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A protease stable in organic solvents from solvent tolerant strain of Pseudomonas aeruginosa.

A solvent tolerant strain of Pseudomonas aeruginosa (PseA) was isolated from soil samples by cyclohexane enrichment in medium. The strain was able to sustain and grow in a wide range of organic solvents. The adaptation of P. aeruginosa cell towards solvents was seen at membrane level in transmission electron micrographs. It also secreted a novel protease, which exhibited remarkable solvent stability and retained most of the activity at least up to 10 days in the presence of hydrophobic organic solvents (log P > or = 2.0) at 25% (v/v) concentrations. The protease was able to withstand as high as 75% concentration of solvents at least up to 48 h. P. aeruginosa strain and its protease, both seem promising for solvent bioremediation, wastewater treatment and carrying out biotransformation in non-aqueous medium.

Cell Proliferation↗

Grouping solvents by statistical analysis of solvent property parameters: implication to polymorph screening.

The success rate of discovering new polymorphs by crystallization from solution may be increased if solvents with diverse properties are used during initial polymorph screening. In this study, eight solvent parameters, including hydrogen bond acceptor propensity, hydrogen bond donor propensity, polarity/dipolarity, dipole moment, dielectric constant, viscosity, surface tension and cohesive energy density (equal to square of solubility parameter), of 96 solvents were collected. Using the cluster statistical analysis of the parameters, these 96 solvents were separated into 15 solvent groups. Such solvent groups may provide guidelines for the judicious choice of solvents with diverse properties for polymorph screening.

Chemistry, Pharmaceutical↗

Encapsulation of hydrophobic drugs in polymeric micelles through co-solvent evaporation: the effect of solvent composition on micellar properties and drug loading.

This study was designed to develop an optimized co-solvent evaporation procedure for the efficient encapsulation of hydrophobic drugs in polymeric micelles of methoxy poly(ethylene oxide)-block-poly(epsilon-caprolactone) (MePEO-b-PCL). MePEO-b-PCL block copolymers having varied MePEO and PCL molecular weights were synthesized, assembled to polymeric micelles, and used for the encapsulation of cyclosporine A (CyA) by a co-solvent evaporation method. The co-solvent composition was varied by changing the type of organic co-solvent (using acetone, acetonitrile and tetrahydrofuran), the ratio of organic to aqueous phase, and their order of addition. Carrier size, morphology and encapsulated CyA levels were defined by dynamic light scattering (DLS), transmission electron microscopy (TEM) and HPLC, respectively, and the effect of co-solvent composition on micellar properties and loaded CyA levels was evaluated. Application of acetone and acetonitrile as the selective co-solvent for the core-forming block led to a decrease in the average diameter of self-assembled structures. When acetone was added to water, a decrease in the ratio of organic to aqueous phase led to an increase in the loading efficiency of CyA in MePEO-b-PCL micelles. A similar trend in CyA loading was observed for MePEO-b-PCL micelles of varied MePEO and PCL block lengths. The ratio of organic to aqueous phase did not affect CyA loading when water was added to acetone. Irrespective of the order of addition, the decrease in the organic to aqueous phase ratio caused a reduction in the average diameter of the empty and CyA loaded micelles. We conclude that the co-solvent evaporation method may be optimized to improve the efficiency of drug encapsulation in polymeric micelles. For CyA encapsulation in MePEO-b-PCL micelles, addition of acetone to water at lower organic to aqueous phase ratio is shown to be the optimum procedure leading to higher drug encapsulation and smaller average diameter for the self-assembled structures.

Cyclosporine↗

Solvent effects on infrared spectra of progesterone in CHCl3/cyclo-C6H12 binary solvent systems.

The infrared spectroscopy studies of the C3 and C20 carbonyl stretching vibrations (upsilon(C=O)) of progesterone in CHCl3/cyclo-C6H12 binary solvent systems were undertaken to investigate the solute-solvent interactions. With the mole fraction of CHC13 in the binary solvent mixtures increase, three types of C3 and C20 carbonyl stretching vibration band of progesterone are observed, respectively. The assignments of upsilon(C=O) of progesterone are discussed in detail. In the CHCl3-rich binary solvent systems or pure CHCl3 solvent, two kinds of solute-solvent hydrogen bonding interactions coexist for C20 C=O. Comparisons are drawn for the solvent sensitivities of upsilon(C=O) for acetophenone and 5alpha-androstan-3,17-dione, respectively.

