Forces causing osmotic pressure.

An analysis of forces acting on a simple system that includes a solvent, solute, and a semipermeable membrane shows the basic mechanism of osmotic pressure can be expressed as any of three forces: that due to the interaction of solute particles with the semipermeable membrane; that due to the cohesiveness of the solvent; or that due to the solute particles interacting with the free surface of the solvent.     

Self-assembly of two-patch particles in solution: a Brownian dynamics simulation study

We study the self-assembly behaviour of two-patch particles with D_∞h symmetry by using Brownian dynamics simulations. The self-assembly process of two-patch particles with diverse patch coverage in two selective solvent conditions is investigated. The patchy particles in a solvent that is bad for patches but good for matrix form linear thread-like structures with low patch coverage, whereas they form 3D network structures with relatively high patch coverage on surface. For patchy particles in a solvent which is good for patches but bad for body, monolayer structures are obtained at high patch coverage, and some cluster structures emerge when surface patch coverage is low.     

Coarse-grained simulations of the salt dependence of the radius of gyration of polyelectrolytes as models for biomolecules in aqueous solution

The salt dependent radius of gyration of a polyelectrolyte in aqueous solution is calculated in an environment where the polyelectrolyte is surrounded by a permeable membrane that exchanges only solvent particles with the bulk. We obtain additionally the scaling exponent of the gyration radius as a function of the polymerization degree, and find that the polyelectrolyte retains a stretched conformation during the condensation and re-expansion process, indicating that these effects are of an electrostatic nature. The solvent quality is also shown to affect the polyelectrolyte conformation, especially for the poor solvent case. These results are obtained using a hybridized Monte Carlo technique with the coarse-grained, dissipative particle dynamics method with fluctuating number of solvent particles. The full range of the electrostatic interactions is included in the simulations, using the Ewald sum method, and the counterions and solvent molecules are included explicitly. In the complex systems mentioned above, the electrostatic interactions and the solvent quality play a key role in understanding phenomena that do not occur in uncharged systems. Our results are compared and validated with the behavior of some biomolecules under similar environments.     

Role of diffusion in nonaqueous enzymology. 1. Theory.

Using a set of standard equations, we have calculated the role of internal and external mass transfer in limiting the rate of enzyme-catalysed reactions in anhydrous organic solvents and supercritical fluids. We have shown that enzyme particles suspended in anhydrous organic solvents will be subject to increasing diffusional limitation as the enzyme activity and particle size increase. Using particle dimensions, as measured by scanning electron microscopy, we have prepared a series of graphs that will enable investigators to determine whether their combination of particle size and activity will result in internal or external diffusional limitations. We have shown that supercritical fluids can be expected to enhance the activity of enzymes in nonaqueous environments as a result of the high diffusivity of the bulk solvent. The plots also clearly indicate that enzyme particles in supercritical fluids require nearly two orders of magnitude less agitation than those suspended in conventional solvents in order to overcome any external mass transfer limitations.     

Effect of the length and effective diameter of F-actin on the filament orientation in liquid crystalline sols measured by x-ray fiber diffraction.

We examined factors that affect the filament orientation in F-actin sols to prepare highly well-oriented liquid crystalline sols suitable for x-ray fiber diffraction structure analysis. Filamentous particles such as F-actin spontaneously align with one another when concentrated above a certain threshold concentration. This alignment is attributed to the excluded volume effect of the particles. In trying to improve the orientation of F-actin sols, we focused on the excluded volume to see how it affects the alignment. The achievable orientation was sensitive to the ionic strength of the solvent; the filaments were better oriented at lower ionic strengths, where the effective diameter of the filament is relatively large. Sols of longer filaments were better oriented than those of shorter filaments at the same concentration, but the best achievable orientation was limited, probably because of the filament flexibility. The best strategy for making well-oriented F-actin sols is therefore to concentrate F-actin filaments of relatively short length (<1 micrometer) by slow centrifugation in a low-ionic-strength solvent (<30 mM).     

