A model for sedimentation in inhomogeneous media. I. Dynamic density gradients from sedimenting co-solutes

Macromolecular sedimentation in inhomogeneous media is of great practical importance. Dynamic density gradients have a long tradition in analytical ultracentrifugation, and are frequently used in preparative ultracentrifugation. In this paper, a new theoretical model for sedimentation in inhomogeneous media is presented, based on finite element solutions of the Lamm equation with spatial and temporal variation of the local solvent density and viscosity. It is applied to macromolecular sedimentation in the presence of a dynamic density gradient formed by the sedimentation of a co-solute at high concentration. It is implemented in the software SEDFIT for the analysis of experimental macromolecular concentration distributions. The model agrees well with the measured sedimentation profiles of a protein in a dynamic cesium chloride gradient, and may provide a measure for the effects of hydration or preferential solvation parameters. General features of protein sedimentation in dynamic density gradients are described.     

Photolysis of formylmethylflavin in aqueous and organic solvents.

The photolysis of formylmethylflavin (FMF), a major intermediate in the photodegradation sequence of riboflavin, has been carried out in water (pH 7.0) and in several organic solvents. FMF produces lumichrome (LC) in organic solvents and LC and lumiflavin (LF) in aqueous solution. FMF and its photoproducts have been analysed using a specific multicomponent spectrophotometric method. FMF undergoes a bimolecular redox reaction on photolysis. The second-order rate constants for the reaction range from 0.66 (chloroform) to 2.44 M(-1) s(-1) (water) and are a linear function of the solvent dielectric constant. A plot of ln k against 1/epsilon is linear for the reactions in 1-butanol, 1-propanol, ethanol, methanol, acetonitrile and water (epsilon approximately 17-79) and non-linear in chloroform and dichloroethane (epsilon approximately 5-10) suggesting a change in reaction mechanism in the two regions. This may be explained on the basis of the existence of a dipolar intermediate along the reaction pathway. The rate of photolysis is governed by the solvation of the intermediate and is thus influenced by the dielectric constant of the medium. The solvent effect on the rate of photolysis of FMF has been expressed in terms of the solvent acceptor number. A linear relationship has been found between ln k and the solvent acceptor number.     

Iodination of insulin in aqueous and organic solvents

1. The iodination of insulin was studied under various experimental conditions in aqueous media and in some organic solvents, by measuring separately the uptake of iodine by the four tyrosyl groups and the relative amounts of monoiodotyrosine and di-iodotyrosine that are formed. In aqueous media from pH1 to pH9 the iodination occurs predominantly on the tyrosyl groups of the A chain. Some organic solvents increase the iodine uptake of the B-chain tyrosyl groups. Their efficacy in promoting iodination of Tyr-B-16 and Tyr-B-26 is in the order: ethylene glycol and propylene glycol approximately methanol and ethanol>dioxan>8m-urea. 2. It is suggested that each of the four tyrosyl groups in insulin has a different environment: Tyr-A-14 is fully exposed to the solvent; Tyr-A-19 is sterically influenced by the environmental structure, possibly by the vicinity of a disulphide interchain bond; Tyr-B-16 is embedded into a non-polar area whose stability is virtually independent of the molecular conformation; Tyr-B-26 is probably in a situation similar to Tyr-B-16 with the difference that its non-polar environment depends on the preservation of the native structure.     

Lipase-catalyzed cellulose acetylation in aqueous and organic media

Screening for lipases capable of catalyzing acetylation of cellulosic substrates was conducted in aqueous buffer solution using water-soluble carboxymethyl cellulose (CMC) as substrate. Lipase A12 from Aspergillus niger (A. niger) showed the most promising acetylation activity among 11 tested commercial microbial lipases and was further applied to catalyzing acetylation of solid cellulose in aqueous solution. This reaction was shown to be feasible with an acetylation extent of 0.16 wt % achieved compared with no detectable acetylation in the absence of enzyme. Pretreatments on cellulose substrate by ultrasonic irradiation and surfactant solution only slightly improved the acetylation extent by 44 and 27%, respectively. Alternatively, this lipase-catalyzed acetylation was remarkably improved with solubilized cellulose as substrate in the dimethyl sulfoxide/paraformaldehyde solvent system, with an acetylation extent (7.87 wt %) nearly 50 times higher than that achieved in aqueous solution. This improvement was attributed to (1) the absence of bulk water and the increase in substrate solubility by the transition of reaction media from aqueous solution to organic solvents and (2) the ability of lipase A12 to remain catalytically active in highly polar DMSO. This discovery that the A. niger lipase was capable of surviving its contact with polar solvents was further confirmed by its considerably preserved catalytic activity on CMC acetylation in aqueous media after enzyme pretreatments with organic solvents of various polarities and in mixture media with the aqueous phase partially replaced by organic solvents.     