Acetophenones↗

Solvent hydrogen-bond network in protein self-assembly: solvation of collagen triple helices in nonaqueous solvents.

Forces between type I collagen triple helices are studied in solvents of varying hydrogen-bonding ability. The swelling of collagen fibers in reconstituted films is controlled by the concentration of soluble polymers that are excluded from the fibers and that compete osmotically with collagen for available solvent. The interaxial spacing between the triple helices as a function of the polymer concentration is measured by x-ray diffraction. Exponential-like changes in the spacing with increasing osmotic stress, qualitatively similar to the forces previously found in aqueous solution, are also seen in formamide and ethylene glycol. These are solvents that, like water, are capable of forming three-dimensional hydrogen-bond networks. In solvents that either cannot form a network or have a greatly impaired ability to form a hydrogen-bonded network, strikingly different behavior is observed. A hard-wall repulsion is seen with collagen solvated by ethanol, 2-propanol, and N,N-dimethylformamide. The spacing between helices hardly changes with increasing polymer concentration until the stress exceeds some threshold where removal of the solvent becomes energetically favorable. No solvation of collagen is observed in dimethoxyethane. In solvents with an intermediate ability to form hydrogen-bonded networks, methanol, 2-methoxyethanol, or N-methylformamide, the change in spacing with polymer concentration is intermediate between exponential-like and hard-wall. These results provide direct evidence that the exponential repulsion observed between collagen helices at 0-8-A surface separations in water is due to the energetic cost associated with perturbing the hydrogen-bonded network of solvent molecules between the collagen surfaces.

Animals↗

Spray freezing into liquid (SFL) particle engineering technology to enhance dissolution of poorly water soluble drugs: organic solvent versus organic/aqueous co-solvent systems.

A spray freezing into liquid (SFL) particle engineering technology has been developed to produce micronized powders to enhance the dissolution of poorly water soluble active pharmaceutical ingredients (APIs). Previously, a tetrahydrofuran (THF)/water co-solvent was used as the solution source in the SFL process. In the present study, an organic system was developed to further enhance the properties of particles produced by SFL. The influence of solution type (e.g. organic versus organic/water) on the physicochemical properties of SFL powders was investigated and compared. The physicochemical properties of SFL carbamazepine (CBZ)/poloxamer 407/PVP K15 (2:1:1 ratio) powders were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), particle size distribution, surface area analysis, contact angle measurement, Karl-Fisher (KF) titration, gas chromatography (GC) analysis, HPLC analysis, and dissolution testing. The CBZ loading in the feed solution of the SFL acetonitrile system was 2.2% (w/w), which was greater than 0.22% (w/w) loading of the THF/water co-solvent system. XRD results indicated CBZ was amorphous in SFL powders produced by either system. SEM micrographs indicated that SFL powders from acetonitrile appeared less porous with a smaller primary particle size than particles from the co-solvent. The M50 (50% cumulative percent undersize) of micronized powder from the SFL acetonitrile system and the THF/water co-solvent system with 0.22% CBZ loading were 680nm and 7.06microm, respectively. The surface area of SFL powders from the acetonitrile and co-solvent systems were 12.89 and 13.31m(2)/g, respectively. The contact angle of the SFL powders against purified water was about 35 degrees for both systems. The SFL powders from both systems exhibited similar and significantly enhanced dissolution rates compared to the bulk CBZ. Acetonitrile was an effective alternative solvent to THF/water co-solvent for use with the SFL micronization process to produce free flowing particles containing CBZ with significantly enhanced wetting and dissolution properties.