A model for sedimentation in inhomogeneous media. II. Compressibility of aqueous and organic solvents

The effects of solvent compressibility on the sedimentation behavior of macromolecules as observed in analytical ultracentrifugation are examined. Expressions for the density and pressure distributions in the solution column are derived and combined with the finite element solution of the Lamm equation in inhomogeneous media to predict the macromolecular concentration distributions under different conditions. Independently, analytical expressions are derived for the sedimentation of non-diffusing particles in the limit of low compressibility. Both models are quantitatively consistent and predict solvent compressibility to result in a reduction of the sedimentation rate along the solution column and a continuous accumulation of solutes in the plateau region. For both organic and aqueous solvents, the calculated deviations from the sedimentation in incompressible media can be very large and substantially above the measurement error. Assuming conventional configurations used for sedimentation velocity experiments in analytical ultracentrifugation, neglect of the compressibility of water leads to systematic errors underestimating sedimentation coefficients by approximately 1% at a rotor speeds of 45000 rpm, but increasing to 2-5% with increasing rotor speeds and decreasing macromolecular size. The proposed finite element solution of the Lamm equation can be used to take solvent compressibility quantitatively into account in direct boundary models for discrete species, sedimentation coefficient distributions or molar mass distributions. Using the analytical expressions for the sedimentation of non-diffusing particles, the ls-g*(s) distribution of apparent sedimentation coefficients is extended to the analysis of sedimentation in compressible solvents. The consideration of solvent compressibility is highly relevant not only when using organic solvents, but also in aqueous solvents when precise sedimentation coefficients are needed, for example, for hydrodynamic modeling.     

Birefringence of Protein Solutions and Biological Systems. I

The quantitative interpretation of birefringence of biological structures such as muscle requires a knowledge of intrinsic birefringence of the components. The intrinsic birefringence of fibrous structures as determined by variation of solvent index is positive while the intrinsic birefringence of proteins in solution is negative as calculated by the Peterlin-Stuart theory. As a first step in clarifying this discrepancy the basis of the Peterlin-Stuart theory has been re-examined. The theory has been recalculated from the standpoint of light scattering and extended to particles whose length is not small compared to the wavelength. The birefringence of a system of particles possessing a shell with index different from the bulk solvent has been obtained in order to interpret measurements in mixed solvents.     

Fluorescence studies on the role of tryptophan in heterogeneous nuclear ribonucleoprotein particles of HeLa cells.

The 40 S heterogeneous nuclear ribonucleoprotein (hnRNP) particles from HeLa cells reveal tryptophan fluorescence with a bi-exponential decay, indicating that only a few of the 'core' proteins contain tryptophan residues. The presence of tryptophan residues distinguishes hnRNP particles from nucleosomes, with which they otherwise share a number of properties. This difference, however, is not essential for protein-RNA binding, as the fluorescence decay remains unchanged when hnRNP particles are dissociated into protein and RNA. However, the Stern-Volmer quenching constant is doubled upon salt dissociation, i.e. tryptophan residues become more accessible to solvent. Thus tryptophan quenching is a useful parameter for monitoring protein-protein interactions in hnRNP particles.     

Microparticles of soy lecithin formed by supercritical processes

Finely divided particles of phospholipids are used to form controlled drug delivery systems called liposomes. Conventional physicochemical methods for preparing these microparticles are hampered by a major drawback-the use of organic solvents that remain at few but inhibitory concentration in the final product. This study aimed to propose an alternative method for preparing microparticles of phospholipids starting from soy lecithin-the process had to be free of solvent or at least, the solvent had to be nontoxic. Two micronization techniques based on the use of supercritical carbon dioxide were investigated: the RESS and the SAS processes. The RESS process failed to separate the particles formed from the cosolvent. Performing the SAS process with ethanol as auxiliary solvent, enabled fine particles to form with size ranging from 1 to 40 microm. Particles were spherical and partly agglomerated and seemed to be free of solvent as shown by preliminary infrared analysis.     

Chromatin model calculations: Arrays of spherical nu bodies.

