scholarly journals A Simple Complex on the Verge of Breakdown: Isolation of the Elusive Cyanoformate Ion

Science ◽  
2014 ◽  
Vol 344 (6179) ◽  
pp. 75-78 ◽  
Author(s):  
Luke J. Murphy ◽  
Katherine N. Robertson ◽  
Scott G. Harroun ◽  
Christa L. Brosseau ◽  
Ulrike Werner-Zwanziger ◽  
...  
Keyword(s):  
Active Site ◽  
Theoretical Calculations ◽  
Acc Oxidase ◽  
Dielectric Medium ◽  
Solution Stability ◽  
Stability Studies ◽  
Simple Complex ◽  
Low Dielectric ◽  
Dielectric Media ◽  
Iron Center

Why does cyanide not react destructively with the proximal iron center at the active site of 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase, an enzyme central to the biosynthesis of ethylene in plants? It has long been postulated that the cyanoformate anion, [NCCO2]–, forms and then decomposes to carbon dioxide and cyanide during this process. We have now isolated and crystallographically characterized this elusive anion as its tetraphenylphosphonium salt. Theoretical calculations show that cyanoformate has a very weak C–C bond and that it is thermodynamically stable only in low dielectric media. Solution stability studies have substantiated the latter result. We propose that cyanoformate shuttles the potentially toxic cyanide away from the low dielectric active site of ACC oxidase before breaking down in the higher dielectric medium of the cell.

scholarly journals Computing Protein pKas Using the TABI Poisson–Boltzmann Solver

2020 ◽  
pp. 2042006
Author(s):  
Jiahui Chen ◽  
Jingzhen Hu ◽  
Yongjia Xu ◽  
Robert Krasny ◽  
Weihua Geng
Keyword(s):  
Boltzmann Distribution ◽  
Dielectric Medium ◽  
Boundary Integral ◽  
Acid Dissociation ◽  
Low Dielectric ◽  
Poisson Boltzmann ◽  
Computing Procedure ◽  
Poisson Boltzmann Equation ◽  
High Dielectric ◽  
Electrostatic Calculations

A common approach to computing protein pKas uses a continuum dielectric model in which the protein is a low dielectric medium with embedded atomic point charges, the solvent is a high dielectric medium with a Boltzmann distribution of ionic charges, and the pKa is related to the electrostatic free energy which is obtained by solving the Poisson–Boltzmann equation. Starting from the model pKa for a titrating residue, the method obtains the intrinsic pKa and then computes the protonation probability for a given pH including site–site interactions. This approach assumes that acid dissociation does not affect protein conformation aside from adding or deleting charges at titratable sites. In this work, we demonstrate our treecode-accelerated boundary integral (TABI) solver for the relevant electrostatic calculations. The pKa computing procedure is enclosed in a convenient Python wrapper which is publicly available at the corresponding author’s website. Predicted results are compared with experimental pKas for several proteins. Among ongoing efforts to improve protein pKa calculations, the advantage of TABI is that it reduces the numerical errors in the electrostatic calculations so that attention can be focused on modeling assumptions.

scholarly journals Understanding the Interaction Modes and Reactivity of Trimedoxime toward MmAChE Inhibited by Nerve Agents: Theoretical and Experimental Aspects

2020 ◽  
Vol 21 (18) ◽  
pp. 6510
Author(s):  
Alexandre A. de Castro ◽  
Daniel A. Polisel ◽  
Bruna T. L. Pereira ◽  
Elaine F. F. da Cunha ◽  
Kamil Kuca ◽  
...  
Keyword(s):  
Experimental Data ◽  
Mus Musculus ◽  
Active Site ◽  
Theoretical Calculations ◽  
Nerve Agents ◽  
The Other ◽  
Chemical Weapons ◽  
Reactivation Process ◽  
Other Hand

Organophosphorus (OP) compounds are used as both chemical weapons and pesticides. However, these agents are very dangerous and toxic to humans, animals, and the environment. Thus, investigations with reactivators have been deeply developed in order to design new antidotes with better efficiency, as well as a greater spectrum of action in the acetylcholinesterase (AChE) reactivation process. With that in mind, in this work, we investigated the behavior of trimedoxime toward the Mus musculus acetylcholinesterase (MmAChE) inhibited by a range of nerve agents, such as chemical weapons. From experimental assays, reactivation percentages were obtained for the reactivation of different AChE–OP complexes. On the other hand, theoretical calculations were performed to assess the differences in interaction modes and the reactivity of trimedoxime within the AChE active site. Comparing theoretical and experimental data, it is possible to notice that the oxime, in most cases, showed better reactivation percentages at higher concentrations, with the best result for the reactivation of the AChE–VX adduct. From this work, it was revealed that the mechanistic process contributes most to the oxime efficiency than the interaction in the site. In this way, this study is important to better understand the reactivation process through trimedoxime, contributing to the proposal of novel antidotes.

Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2-Dichloroethane and Water in Cyclohexane

1995 ◽  
Vol 117 (47) ◽  
pp. 11809-11810 ◽  
Author(s):  
William L. Jorgensen ◽  
Nora A. McDonald ◽  
Massimo Selmi ◽  
Paul R. Rablen
Keyword(s):  
Low Dielectric ◽  
Dielectric Media

Spectroscopic studies of the coupled binuclear ferric active site in methemerythrins and oxyhemerythrin: the electronic structure of each iron center and the iron-oxo and iron-peroxide bonds

1989 ◽  
Vol 111 (13) ◽  
pp. 4688-4704 ◽  
Author(s):  
Richard C. Reem ◽  
James M. McCormick ◽  
David E. Richardson ◽  
Frank J. Devlin ◽  
Philip J. Stephens ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Active Site ◽  
Spectroscopic Studies ◽  
Iron Center

Solution stability studies of the subunit components of meningococcal C oligosaccharide‒CRM197 conjugate vaccines

2001 ◽  
Vol 33 (2) ◽  
pp. 91 ◽  
Author(s):  
Mei M. Ho ◽  
Xavier Lemercinier ◽  
Barbara Bolgiano ◽  
Dennis Crane ◽  
Michael J. Corbel
Keyword(s):  
Solution Stability ◽  
Stability Studies ◽  
Conjugate Vaccines

scholarly journals Light in dielectric media and scalar fields in a de Sitter spacetime

2021 ◽  
Vol 81 (8) ◽  
Author(s):  
I. A. Pedrosa ◽  
B. F. Ramos ◽  
K. Bakke
Keyword(s):  
Scalar Field ◽  
Coherent States ◽  
Scalar Fields ◽  
Dielectric Medium ◽  
De Sitter Spacetime ◽  
De Sitter ◽  
Expectation Values ◽  
Dielectric Media ◽  
Sitter Spacetime ◽  
Constant Rate

AbstractIn the present work we discuss the behavior of light in a linear dielectric medium with a time-varying electric permittivity that increases exponentially at a constant rate and of a scalar field in a de Sitter spacetime, in both the classical and quantum contexts. Notably, we find that the behavior of these two systems are identical and can be described by similar Hamiltonians. By using the Lewis–Riesenfeld invariant method together with Fock states we solve the time-dependent Schrödinger equation for this problem and use its solutions to construct coherent states for the scalar field. Finally, we employ both the Fock and coherent states to evaluate some important properties of the quantized scalar field, such as expectation values of the amplitude and momentum of each mode their variances and the respective uncertainty principle.

scholarly journals The Physics of Tachyons IV. Tachyon Electrodynamics

1998 ◽  
Vol 51 (3) ◽  
pp. 477
Author(s):  
Ross L. Dawe ◽  
Kenneth C. Hines
Keyword(s):  
Dipole Moment ◽  
Collision Energy ◽  
Cherenkov Radiation ◽  
Mathematical Proof ◽  
Dielectric Materials ◽  
Dielectric Medium ◽  
Current Loop ◽  
Dielectric Media ◽  
Viable Approach ◽  
New Formulation

A new formulation of the theory of tachyons using the same two postulates as in specialrelativity is applied to the electrodynamics of material media. A discussion of Lagrange’s equations and Hamilton’s equations for ‘classical’ charged tachyons shows that such a formalism is a viable approach. An essay is included on why tachyons can be considered to be localised particles for the purpose of calculations. Tachyonic transformations of the electromagneticfields D, P, H and M are shown to be the same as for bradyonic transformations. Examples discussed include the electric dipole moment of a tachyonic current loop, constitutive equations, polarisation in tachyonic dielectric materials and the velocity of light in tachyonic dielectric media. This is followed by discussions of the collision energy loss for charged tachyonsinteracting with a material medium and a mathematical proof that tachyons cannot emit Cherenkov radiation when passing through a bradyonic dielectric medium.

Phage display screening in low dielectric media

2008 ◽  
Vol 21 (5) ◽  
pp. 330-337 ◽  
Author(s):  
Linus Olofsson ◽  
Pernilla Söderberg ◽  
Jonas Ankarloo ◽  
Ian A. Nicholls
Keyword(s):  
Phage Display ◽  
Low Dielectric ◽  
Dielectric Media
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