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.     

Excluded volume effects in gene stretching

We investigate the effects excluded volume on the stretching of a single DNA in solution. We find that for small force F, the extension h is not linear in F but proportion to F(gamma), with gamma = (1 - nu)/nu, where nu is the well-known universal correlation length exponent. A freely joint chain model with the segment length chosen to reproduce the small extension behavior gives excellent fit to the experimental data of lambda-phage DNA over the whole experimental range. We show that excluded volume effects are stronger in two dimensions and derive results in two dimensions that are different from the three-dimensional results. This suggests experiments to be performed in these lower dimensions.     

Range of the solvation pressure between lipid membranes: dependence on the packing density of solvent molecules

Well-ordered multilamellar arrays of liquid-crystalline phosphatidylcholine and equimolar phosphatidylcholine-cholesterol bilayers have been formed in the nonaqueous solvents formamide and 1,3-propanediol. The organization of these bilayers and the interactions between apposing bilayer surfaces have been investigated by X-ray diffraction analysis of liposomes compressed by applied osmotic pressures up to 6 X 10(7) dyn/cm2 (60 atm). The structure of egg phosphatidylcholine (EPC) bilayers in these solvents is quite different than in water, with the bilayer thickness being largest in water, 3 A narrower in formamide, and 6 A narrower in 1,3-propanediol. The incorporation of equimolar cholesterol increases the thickness of EPC bilayers immersed in each solvent, by over 10 A in the case of 1,3-propanediol. The osmotic pressures of various concentrations of the neutral polymer poly(vinylpyrrolidone) dissolved in formamide or 1,3-propanediol have been measured with a custom-built membrane osmometer. These measurements are used to obtain the distance dependence of the repulsive solvation pressure between apposing bilayer surfaces. For each solvent, the solvation pressure decreases exponentially with distance between bilayer surfaces. However, for both EPC and EPC-cholesterol bilayers, the decay length and magnitude of this repulsive pressure strongly depend on the solvent. The decay length for EPC bilayers in water, formamide, and 1,3-propanediol is found to be 1.7, 2.4, and 2.6 A, respectively, whereas the decay length for equimolar EPC-cholesterol bilayers in water, formamide, and 1,3-propanediol is found to be 2.1, 2.9, and 3.1 A, respectively. These data indicate that the decay length is inversely proportional to the cube root of the number of solvent molecules per unit volume.(ABSTRACT TRUNCATED AT 250 WORDS)     

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.     

Buoyant density and solvation of magnesium DNA

The buoyant density of T-4 DNA was determined by equilibrium sedimentation in a density gradient, of mixed solutions of cesium and magnesium chlorides and bromides. The preferential hydration was calculated from these data, allowing appropriately for the exchange equilibrium of DNA with Cs⁺ and Mg⁺⁺ ions. The charge and intrinsic solvation of the counterions were found to have no appreciable effect on the hydration of the DNA, the extent of solvation depending only on the thermodynamic, activity of the water. Various reasonable hypotheses are discussed to account for these results.     

Excluded volume as a determinant of macromolecular structure and reactivity

The effect of excluded volume on the thermodynamic activity of globular macromolecules and macromolecular complexes in solution is studied in the hard-particle approximation. Activity coefficients are calculated as a function of the fraction of total volume occupied by macromolecules using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of volume occupied by globular macromolecules increases, including the following: (i) Compact quasi-spherical macromolecular conformations become increasingly energetically favored over extended anisometric conformations. (ii) Self- and heteroassociation processes are enhanced, particularly those leading to the formation of compact quasi-spherical aggregates. (iii) Depending upon the details of the reaction mechanism, the rate of an enzyme-catalyzed reaction may monotonically decrease, go through a maximum, or exhibit more complex behavior. A given degree of volume occupancy by larger macromolecules is predicted to have less effect on the structure and self-association of smaller macromolecules than the same degree of volume occupancy by smaller macromolecules has on the structure and self-association of larger macromolecules.     

Comparing brain networks of different size and connectivity density using graph theory

Graph theory is a valuable framework to study the organization of functional and anatomical connections in the brain. Its use for comparing network topologies, however, is not without difficulties. Graph measures may be influenced by the number of nodes (N) and the average degree (k) of the network. The explicit form of that influence depends on the type of network topology, which is usually unknown for experimental data. Direct comparisons of graph measures between empirical networks with different N and/or k can therefore yield spurious results. We list benefits and pitfalls of various approaches that intend to overcome these difficulties. We discuss the initial graph definition of unweighted graphs via fixed thresholds, average degrees or edge densities, and the use of weighted graphs. For instance, choosing a threshold to fix N and k does eliminate size and density effects but may lead to modifications of the network by enforcing (ignoring) non-significant (significant) connections. Opposed to fixing N and k, graph measures are often normalized via random surrogates but, in fact, this may even increase the sensitivity to differences in N and k for the commonly used clustering coefficient and small-world index. To avoid such a bias we tried to estimate the N,k-dependence for empirical networks, which can serve to correct for size effects, if successful. We also add a number of methods used in social sciences that build on statistics of local network structures including exponential random graph models and motif counting. We show that none of the here-investigated methods allows for a reliable and fully unbiased comparison, but some perform better than others.     