Chromatin fibers consists of globular nucleohistone particles (designated nu bodies) along the length of the chromatin DNA with approximately 6-to7-fold compaction of the DNA within the nu bodies. We have calculated theoretical small-angle x-ray scattering curves and have compared these with experimental data in the literature. Several models predict maxima at the correct angles. The first maximum (approximately 110 degrees A) results from interparticle interference, while both the spatial arrangement and the structure factor the nu bodies can contribute to the additional small-angle maxima. These calculations suggest models which can account for the electron microscopic observation that chromatin is seen as either approximately 100-or approximately 200-to 250 degrees A-diameter fibers, depending on the solvent conditions. They also account for the limited orientability of the x-ray pattern from pulled chromatin fibers.     

Calculation of protein form birefringence using the finite element method.

An approach based on the finite element method (FEM) is employed to calculate the optical properties of macromolecules, specifically form birefringence. Macromolecules are treated as arbitrarily shaped particles suspended in a solvent of refraction index n1. The form birefringence of the solution is calculated as the difference in its refractive index when all the particles of refractive index n2 are either parallel to or normal to the direction of the polarization of light. Since the particles of interest are small compared to the wavelength of light, a quasi-static approximation for the refractive index is used, i.e., that it is equal to the square root of the dielectric constant of the suspension. The average dielectric constant of the mixture is calculated using the finite element method. This approach has been tested for ellipsoidal particles and a good agreement with theoretical results has been obtained. Also, numerical results for the motor domains of ncd and kinesin, small arbitrarily shaped proteins with known x-ray structures, show reasonable agreement with the experimental data obtained from transient electric birefringence experiments.     

Bilayers of nucleosome core particles

Among the multiple effects involved in chromatin condensation and decondensation processes, interactions between nucleosome core particles are suspected to play a crucial role. We analyze them in the absence of linker DNA and added proteins, after the self-assembly of isolated nucleosome core particles under controlled ionic conditions. We describe an original lamellar mesophase forming tubules on the mesoscopic scale. High resolution imaging of cryosections of vitrified samples reveals how nucleosome core particles stack on top of one another into columns which themselves align to form bilayers that repel one another through a solvent layer. We deduce from this structural organization how the particles interact through attractive interactions between top and bottom faces and lateral polar interactions that originate in the heterogeneous charge distribution at the surface of the particle. These interactions, at work under conditions comparable with those found in the living cell, should be of importance in the mechanisms governing chromatin compaction in vivo.     

Structure of human serum lipoproteins in solution. II. Small-angle x-ray scattering study of HDL and LDL.

Two human serum lipoprotein particles, HDL₃ and LDL, were studied in solution in solvents of variable density (NaBr in water) by small-angle X-ray scattering using a position-sensitive proportional counter. The data were analysed using the theoretical approach outlined in the accompanying paper (Luzzati et al., 1976). The structures of the particles were found to be independent of the salt concentration of the solution (i.e. the particles are impenetrable to NaBr). Density heterogeneities are negligible and size and shape heterogeneities appear to be small.The particle structures could be quantitatively described in terms of a set of parameters and of a few one-dimensional functions. The parameters are the volume, radius of gyration and surface area of the shape functions; the second moment and square average of the electron density contrast at buoyancy; the electron density level, volume, radius of gyration and surface area of the hydrocarbon and polar regions. The one-dimensional functions are: the distribution of chords, the spherical average of the shape function and of the electron density at buoyancy, and the fraction of each spherical shell occupied by the hydrocarbon and polar regions. These parameters and functions are internally consistent and agree with the chemical data confirming the assumptions made in their derivation.The results are compatible with the shape of the particle being compact and quasi-spherical although with deeply convoluted surfaces. They also indicate that the outer layers of the particles are occupied by the proteins and the polar groups of phospholipids and free cholesterol, and the cores by neutral lipids. The maximum diameters of the particles are 130Å and 280Å for HDL₃ and LDL, respectively, while the hydrocarbon cores have diameters of 80Å and 230Å, respectively. The solvent is considered to penetrate to 25Å from the center of the HDL₃ particle with a minimum solvation at a radius of 45Å. In the case of LDL, the solvent penetrates to 55Å from the center of the particle. The lipids in the cores of the particles, particularly the cholesterol esters, appear to display a micelle-like organization with the steroid nuclei segregated in regions distinct from those occupied by the hydrocarbon chains.Although the data are consistent with several aspects of previously proposed models, they indicate that the structures of the HDL₃ and LDL particles are more complex than previously believed.     

