scholarly journals Stability of unimolecular films of 32P-labelled lecithin

1967 ◽  
Vol 105 (1) ◽  
pp. 401-407 ◽  
Author(s):  
H. Hauser ◽  
R. M. C. Dawson
Keyword(s):  
Pressure Change ◽  
Ion Concentration ◽  
Hydrolysis Rate ◽  
Ion Distribution ◽  
Rapid Perfusion ◽  
Poisson Boltzmann ◽  
Rate Of Hydrolysis ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Hydrolysis Of

1. The stability of monolayers of a highly unsaturated yeast lecithin labelled with 32P has been investigated by a surface radioactivity technique. 2. Lecithin films on distilled water at all surface pressures between 6 and 48dynes/cm. were completely stable on rapid perfusion of the subphase and on addition of ionic amphipathic substances to the film. 3. Ultrasonically treated lecithin added to the subphase caused a slow loss of surface radioactivity but little pressure change. 4. The addition of proteins to the subphase caused negligible changes in the film even when conditions were favourable for electrostatic heterocoagulation and penetration. 5. Lecithin films were not hydrolysed by a strongly acid subphase at room temperature. The very low rate of hydrolysis produced by alkali was proportional to the subphase OH−ion concentration: the apparent activation energy and temperature coefficient (Q10) of the reaction were 14250 cal. and 2·37 respectively. 6. Alkaline hydrolysis of lecithin monolayers was markedly stimulated by adding methanol (10–20%, v/v) to the subphase. The addition of ionic amphipaths to the monolayer had the expected type of effect on the hydrolysis rate, but its magnitude was far less than that suggested by an application of the Poisson–Boltzmann equation for ion distribution at a charged interface (Davies & Rideal, 1963).

Examining sharp restart in a Monte Carlo method for the linearized Poisson–Boltzmann equation

2020 ◽  
Vol 26 (3) ◽  
pp. 223-244
Author(s):  
W. John Thrasher ◽  
Michael Mascagni
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Algorithm ◽  
Significant Bias ◽  
Poisson Boltzmann ◽  
Electrostatic Free Energy ◽  
Poisson Boltzmann Equation ◽  
The Stability ◽  
Potential Methods ◽  
The Individual

AbstractIt has been shown that when using a Monte Carlo algorithm to estimate the electrostatic free energy of a biomolecule in a solution, individual random walks can become entrapped in the geometry. We examine a proposed solution, using a sharp restart during the Walk-on-Subdomains step, in more detail. We show that the point at which this solution introduces significant bias is related to properties intrinsic to the molecule being examined. We also examine two potential methods of generating a sharp restart point and show that they both cause no significant bias in the examined molecules and increase the stability of the run times of the individual walks.

Study and modeling of mechanisms of cholinesterasis reactions in order to improve their catalytic properties in the neutralization reactions of organophosphorous compounds

2020 ◽  
pp. 134-174
Author(s):  
Sergey Varfolomeev ◽  
Bella Grigorenko ◽  
Sofya Lushchekina ◽  
Patrick Masson ◽  
Galina Mahaeva ◽  
...  
Keyword(s):  
First Generation ◽  
Organophosphorus Compounds ◽  
Protein Molecule ◽  
Catalytic Antibodies ◽  
High Rate ◽  
Biological Targets ◽  
Organophosphorous Compounds ◽  
Rate Of Hydrolysis ◽  
The Stability ◽  
Hydrolysis Of