Chemical Engineering↗

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled using estimators based on the solvent exposed solute surface area. In this paper, we analyze the accuracy of linear surface area models for predicting the van der Waals solute-solvent interaction energies of native and non-native protein conformations, peptides and small molecules, and the desolvation penalty of protein-protein and protein-ligand binding complexes. The target values are obtained from explicit solvent simulations and from a continuum solvent van der Waals interaction energy model. The results indicate that the standard surface area model, while useful on a coarse-grained scale, may not be accurate or transferable enough for high resolution modeling studies of protein folding and binding. The continuum model constructed in the course of this study provides one path for the development of a computationally efficient implicit solvent nonpolar hydration free energy estimator suitable for high-resolution structural and thermodynamic modeling of biological macromolecules.

Amino Acid Sequence↗

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment.

Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Differences in conformational sampling of DNA with two sets of atomic radii that are used to define the dielectric interface between the solute and the continuum dielectric model of the solvent are investigated. Results suggest that depending on the choice of atomic radii agreement is either closer to experimental data or to explicit solvent simulations. Furthermore, partial conformational transitions toward A-DNA conformations when salt is added within the implicit solvent framework are observed.

Computer Simulation↗

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

Computer Simulation↗

Addition of polar organic solvents can improve the product selectivity of cyclodextrin glycosyltransferase. Solvent effects on cgtase.

Cyclodextrin glycosyltransferase (EC 2.4.1.19, CGTase) is an enzyme that produces cyclodextrins from starch via an intramolecular transglycosylation reaction. Addition of small amounts (10% v/v) of polar organic solvents can affect both the overall production yield and the type of cyclodextrin produced from a maltodextrin substrate under simulated industrial process conditions. Using CGTase from Thermoanaerobacter sp. all solvents produced an increase in cyclodextrin yield when compared with a control, the greatest increase being obtained with addition of ethanol (26%). In addition product selectivity was affected by the nature of the organic solvent used: beta-cyclodextrin was favoured in the absence of any solvent and on the addition of dimethylsulphoxide, t-butanol and dimethylformanide while alpha-cyclodextrin was favoured by addition of acetonitrile, ethanol and tetrahydrofuran. With CGTase from Bacillus circulans strain 251 relatively smaller increases in overall cyclodextrin production were achieved (between 5-10%). Addition of t-butanol to a B. circulans catalysed reaction however did produce the largest selectivity for beta-cyclodextrin of any solvent-enzyme combination (82%). The effect of solvent addition was shown not to be related to the product inhibition of CGTase, but may be related to reduced competition from the intermolecular transglycosylation reaction that causes degradation of cyclodextrin products. This rate of this reaction was shown to be dependent on the nature of the organic solvent used.

Journal Article↗

Noise and solvent, alcohol and solvent: two dangerous interactions on auditory function.

While noise exposure is the most significant contributor to occupational hearing loss, recent evidence points to solvents and their interactions as additional contributors to occupational deafness. Furthermore, due to the metabolic competitive inhibition between aromatic solvents and ethanol, the solvent toxicity can be even enhanced in certain circumstances. So, two dangerous interactions: noise and solvents, solvents and ethanol deserve to be taken into consideration in an exhaustive preventive policy. Based on the investigations reviewed in the present study, it appears that the combined effects of an exposure to noise and solvent exceed the summation of the damage produced by each agent alone. Such a statement can be also made for a combined exposure to solvent and ethanol. It is therefore important to bear in mind that noise effects can be exacerbated by non-acoustic agents. Thus, if our noise regulations have to be more effective, it is necessary to take into consideration the ototoxic effects of noise in a multifactorial environment.

Journal Article↗

Cometabolism of chlorinated solvents and binary chlorinated solvent mixtures using M. trichosporium OB3b PP358.