Molecular dynamics simulation study of the static and dynamic properties of a model colloidal suspension with explicit solvent

Molecular dynamics simulation was used to study a colloidal suspension with explicit solvent to determine how inclusion of the solvent affects the structure and dynamics of the system. The solute was modelled as a hard-core particle enclosed in a Weeks–Chandler–Andersen (WCA) potential shell, while the solvent was modelled as a simple WCA fluid. We found that when the solute–solvent interaction included a hard core equal to half of the solute hard-core diameter, large depletion effects arose, leading to an effective attraction and large deviations from hard-sphere structure for the colloidal component. It was found that these effects could be eliminated by reducing the hard-core distance parameter in the solute–solvent interaction, thus allowing the solvent to penetrate closer to the colloidal particles. Three different values for the solute–solvent hard-core parameter were systematically studied by comparing the static structure factor and radial distribution function to the predictions of the Percus–Yevick theory for hard spheres. When the optimal value of the solute–solvent hard-core interaction parameter was found, this model was then used to study the dynamical behaviour of the colloidal suspension. This was done by first measuring the velocity autocorrelation function (VACF) over a large range of packing fractions. We found that this model predicted the sign of the long-time tail in the VACF in agreement with experimental values, something that single component hard-sphere systems have failed to do. The intermediate scattering functions at low wavevector were briefly studied to determine their behaviour in a dilute system. It was found that they could be modelled using a simple diffusion equation with a wavevector independent diffusion coefficient, making this model an excellent analogue of experimentally studied hard-sphere colloids.     

Solvent structure and enzyme activity

Enzymes are fluctuating particles in thermal equilibrium with their solvent environment. A variety of models of enzyme action have postulated selective excitation of enzyme vibrational modes or triggering of correlated motion of catalytic groups through collisions with solvent particles as the basis of catalytic activity. Solvent composition and structure are expected to influence such interactions. Solutes such as p-dioxane, t-butanol, and tetraalkylammonium chlorides are known to be strong perturbants of the structure of water. However, when the kinetic parameters of two enzymes, carboxypeptidase A and alpha-chymotrypsin, were examined carefully in aqueous mixtures containing these solutes, no significant influence of solvent structure or mass composition on the catalytic rate constant was found. The results indicate, furthermore, that, within the low viscosity limit, fluctuations in enzyme structure that are responsible for activated processes in the catalytically rate limiting step appear not to be significantly influenced by dynamic processes in the bulk solvent.     

Bile acids. LXXII. High-performance liquid chromatographic analysis of bile acid coenzyme A derivatives

The mobilities of coenzyme A and coenzyme A derivatives of cholate, chenodeoxycholate, deoxycholate, lithocholate, and their 5 alpha analogs were studied in reversed-phase high-performance liquid chromatography. With a C18 Radial-PAK A cartridge (10-micron particles) and a solvent mixture of 2-propanol/10 mM phosphate buffer (pH 7.0, 140:360), separation of the chenodeoxycholyl and deoxycholyl coenzyme A derivatives was not observed. An increase in ionic strength of the buffer to 50 mM afforded separation, which was markedly augmented with a C18 Radial-PAK A cartridge with 5-micron particles. Lowering the pH of the buffer to 5.5 did not materially change the separations regardless of the ionic strength. Quantitation was carried out to a lower level of 8.5 X 10(-12) mol.     

Magnetic cross-relaxation among protons in protein solutions.