“Biocleaners” or “bioscavengers” are biological objects (enzymes, catalytic antibodies) that are capable of binding and/or hydrolyzing organophosphorus compounds (OPC). Their use seems to be the most effective alternative to traditional antidotes to neutralize or detoxify OPC. The introduction of bioscavengers allows neutralizing toxicant molecules in the bloodstream before they reach their biological targets, thereby providing protection against poisoning. Bioscavengers of the first-generation neutralized OPC molecules by stoichiometrically binding to them. The safety and efficacy of human butyrylcholinesterase (BChE) for protecting against OPC poisoning has been shown. However, the stoichiometric neutralization of OPC requires the introduction of a huge amount of expensive biopharmaceuticals. Catalytic bioscavengers that hydrolytically neutralize OPC were introduced at a much lower dose to achieve the same degree of effectiveness. The most effective catalytic bioscavengers are enzymes. The most promising enzymes are artificial mammalian paraoxonase mutants and bacterial phosphotriesterases. However, studies of other enzymes, such as prolidases, oxidases, artificial mutants of cholinesterases and carboxyl esterases and catalytic antibodies are actively ongoing. Since OPC are pseudosubstrates of cholinesterases (ChEs), a detailed description of the mechanisms of inhibition, dealkylation, and spontaneous reactivation of phosphorylated ChEs is critical for the development of ChEs mutants with a high rate of hydrolysis of OPC. The review presents an analysis of different views on the mechanisms of interaction of ChEs with OPC, discusses the possible directions of creating effective catalytic biological traps based on BChE and changes in their mechanism of action as compared to the native enzyme. A separate section is devoted to the effect of mutations, both polymorphic and artificial, on the stability of the protein molecule of BChE.

Mechanistic Information from the Effect of Pressure on the Kinetics of Hydrolysis of Iodopentaaquochromium(III) Ion

1975 ◽  
Vol 53 (24) ◽  
pp. 3697-3701 ◽  
Author(s):  
Milton Cornelius Weekes ◽  
Thomas Wilson Swaddle
Keyword(s):  
Ionic Strength ◽  
Hydrogen Ion ◽  
Ion Concentration ◽  
Hydrogen Ion Concentration ◽  
Kinetics Of Hydrolysis ◽  
Rate Of Hydrolysis ◽  
Kinetics Of ◽  
Hydrolysis Of ◽  
Aqueous Hclo ◽  
Conjugate Base

The rate of hydrolysis of iodopentaaquochromium(III) ion has been measured as a function of pressure (0.1 to 250 MPa) and hydrogen ion concentration (0.1 to 1.0 mol kg−1) at 298.2 K and ionic strength 1.0 mol kg−1 (aqueous HClO4–LiClO4). The volumes of activation for the acid independent and inversely acid dependent hydrolysis pathways are −5.4 ± 0.5 and −1.6 ± 0.3 cm3 mol−1 respectively, and are not detectably pressure-dependent. Consideration of these values, together with the molar volume change of −3.3 ± 0.3 cm3 mol−1 determined dilatometrically for the completed hydrolysis reaction, indicates that the mechanisms of the two pathways are associative interchange (Ia) and dissociative conjugate base (Dcb) respectively.

BION-2: Predicting Positions of Non-Specifically Bound ions on Protein Surface by a Gaussian-based Treatment of Electrostatic Environment

2020 ◽  
Author(s):  
Mihiri Shashikala ◽  
Arghya Chakravorty ◽  
Shailesh Pandey ◽  
Emil Alexov
Keyword(s):  
Thermal Fluctuation ◽  
Computational Method ◽  
Ion Concentration ◽  
Biological Processes ◽  
Poisson Boltzmann ◽  
Concentration Changes ◽  
Energy Of Interaction ◽  
Poisson Boltzmann Equation

Abstract Background: Ions play significant roles in biological processes - they may specifically bind to a protein site or bind non-specifically on its surface. Though, the role of specifically bound ions range from actively providing structural compactness via coordination of charge-charge interactions to numerous enzymatic activities, non-specifically surface-bound ions are also crucial to maintaining a protein’s stability, responding to pH and ion concentration changes and contributing to other biological processes. However, experimental determination of positions of non-specifically bound ions is not trivial since they may have low residential time and experience significant thermal fluctuation of their positions. Results: Here we report a new release of a computational method, the BION-2 method, that predicts positions of non-specifically surface-bound ions. The BION-2 utilizes the Gaussian-based treatment of ions within the framework of the modified Poisson-Boltzmann equation, that does not require a sharp boundary between the protein and water phase. Thus, the predictions are done by the balance of the energy of interaction between the protein charges and the corresponding ions, and the de-solvation penalty of the ions as they approach the protein. Conclusions: The BION-2 is tested against experimentally determined ion’s positions, with both X-ray and NMR determined positions, and it is demonstrated that it outperforms the old BION and molecular dynamics tools. The BION-2 is available as a web server as well.