A universal gradient apparatus for multiple organic solvents. II. Fractionation and elution of serum lipids.

Chromatography of serum lipids on a silicic acid column by gradient elution and with continuous detection is described. The gradient is formed in a new organic gradient device based on the principle of E. Peterson and H. A. Sober ((1959) Anal. Chem.31, 857), starting from six initial organic solvents. The detection is realized by flame ionization on a LCM2 liquid chromatography detector (Pye-Unicam). The technique is less solvent- and time-consuming and is of interest in preparative separation and analysis of lipophilic substances.     

Studies of the conformation of apomyoglobin in aqueous solutions and denaturing organic solvents.

The properties of apomyoglobin were examined in aqueous solutions and various helix- and random-coil-forming solvents by solvent perturbation, optical rotation, circular dichroism, and viscosity measurements. The solvent perturbation data obtained in neutral aqueous solutions suggest 25–40% exposure of the two tryptophyl residues and 50–60% exposure of the three tyrosyls. The estimates of burial of these groups are in the ranges expected for myoglobin based on its X-ray structure. In the helicogenic alcohols, methanol, ethanol, 2-chloroethanol, trifluoroethanol, and 1-propyl alcohol, as well as in acidic solutions, 8 M urea and 6M guanidine hydrochloride, essentially all the tryptophyl and tyrosyl residues are found to be exposed to solvent based on this method. Analysis of the ORD and CD data indicates that in the alcohols the α-helix content of apomyoglobin has in most cases changed from 58–59% to about 80–95%. Analysis of the intrinsic viscosity data based on the equations of Simha and Kirkwood and Auer indicates that the polypeptide chain in these solvents has the dimensions of fully extended α-helical rods, with lengths of 221–251 Å and mean diameters of 12.8–13.6 Å. It is concluded that apomyoglobin in the various alcohols must have an extended but somewhat irregular rodlike structure, having a few bend or irregular sequences between the α-helical segments due largely to the presence of the four proline residues, 37, 88, 100, and 120 in the amino acid sequence.     

Enzyme engineering for nonaqueous solvents. II. Additive effects of mutations on the stability and activity of subtilisin E in polar organic media.

Single amino acid substitutions increase the activity and stability of subtilisin E in mixtures of organic solvents and water, and the effects of these mutations are additive. A variant of subtilisin E that exhibits higher activity in mixtures of dimethylformamide (DMF) and water (Q103R) was created by random mutagenesis combined with screening for improved activity (K. Chen and F. H. Arnold, in preparation). Another mutation, N218S, known to improve both the activity and stability of subtilisin BPN', also improves the activity and stability of subtilisin E in the presence of DMF. The effects of the two substitutions on transition-state stabilization are additive. Furthermore, the Q103R mutation that improves activity has no deleterious effect on subtilisin stability. The double mutant Q103R+N218S is 10 times more active than the wild-type enzyme in 20% (v/v) DMF and twice as stable in 40% DMF. Although the effects of single mutations can be impressive, a practical strategy for engineering enzymes that function in nonaqueous solvents will most likely require multiple changes in the amino acid sequence. These results demonstrate the excellent potential for engineering nonaqueous-solvent-compatible enzymes.     

The molecular size and shape of the Folch-Pi apoprotein in aqueous and organic solvents.

In 1% acetic acid, sedimentation velocity measurements and equilibrium ultracentrifuge experiments demonstrate that the Folch-Pi apoprotein is not monodisperse. The weight-average molecular weight calculated from ultracentrifuge experiments and combining sedimentation coefficient and viscosity measurements, ranged from 64000 to 80000. The intrinsic viscosity value suggests an asymetric shape for the apoprotein if a low value of hydration is considered. In dioxan/1% acetic acid (2:3, v/v) a smaller sedimentation coefficient was found, the intrinsic viscosity value remaining identical to that in 4% acetic acid. In pure 2-chloroethanol, light-scattering experiments led to a molecular weight of 165000 indicating that even in this solvent the protein is not monomeric. Intrinsic viscosity and light scattering measurements on the one hand, primary sequence on the other hand (six proline residues per monomer of Mr 23500) suggest that the molecule in 2-chloroethanol may consist of rod-like segments with flexible junctions.     