The magnetic spin-lattice relaxation rates of solvent water nuclei are known to increase upon addition of diamagnetic solute protein. This enhancement of the relaxation rate is a function of magnetic field, and the orientational relaxation time of the protein molecules can be deduced from analysis of the field-dependent relaxation rates. Although the nature of the interactions that convey information about the dynamics of protein motion to the solvent molecules is not established, it is known that there is a contribution to the relaxation rates of solvent protons that plays no role in the relaxation of solvent deuterons and 17O nuclei. We show here that the additional interaction arises from a cross-relaxation process between solvent and solute protons. We introduce a heuristic three-parameter model in which protein protons and solvent protons are considered as two separate thermodynamic systems that interact across the protein-solvent interface. The three parameters are the intrinsic relaxation rates of each system and a cross-relaxation term. The sign of the latter term must always be positive, for all values of magnetic field, in order for magnetization energy to flow from the hotter to the cooler system. We find that the magnetic field-dependence of the cross-relaxation contribution is much like that of the remaining solvent proton relaxation, i.e., about the same as the deuteron relaxation field dependence. This finding is not compatible with the predictions of expressions for the cross-relaxation that have been used by other authors, but not applied to data over a wide range of magnetic field strength. The model predicts that the relaxation behavior of both the protein protons and the solvent protons is the sum of two exponentials, the relative contributions of which would vary with protein concentration and solvent isotopic composition in a fashion suggestive of the presence of two classes of protein protons, when there is in reality only one. This finding has immediate implications for the interpretation of published proton relaxation rates in complex systems such as tissues; these data should be reexamined with cross-relaxation taken into account.     

The inhibitory effect of extracts of cigarette tar on electron transport of mitochondria and submitochondrial particles.

Acetonitrile extracts of cigarette tar inhibit state 3 and state 4 respiration of intact mitochondria. Exposure of respiring submitochondrial particles to acetonitrile extracts of cigarette tar results in a dose-dependent inhibition of oxygen consumption and reduced nicotinamide adenine dinucleotide (NADH) oxidation. This inhibition was not due to a solvent effect since acetonitrile alone did not alter oxygen consumption or NADH oxidation. Intact mitochondria are less sensitive to extracts of tar than submitochondrial particles. The NADH-ubiquinone (Q) reductase complex is more sensitive to inhibition by tar extract than the succinate-Q reductase and cytochrome complexes. Nicotine or catechol did not inhibit respiration of intact mitochondria. Treatment of submitochondrial particles with cigarette tar results in the formation of hydroxyl radicals, detected by electron spin resonance (ESR) spin trapping. The ESR signal attributable to the hydroxyl radical spin adduct requires the presence of NADH and is completely abolished by catalase and to a lesser extent superoxide dismutase (SOD). Catalase and SOD did not protect the mitochondrial respiratory chain from inhibition by tar extract, indicating that the radicals detected by ESR spin trapping are not responsible for the inhibition of the electron transport. We propose that tar causes at least two effects: (1) Tar components interact with the electron transport chain and inhibit electron flow, and (2) tar components interact with the electron transport chain, ultimately to form hydroxyl radicals.     

Solvent Structure and Enzyme Activity

Abstract

Enzymes are fluctuating particles in thermal equilibrium with their solvent environment. A variety of models of enzyme action have postulated selective excitation of enzyme vibrational modes or triggering of correlated motion of catalytic groups through collisions with solvent particles as the basis of catalytic activity. Solvent composition and structure are expected to influence such interactions. Solutes such as p-dioxane, t-butanol, and tetraalkylammonium chlorides are known to be strong perturbants of the structure of water. However, when the kinetic parameters of two enzymes, carboxypeptidase A and α-chymotrypsin, were examined carefully in aqueous mixtures containing these solutes, no significant influence of solvent structure or mass composition on the catalytic rate constant was found. The results indicate, furthermore, that, within the low viscosity limit, fluctuations in enzyme structure that are responsible for activated processes in the catalytically rate limiting step appear not to be significantly influenced by dynamic processes in the bulk solvent.     

A neutral pH acrylamide gel electrophoretic system for histones and other basic proteins.

A method has been devised whereby measurement of the acid-labile sulfide content of spinach subchloroplast particles is free of interference resulting from the presence of Triton X-100. Quantitative extraction into an organic solvent allows accurate detection of micromolar concentrations of sulfide.