The mutant methanotroph, Methylosinus trichosporium OB3b PP358, which constitutively expresses soluble methane monooxygenase (sMMO), was used to study the degradation kinetics of individual chlorinated solvents and binary solvent mixtures. Although sMMO's broad specificity permits a wide range of chlorinated solvents to be degraded, it creates the potential for competitive inhibition of degradation rates in mixtures because multiple chemicals are simultaneously available to the enzyme. To effectively design both ex-situ and in-situ groundwater bioremediation systems using strain PP358, kinetic parameters for chlorinated solvent degradation and accurate kinetic expressions to account for inhibition in mixtures are required. Toward this end, the degradation parameters for six prevalent chlorinated solvents and the verification of enzyme competition model for binary mixtures were the focus of this investigation. M. trichosporium OB3b PP358 degraded trichloroethylene (TCE), chloroform, cis-1,2-dichloroethylene (c-DCE), trans-1,2-dichloroethylene (t-DCE), and 1, 1-dichloroethylene (1,1-DCE) rapidly, with maximum substrate transformation rates of >20.8, 3.1, 9.5 24.8, and >7.5 mg/mg-day, respectively. 1,1,1-trichloroethane (TCA) was not significantly degraded. Half-saturation coefficients ranged from 1 to greater than 10 mg/L. Competition experiments were carried out to observe the effect of a second solvent on degradation rates and to verify the applicability of the Monod model adjusted for competitive inhibition. Binary mixtures of 0.3->0.5 mg/L TCE with up to 5 mg/L c-DCE and up to 7 mg/L 1,1,1-TCA were studied with 20 mM of formate and no growth substrate. No competition was observed at any of these concentrations. Additional competition experiments, using binary mixtures of t-DCE with TCE and t-DCE with c-DCE, were conducted at higher concentrations (i.e., 7-18 mg/L) and enzyme competition was observed. Predictions from a competitive inhibition model compared well with experimental data for these mixtures.

Bacteria↗

Effects of organic solvents and solvent-atrazine interactions on two algae, Chlorella vulgaris and Selenastrum capricornutum.

When assessing pesticides toxicity on test organisms, the use of organic solvents is frequently required to formulate solutions of pesticides having low or moderate water solubility. These solvents may influence the results of toxicity tests. This study examined the effects of ethanol and dimethyl sulfoxide (DMSO) on two species of algae, Chlorella vulgaris and Selenastrum capricornutum. The interactives effects of these organic solvents with various concentrations of atrazine were tested to analyse how these solvents can affect the toxicity of atrazine. Toxicity was measured as the change in chlorophyll (a) content (estimated via fluorescence) in cultures of the test organism that were incubated over a 96-h period at standard conditions of temperature and light. In the absence of atrazine, ethanol was toxic to both algae, yielding significant inhibition of chlorophyll (a) content at concentrations as low as 0.05%. Morever, S. capricornutum was less sensitive to ethanol than was C. vulgaris. DMSO did not show any toxic effects on either chlorophycea. At concentrations up to 0.5%, DMSO interacted additively with atrazine for both chlorophycea. An additive response was also observed with ethanol towards S. capricornutum. For C. vulgaris, ethanol interacted antagonistically at most of atrazine concentrations and gave few additive and synergistic interactions. An additive response of an atrazine-solvent mixture indicate the inherent toxicity of the atrazine. Since DMSO generally gave additive responses for both algae, it can be considered as an adequate organic solvent to use in bioassays.

Atrazine↗

Excluded volume approximation to protein-solvent interaction. The solvent contact model.

Important properties of globular proteins, such as the stability of its folded state, depend sensitively on interactions with solvent molecules. Existing methods for estimating these interactions, such as the geometrical surface model, are either physically misleading or too time consuming to be applied routinely in energy calculations. As an alternative, we derive here a simple model for the interactions between protein atoms and solvent atoms in the first hydration layer, the solvent contact model, based on the conservation of the total number of atomic contacts, a consequence of the excluded-volume effect. The model has the conceptual advantage that protein-protein contacts and protein-solvent contacts are treated in the same language and the technical advantage that the solvent term becomes a particularly simple function of interatomic distances. The model allows rapid calculation of any physical property that depends only on the number and type of protein-solvent nearest-neighbor contacts. We propose use of the method in the calculation of protein solvation energies, conformational energy calculations, and molecular dynamics simulations.