A simple preparation of half N-acetylated chitosan highly soluble in water and aqueous organic solvents

A simple and improved method of preparing highly soluble chitosan (half N-acetylated chitosan) was developed using a series of chitosan samples of low molecular weights, and the solubility of the half N-acetylated chitosan in water and organic solvents was investigated in detail. To reduce the molecular weight, chitosan was treated with NaBO3 under the condition that chitosan was homogeneously dissolved in aqueous acetic acid. Weight-average molecular weights of the obtained chitosan samples were determined using a size-exclusion chromatography system equipped with a low-angle laser light-scattering photometer. Each chitosan sample was then N-acetylated with acetic anhydride under the condition that chitosan was homogeneously dissolved in aqueous acetic acid again. The water solubility of the half N-acetylated chitosan thus prepared increased with decreasing molecular weight. From 1H NMR spectroscopy, it was suggested that the sequence of N-acetylglucosamine and glucosamine residues was random. The solubility of the half N-acetylated chitosan of low molecular weight was rather high even in aqueous dimethylacetamide and dimethylsulfoxide.     

A model of interfacial inactivation for papain in aqueous organic biphasic systems

A model was proposed to describe the effects of the main factors in aqueous-organic two-liquid-phase media on the stability of papain. The relationships between the half-life of papain activity and these factors including interfacial tension, stirring rate, phase volume ratio and temperature were investigated. The results showed that these factors had notable effects on papain stability except temperature. The correlation coefficient between the model and the experimental data were 0.829, which indicated the model is practicable.     

The activity of PEG-modified chymotrypsin in aqueous and organic media

Summary Polyethylene glycol-modified chymotrypsin was prepared by activation of monomethoxypolyethylene glycols with phenylchloroformates and subsequent coupling with free enzyme. The modification was correlated with enzyme activity in aqueous solution and in organic solvents. The activity in aqueous solution was high (80% of that of non-modified enzyme), even at high degrees of modification. The modified protease was soluble in benzene and DMF and catalyzed transesterification in cyclohexane.     

Designing enzymes for use in organic solvents.

Enzymes are routinely used in organic solvents where numerous reactions of interest to synthetic and polymer chemists can be performed with high selectivity. Recently, it has become apparent that the catalytic properties of an enzyme can be tailored to a specific catalytic requirement by the use of solvent and protein engineering. The former involves altering the polarity, hydrophobicity, water content, etc., of the organic milieu, while the later applies site-directed mutagenesis to alter the physicochemical properties of the biocatalyst. The dominant effects of organic solvents on enzyme structure and function, and the potential of solvent and protein engineering to design enzymes to function optimally in organic media, are the major foci of this review.     

Structure and activity of alpha-chymotrypsin and trypsin in aqueous organic media

The effects of different concentrations (20-95%) of organic solvents (ethanol, 1,4-dioxane and acetonitrile) were studied on alpha-chymotrypsin and trypsin from bovine pancreas. The changes in secondary structure were followed by CD measurements, and the apparent Michaelis constants (KMapp) and the stabilities of the enzymes were determined. Significant alterations in the CD spectra were found for both enzymes at the different organic solvent concentrations. The apparent KM values of trypsin and alpha-chymotrypsin decreased as the low solvent concentrations were elevated, but then increased in the presence of higher organic solvent concentrations. The stabilities of the enzymes changed on increase of the organic solvent concentration; trypsin exhibited a higher stability than that of alpha-chymotrypsin in all organic solvents. These results show that at an organic solvent content of 95% the manifestation of an enzyme activity similar to that measured in water can be attributed to the similar compositions of the secondary structural elements.     

A sensor for superoxide in aqueous and organic/aqueous media based on immobilized cytochrome c on binary self-assembled monolayers

A method for the electrochemical detection of superoxide radical was developed, based on cytochrome c (cyt c) immobilized on the binary self-assembled monolayers (SAMs) of thioctic acid (T-COOH) and thioctic amide (T-NH2) on gold electrode. The sensor works by electrochemically detecting cyt c reduced by the superoxide radical generated by a xanthine-XOD system. The electrochemical properties of immobilized cyt c were investigated in aqueous buffer and in a mixture of aqueous and organic solvents. The interaction of superoxide radical with the modified electrode was characterized in phosphate buffer solution (PBS) and in the mixtures of both PBS and dimethyl sulfoxide (DMSO) and PBS and glycerol (Gly). The results showed that the sensors responded immediately to superoxide radical in PBS and gave a steady-state anodic current within 10s during the generation of superoxide radical. In 40% DMSO and in 30% Gly solution, the current response reached a steady-state anodic current within 20s. The sensor could also be used to estimate superoxide dismutase (SOD).     

