Computational Study ◽  
Glycerol Phosphate ◽  
Structural Alterations ◽  
Phosphate Synthase

Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase

Biochemistry ◽  
2018 ◽  
Vol 57 (23) ◽  
pp. 3265-3277 ◽  
Author(s):  
Sandra Schlee ◽  
Thomas Klein ◽  
Magdalena Schumacher ◽  
Julian Nazet ◽  
Rainer Merkl ◽  
...  
Keyword(s):  
Active Site ◽  
Glycerol Phosphate ◽  
Loop Dynamics ◽  
Relationship Of ◽  
Phosphate Synthase

scholarly journals Controlling Active Site Loop Dynamics in the (β/α)8 Barrel Enzyme Indole-3-Glycerol Phosphate Synthase

Catalysts ◽  
2016 ◽  
Vol 6 (9) ◽  
pp. 129 ◽  
Author(s):  
Kathleen O’Rourke ◽  
Aneta Jelowicki ◽  
David Boehr
Keyword(s):  
Active Site ◽  
Glycerol Phosphate ◽  
Loop Dynamics ◽  
Phosphate Synthase

Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome

2020 ◽  
Author(s):  
Jon Uranga ◽  
Lukas Hasecke ◽  
Jonny Proppe ◽  
Jan Fingerhut ◽  
Ricardo A. Mata
Keyword(s):  
Active Site ◽  
Boronic Acid ◽  
Computational Study ◽  
Ubiquitin Proteasome System ◽  
Bayesian Optimization ◽  
Inhibition Mechanism ◽  
20S Proteasome ◽  
Acid Base ◽  
Ubiquitin Proteasome ◽  
Infection Cycles

The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor.

scholarly journals Photoprotective Properties of Eumelanin: Computational Insights into the Photophysics of a Catechol:Quinone Heterodimer Model System

Photochem ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 26-37
Author(s):  
Victoria C. Frederick ◽  
Thomas A. Ashy ◽  
Barbara Marchetti ◽  
Michael N. R. Ashfold ◽  
Tolga N. V. Karsili
Keyword(s):  
Ground State ◽  
Sandwich Structure ◽  
Computational Study ◽  
Minimum Energy ◽  
Carbonyl Oxygen ◽  
Model System ◽  
Molecular Structures ◽  
Uv Damage ◽  
Chromosomal Dna ◽  
Relevant Model

Melanins are skin-centered molecular structures that block harmful UV radiation from the sun and help protect chromosomal DNA from UV damage. Understanding the photodynamics of the chromophores that make up eumelanin is therefore paramount. This manuscript presents a multi-reference computational study of the mechanisms responsible for the experimentally observed photostability of a melanin-relevant model heterodimer comprising a catechol (C)–benzoquinone (Q) pair. The present results validate a recently proposed photoinduced intermolecular transfer of an H atom from an OH moiety of C to a carbonyl-oxygen atom of the Q. Photoexcitation of the ground state C:Q heterodimer (which has a π-stacked “sandwich” structure) results in population of a locally excited ππ* state (on Q), which develops increasing charge-transfer (biradical) character as it evolves to a “hinged” minimum energy geometry and drives proton transfer (i.e., net H atom transfer) from C to Q. The study provides further insights into excited state decay mechanisms that could contribute to the photostability afforded by the bulk polymeric structure of eumelanin.

Identification of the active site of human mitochondrial malonyl-coenzyme a decarboxylase: A combined computational study

2016 ◽  
Vol 84 (6) ◽  
pp. 792-802 ◽  
Author(s):  
Baoping Ling ◽  
Yuxia Liu ◽  
Xiaoping Li ◽  
Zhiguo Wang ◽  
Siwei Bi
Keyword(s):  
Active Site ◽  
Coenzyme A ◽  
Computational Study

Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study

2007 ◽  
Vol 47 (4) ◽  
pp. 1590-1598 ◽  
Author(s):  
Paul Czodrowski ◽  
Christoph A. Sotriffer ◽  
Gerhard Klebe
Keyword(s):  
Active Site ◽  
Computational Study ◽  
Hiv 1

scholarly journals A novel inhibitor of indole-3-glycerol phosphate synthase with activity against multidrug-resistant Mycobacterium tuberculosis

FEBS Journal ◽  
2008 ◽  
Vol 276 (1) ◽  
pp. 144-154 ◽  
Author(s):  
Hongbo Shen ◽  
Feifei Wang ◽  
Ying Zhang ◽  
Qiang Huang ◽  
Shengfeng Xu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Multidrug Resistant ◽  
Glycerol Phosphate ◽  
Phosphate Synthase
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