scholarly journals Genetic control of the hydrolysis of aromatic esters by sheep plasma A-esterase

1966 ◽  
Vol 7 (3) ◽  
pp. 373-382 ◽  
Author(s):  
R. M. Lee
Keyword(s):  
Esterase Activity ◽  
Phosphate Esters ◽  
Hydrolysis Rate ◽  
Aromatic Esters ◽  
Hydrolysis Rates ◽  
Rate Of Hydrolysis ◽  
Hydrolysis Of ◽  
Naphthyl Acetate ◽  
Genetic Marking ◽  
Genetic Hypothesis

1. The rate of hydrolysis by sheep plasma of some carboxylic and phosphate esters has been determined for a random flock, and for a flock previously selected for its ability to hydrolyse di-(2-chloroethyl) aryl phosphates.2. A discontinuous variation in hydrolysis rate was found with all substrates tested and, using combinations of substrates, six types of plasma could be distinguished, each type having a different pattern of esterase activity.3. The most useful substrates for distinguishing between phenotypes were 1-naphthyl acetate and 4-ethoxycarbonylcoumarin-7-yl acetate. Three rates of hydrolysis were possible for each of these esters, and the highest rate for one was invariably combined with the lowest rate for the other, although the converse did not apply.4. To explain these results, and those of Lee (1964), it has been postulated that the quantitative production of esterase hydrolysing 1-naphthyl acetate is governed by the presence of an allele, termed Esa, at a particular gene locus. Similarly, the production of esterase hydrolysing 4-ethoxycarbonylcoumarin-7-yl acetate is determined by allele Esb, and where neither substrate is attacked the presence of a third allele, Esc, is proposed.5. The hydrolysis rates of haloxon, 1-naphthyl butyrate and 4-nitrophenyl butyrate varied in the same way as that of 1-naphthyl acetate, whereas the hydrolysis of indophenyl acetate followed the same pattern as that of 4-ethoxycarbonylcoumarin-7-yl acetate. The variation in hydrolysis rate of Coroxon could be explained by assuming that Esa and Esb are equal in this respect.6. A mating experiment produced results which were in accordance with the genetic hypothesis, but were too few in number to provide confirmation.7. The genetic marking of six types of sheep is possible, utilizing the variation in plasma A-esterase activity.

scholarly journals BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics

2020 ◽  
Vol 22 (1) ◽  
pp. 272
Author(s):  
H. B. Mihiri Shashikala ◽  
Arghya Chakravorty ◽  
Shailesh Kumar Panday ◽  
Emil Alexov
Keyword(s):  
Thermal Fluctuation ◽  
Computational Method ◽  
Ion Concentration ◽  
Biological Processes ◽  
Poisson Boltzmann ◽  
Concentration Changes ◽  
Energy Of Interaction ◽  
Poisson Boltzmann Equation

Ions play significant roles in biological processes—they may specifically bind to a protein site or bind non-specifically on its surface. Although the role of specifically bound ions ranges from actively providing structural compactness via coordination of charge–charge interactions to numerous enzymatic activities, non-specifically surface-bound ions are also crucial to maintaining a protein’s stability, responding to pH and ion concentration changes, and contributing to other biological processes. However, the experimental determination of the positions of non-specifically bound ions is not trivial, since they may have a low residential time and experience significant thermal fluctuation of their positions. Here, we report a new release of a computational method, the BION-2 method, that predicts the positions of non-specifically surface-bound ions. The BION-2 utilizes the Gaussian-based treatment of ions within the framework of the modified Poisson–Boltzmann equation, which does not require a sharp boundary between the protein and water phase. Thus, the predictions are done by the balance of the energy of interaction between the protein charges and the corresponding ions and the de-solvation penalty of the ions as they approach the protein. The BION-2 is tested against experimentally determined ion’s positions and it is demonstrated that it outperforms the old BION and other available tools.

scholarly journals Ability of the Poisson–Boltzmann equation to capture molecular dynamics predicted ion distribution around polyelectrolytes