Improved stability and catalytic activity of chemically modified papain in aqueous organic solvents

Papain was modified with the anhydrides of various monocarboxylic (acetic or propionic) and dicarboxylic (citraconic, maleic or succinic) acids. 7–10 of the 11 primary amino groups of the enzyme were modified. The organic solvent tolerances of the modified enzyme forms were increased (especially in the concentration range of 10–60%) in comparison with the unmodified enzyme. Acylation enhanced the catalytic activity and stability of papain both in buffer and in aqueous organic solvents (ethanol and acetonitrile). Decrease of the positive charges on the surface of papain resulted in a higher enzyme stability than when they were replaced by negative charges. The kinetic parameters revealed that in aqueous ethanol the maximum rates (V_max) and Michaelis constants (K_M) of the modified papain forms were increased, and higher catalytic efficiencies (k_cat/K_M) were detected as compared with the native enzyme. The results of near-UV circular dichroism and tryptophan fluorescence spectroscopic studies suggested that the modifications caused only local changes around the aromatic residues. The modified enzyme forms led to higher N-acetyl-l-tyrosine ethyl ester synthesis conversions in aqueous ethanol; acetyl and propionyl papain furnishing the highest productivity.     

Lipase-catalyzed synthesis of precursor dipeptides of RGD in aqueous water-miscible organic solvents

PPL-catalyzed synthesis of the precursor dipeptides of RGD as a cellular adhesion factor, Benzyl-Arg-Gly-NH2 and CBZ-Gly-Asp-NH2, was conducted in water-organic cosolvents systems. Five water-miscible organic solvents, which have some advantage over the water-immiscible organic solvent systems or the anhydrous organic solvent systems used often in protease-catalyzed synthesis of a peptide bond, were tested. The reaction condition of PPL-catalyzed synthesis of the dipeptides was optimized by examining the main factors affecting the product yield. The optimal reaction condition for the synthesis of Benzyl-Arg-Gly-NH2 was set up as pH 8.0, 15 degrees C in 40% MeOH for 10 h with the maximum yield of 73.6%. The optimum condition for the synthesis of CBZ-Gly-Asp-NH2 was pH 7.0, 15 degrees C in 50% MeOH for 10h with the maximum yield of 67.0%.     

Transport of bacteria in porous media: II. A model for convective Transport and growth

A model is presented for the coupled processes of bacterial growth and convective transport of bacteria has been modeled using a fractional flow approach. The various mechanisms of bacteria retention can be incorporated into the model through selection of an appropriate shape of the fractional flow curve. Permeability reduction due to pore plugging by bacteria was simulated using the effective medium theory. In porous media, the rates of transport and growth of bacteria, the generation of metabolic products, and the consumption of nutrients are strongly coupled processes. Consequently, the set of governing conservation equations form a set of coupled, nonlinear partial differential equations that were solved numerically. Reasonably good agreement between the model and experimental data has been obtained indicating that the physical processes incorporated in the model are adequate. The model has been used to predict the in situ transport and growth of bacteria, nutrient consumption, and metabolite production. It can be particularly useful in simulating laboratory experiments and in scaling microbial-enhanced oil recovery or bioremediation processes to the field. (c) 1994 John Wiley & Sons, Inc.     

Tyrosinase inactivation in organic solvents.

The inactivation of the catecholase activity of mushroom tyrosinase was investigated under nonaqueous conditions. The enzyme was immobilized on glass beads, and assays were conducted in chloroform, toluene, amyl acetate, isopropyl ether, and butanol. The reaction components were pre-equilibrated for 2 weeks with a saturated salt solution at a water activity of 0.90. The initial reaction velocity varied between 1.3 x 10(3) mol product/((mol enzyme)(min)) in toluene and 8.7 x 10(3) mol product/((mol enzyme)(min)) in amyl acetate. The turnover number varied between 8.1 x 10(3) mol product/mol enzyme in toluene and 7.2 x 10(4) mol product/mol enzyme in amyl acetate. In each solvent, the tyrosinase reaction inactivation parameters were represented by a probabilistic model. Changes in the probability of inactivation were followed throughout the course of the reaction using a second model which relates the reaction velocity to the amount of product formed. These models reveal that the inactivation rate of tyrosinase decreases as the reaction progresses, and that the inactivation kinetics are independent of the quinone concentration in toluene, chloroform, butanol, and amyl acetate. Significant effects of quinone concentration were, however, observed in isopropyl ether. The likelihood of inactivation of the enzyme was found to be greatest toward the beginning of the reaction. In the latter phase of the reaction, inactivation probability was less and tended to remain constant until the completion of the reaction.