Amino Acids↗

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

This paper reviews a recently developed method for calculating the total conformational free energy of a solute macromolecule in water solvent. The method consists of a relatively short simulation by molecular dynamics with explicit solvent molecules (ES) to produce a set of microstates of the macroscopic conformation. Conformational internal solute energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) surface energy-dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions and of the polarization of water solvent by the solute's charges. We have earlier applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins), and have obtained good discrimination in favor of the native conformations in all instances. These results are summarized and further analyzed to show that, on average, three major component terms of the free energy all contribute in favor of discrimination. We discuss possible improvements of the ES/IS method. It is shown how the force field can be made self-consistent by adapting the parameters for calculation of surface and polarization free energies closely to the molecular mechanics force field used in the dynamics simulation, using established simulation methods to compute free energies for cavity formation and a charging process with the molecular mechanics force field to provide a set of (quasi-experimental) reference data that can be used to refine the parameters of the continuum models. The molecular surface area together with a microscopic surface free energy near 70 cal/(mol A2) is found to be a consistent descriptor of the cavity free energy. Preliminary results indicate that a linear-response approximation for the polarization of water solvent reaction near typical polar and charged protein groups is accurate to within approximately 90%.

Algorithms↗

Solvent effects on infrared spectra of 2-acetylthiophene in organic solvents.

Infrared spectroscopy studies of 2-acetylthiophene (ACTH) in 18 different organic solvents, both polar and non-polar, were undertaken to investigate the solvent-solute interactions. The frequencies of carbonyl stretching vibration upsilon(C=O) of ACTH were correlated with the properties such as the solvent acceptor number (AN) and the linear solvation energy relationships (LSER). The solvent-induced stretching vibration frequency shifts showed a better correlation with the LSER than the AN. A six-membered ring-like hydrogen bonding structure was presented and the solvent effects of ACTH in alcohol solvents were investigated in detail.

Hydrogen Bonding↗

Electrochemistry of cytochrome C in aqueous and mixed solvent solutions: thermodynamics, kinetics, and the effect of solvent dielectric constant.

The solvent dielectric constant is considered an important factor in determining the redox potential of the heme-containing protein cytochrome c in solution. In this study, we investigate the electrochemical response of cytochrome c in aqueous/organic solvent mixtures (100% aqueous buffer, 30% acetonitrile, 40% dimethyl sulfoxide, and 50% methanol), reporting the redox potential (E degrees'), enthalpy, and entropy of reduction. The temperature dependence of the solvent dielectric constant (epsilon) was also measured. The results show that epsilon alone cannot regulate the E degrees' of cytochrome c in mixed solvent systems. The implications of the temperature dependence of epsilon on the validity of the thermodynamic data are also discussed. The effect of solvent and temperature on the electron-transfer rate constant, k(s), was determined in each solvent mixture. A substantial increase in the activation energy for electron transfer was observed in 40% DMSO.

Animals↗

Solvent extraction as an adjunct to rendering: the effect on BSE and scrapie agents of hot solvents followed by dry heat and steam.

The study was designed to determine the effect on bovine spongiform encephalopathy (BSE) and scrapie agents of the solvent extraction processes used in the past by British renderers. The raw material was mouse spleen infected with either the 22A strain of scrapie agent or the 301V strain of BSE agent. Samples were exposed to hexane, heptane, petroleum spirit or perchlorethylene at the relevant temperatures for the appropriate times. Control samples were exposed to the same range of temperatures for the same range of times in saline. Other samples were exposed to the hot solvents, followed by treatment with dry heat at 100 degrees C for 30 minutes and steam at 100 degrees C for 30 minutes. Further samples were exposed only to the dry heat and steam cycles. No single complete process was significantly more effective than any of the others, and they all produced only slight inactivation, less than one log on average for both strains of agent. The average degree of inactivation produced by exposure to hot saline was generally comparable to that produced by exposure to the hot solvents. This was also true for the samples exposed only to dry heat and steam compared with those exposed to hot solvent before treatment with dry heat and steam, and suggests that the slight inactivation was caused by the heat rather than by the solvents. It is concluded that the solvent extraction processes used by renderers in Britain had little capacity to inactivate BSE and scrapie agents.

Abattoirs↗