2017 ◽  
Vol 19 (36) ◽  
pp. 24583-24593 ◽  
Author(s):  
Piotr Batys ◽  
Sohvi Luukkonen ◽  
Maria Sammalkorpi
Keyword(s):  
Molecular Dynamics ◽  
Boltzmann Equation ◽  
Charge Density ◽  
Layer Thickness ◽  
Mean Field ◽  
Ion Distribution ◽  
Line Charge ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Ion condensation around polyelectrolytes is examined computationally at all-atom and mean field detail levels to extract the practical limits of a PB model; the condensed ion layer thickness is found to depend solely on polyelectrolyte line charge density.

scholarly journals Antitumour Metallocenes: Effect of DMSO on the Stability of Cp2TiX2 and Implications for Anticancer Activity

1998 ◽  
Vol 5 (4) ◽  
pp. 207-215 ◽  
Author(s):  
George Mokdsi ◽  
Margaret M. Harding
Keyword(s):  
Nmr Spectroscopy ◽  
Aqueous Solutions ◽  
Anticancer Activity ◽  
Active Species ◽  
Aromatic Rings ◽  
Cyclopentadienyl Ligands ◽  
Rate Of Hydrolysis ◽  
The Stability ◽  
Rapid Hydrolysis ◽  
Hydrolysis Of

The rate of hydrolysis of the aromatic rings of Cp2TiX2 [X = CI 1, O2CCCl3  8 and O2CCH2NH3Cl  13], in aqueous solutions, 10%DMSO and 100% DMSO have been studied by H1NMR spectroscopy. Rapid hydrolysis of both the carboxylate and cyclopentadienyl ligands in Cp2TiX2[X = O2CCCl3,O2CCH2NH3Cl] occurs in DMSO to give biologically inactive species. The rate of these reactions are concentration dependent as dilution of these samples with saline or water to give the therapeutic conditions of 10%DMSO/90%H2O slows the hydrolysis chemistry. In contrast, samples of Cp2TiX2 [X = CI 1, O2CCH2NH3Cl  13], dissolved in water give solutions containing the presumed antitumour active species in which the halide or glycine ligands have been hydrolysed but the Cp rings remain metal bound.

scholarly journals Hydrolysis of GTP by Sec4 protein plays an important role in vesicular transport and is stimulated by a GTPase-activating protein in Saccharomyces cerevisiae.

1992 ◽  
Vol 12 (5) ◽  
pp. 2017-2028 ◽  
Author(s):  
N C Walworth ◽  
P Brennwald ◽  
A K Kabcenell ◽  
M Garrett ◽  
P Novick
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Synthetic Lethality ◽  
Vesicular Transport ◽  
Yeast Cells ◽  
Hydrolysis Rate ◽  
Phosphoryl Group ◽  
Absolute Level ◽  
Yeast Saccharomyces Cerevisiae ◽  
Rate Of Hydrolysis ◽  
Hydrolysis Of

Sec4, a GTP-binding protein of the ras superfamily, is required for exocytosis in the budding yeast Saccharomyces cerevisiae. To test the role of GTP hydrolysis in Sec4 function, we constructed a mutation, Q-79----L, analogous to the oncogenic mutation of Q-61----L in Ras, in a region of Sec4 predicted to interact with the phosphoryl group of GTP. The sec4-leu79 mutation lowers the intrinsic hydrolysis rate to unmeasurable levels. A component of a yeast lysate specifically stimulates the hydrolysis of GTP by Sec4, while the rate of hydrolysis of GTP by Sec4-Leu79 can be stimulated by this GAP activity to only 30% of the stimulated hydrolysis rate of the wild-type protein. The decreased rate of hydrolysis results in the accumulation of the Sec4-Leu79 protein in its GTP-bound form in an overproducing yeast strain. The sec4-leu79 allele can function as the sole copy of sec4 in yeast cells. However, it causes recessive, cold-sensitive growth, a slowing of invertase secretion, and accumulation of secretory vesicles and displays synthetic lethality with a subset of other secretory mutants, indicative of a partial loss of Sec4 function. While the level of Ras function reflects the absolute level of GTP-bound protein, our results suggest that the ability of Sec4 to cycle between its GTP and GDP bound forms is important for its function in vesicular transport, supporting a mechanism for Sec4 function which is distinct from that of the Ras protein.

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