Effects of Protonation State on a Tyrosine−Histidine Bioinspired Redox Mediator†

2010 ◽  
Vol 114 (45) ◽  
pp. 14450-14457 ◽  
Author(s):  
Gary F. Moore ◽  
Michael Hambourger ◽  
Gerdenis Kodis ◽  
Weston Michl ◽  
Devens Gust ◽  
...  
Keyword(s):  
Redox Mediator ◽  
Protonation State

Redox Mediator‐Based Microbial Biosensors for Acute Water Toxicity Assessment: A Critical Review

2020 ◽  
Vol 7 (12) ◽  
pp. 2513-2526 ◽  
Author(s):  
Deyu Fang ◽  
Guanyue Gao ◽  
Yajie Yang ◽  
Yu Wang ◽  
Lijuan Gao ◽  
...  
Keyword(s):  
Critical Review ◽  
Toxicity Assessment ◽  
Redox Mediator ◽  
Water Toxicity

Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid

2011 ◽  
Vol 79 (7) ◽  
pp. 2076-2085 ◽  
Author(s):  
Verónica I. Dumit ◽  
Néstor Cortez ◽  
G. Matthias Ullmann
Keyword(s):  
Carboxylic Acid ◽  
Active Site ◽  
Protonation State

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

scholarly journals Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease

2021 ◽  
Vol 120 (3) ◽  
pp. 204a-205a
Author(s):  
Anna Pavlova ◽  
Diane L. Lynch ◽  
Micholas Dean Smith ◽  
Jeremy D. Smith ◽  
James C. Gumbart
Keyword(s):  
Protonation State ◽  
Inhibitor Binding ◽  
Main Protease

Electrochemically active hydroquinone-based redox mediator for flexible energy storage system with improved charge storing ability

2021 ◽  
Vol 588 ◽  
pp. 62-69
Author(s):  
Hyeonggeun Choi ◽  
Min-Cheol Kim ◽  
Yeonsu Park ◽  
Suok Lee ◽  
Wook Ahn ◽  
...  
Keyword(s):  
Energy Storage ◽  
Storage System ◽  
Energy Storage System ◽  
Redox Mediator ◽  
Electrochemically Active

Helical Copper Redox Mediator with Low Electron Recombination for Dye-Sensitized Solar Cells

2021 ◽  
Author(s):  
Zijian Deng ◽  
Xichuan Yang ◽  
Kaiyuan Yang ◽  
Li Zhang ◽  
Haoxin Wang ◽  
...  
Keyword(s):  
Solar Cells ◽  
Dye Sensitized Solar Cells ◽  
Redox Mediator ◽  
Electron Recombination ◽  
Dye Sensitized ◽  
Sensitized Solar Cells

scholarly journals A QM/MM Evaluation of the Missing Step in the Reduction Mechanism of HMG-CoA by Human HMG-CoA Reductase

Processes ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 1085
Author(s):  
Paula Mihaljević-Jurič ◽  
Sérgio F. Sousa
Keyword(s):  
Mevalonate Pathway ◽  
Atomic Level ◽  
Amino Acid Residues ◽  
Protonation State ◽  
Primary Target ◽  
Cholesterol Levels ◽  
The Subject ◽  
Electron Reduction ◽  
Dynamics Simulations ◽  
Coa Reductase

Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. A second reduction step of this reaction mechanism has been the subject of much speculation in the literature, with different conflicting theories persisting to the present day. In this study, the different mechanistic hypotheses were evaluated with atomic-level detail through a combination of molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The obtained Gibbs free activation and Gibbs free reaction energy (15 kcal mol−1 and −40 kcal mol−1) show that this hydride step takes place with the involvement of a cationic His405 and Lys639, and a neutral Glu98, while Asp715 remains in an anionic state. The results provide an atomic-level portrait of this step, clearly demonstrating the nature and protonation state of the amino acid residues involved, the energetics associated, and the structure and charge of the key participating atoms in the several intermediate states, finally elucidating this missing step.

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