Determination of particle sedimentation rate by ultrasonic interferometry: Role of particle size,density and volume fraction

The sedimentation rate (SR) of non-aggregated spherical particles in suspension was determined using an ultrasonic interferometry technique (Echo-Cell); this method is based on A-mode echography and measures the rate of formation of a sediment on a solid plate during settling. The particle accumulation rate, which is related to SR, is obtained from the interference of two waves reflected by two interfaces: one between the plate and the sediment and the other between the sediment and the suspension. Studies were carried out at 25°C using latex spheres of different diameters (7 to 20 μm) and densities (1.062 to 1.190 g/cm³) suspended in distilled water at various volume fractions (1% to 5%). As anticipated by the Stokes model, linear relations were found between SR and both particle density and the square of particle radius. Experimental SR values decreased with increasing suspension particle concentration; these concentration effects were in good agreement with those predicted by the Steinour model. Our results thus serve to validate the theoretical aspects of the Echo-Cell method and suggest its usefulness as a tool for studies of RBC interaction and RBC aggregation.     

Excluded volume effects on the partition of macromolecules between two liquid phases

Partition parameters of several proteins and other macromolecules are measured in an aqueous two-phase liquid system containing polyethylene glycol and phosphate buffer. Distribution of macromolecules is a function of the relative volume excluded to the macromolecules in the two phases. A simple model with no adjustable parameters yields covolumes of the macromolecules with the polyethylene glycol. Covolumes are used to estimate effective molecular volumes and the magnitudes of excluded volume effects. The same approach is applied to mixtures of macromolecules.     

Isolation of human monocytes according to volume and density

Human peripheral blood monocytes were obtained in very pure preparations by using buoyant density gradient centrifugation followed by velocity sedimentation. We introduced several modifications in the experimental procedure in order to take advantage of the minimal differences in cell density and size between monocytes and lymphocytes. Previous methods used to isolate monocytes based on their physical properties are reviewed, and the theory of velocity sedimentation is discussed with regard to the differences in the methodology used, which account for the different results we obtained.     

Separation of lymphoid-line cells according to volume and density

Velocity sedimentation and isopycnic centrifugation was used to separate exponentially growing RAJI lymphoid line cells according to size and density. Mixtures of Ficoll, Isopaque and tissue culture medium were used as gradient media. These media had a constant pH, were isotonic, and did not have any significant harmful effect on the cells. The observed variation in cell size paralleled the progression of the cells through the cell cycle, as assessed by thymidine incorporation and impulse cytophotometric determination of DNA contents. Differences in cell density did not reflect the cell cycle phase. No correlation could be established between cell size and density. Velocity sedimentation could be used to obtain cell populations which were relatively pure according to cell cycle phase and growing synchronously for at least 24 h.     

Measurement of preferential solvation of some glucans in mixed solvent systems by gel-permeation chromatography

Preferential solvation of the glucans amylose, pullulan, and dextran in binary dimethyl-sulfoxide/water (DMSO/H₂O) solvent mixtures has been measured using gel-permeation chromatography. The preferential solvation behavior of the three glucans in DMSO/H₂O solvent mixtures is indistinguishable in the experiments reported. In solvent mixtures with mol ratio DMSO/H₂O less than 1:2, all three glucans are solvated preferentially by H₂O. The maximum extent of preferential solvation by H₂O is about 2.5 mol H₂O/mol of glucose residues. When the DMSO/H₂O mol ratio exceeds 1:2, DMSO solvates the glucans preferentially to a maximum extent of about 1 mol DMSO/mol of glucose residues. An interpretation of the change in preferential solvation with mixed solvent composition is suggested in terms of the known characteristics of the binary solvent system, and the relationship of preferential solvation, reported here, to the absolute solvation of the glucan chains is discussed.     

Canopy seed bank structure in relation to: fire,tree size and density

To assess the canopy seed bank structure of Pinus halepensis, we measured the level of serotiny and the seed bank size and density of trees in unburned stands and post-fire regenerated stands in Israel. We analysed the effects of tree size, tree density and fire history on the level of serotiny. The level of serotiny decreased with an increase in tree height. The high level of serotiny in short trees could be explained by selection to increase regeneration chances after burning at pre-mature age. Also, limitation of long-distance seed dispersal opportunities in short trees may favour high serotiny levels. The level of serotiny was higher in post-fire stands than in unburned stands, suggesting a fast selection for serotiny by fire. Unburned stands had a higher total stand seed density than post-fire regenerated stands, but the proportion of seeds in serotinous cones of the total stand seed density was higher in post-fire regenerated stands. The fact that P. halepensis bears simultaneously serotinous and non-serotinous cones reflects its dual strategy as both a post-fire obligate seeder, mainly from serotinous cones and an early coloniser during fire-free periods, mainly from non-serotinous cones. The relative investment in these strategies is dependent on fire history and varies with tree height. Furthermore, mature brown cones can contribute to post-fire regeneration in case of spring fires, and serotinous cones are known to open partially also in dry spell events. Thus, post-fire regeneration and invasion are strategies, which seem to complement each other.     

Airway thermal volume in humans and its relation to body size

Serikov, Vladimir B., E. Heidi Jerome, Neal W. Fleming,Peter G. Moore, Frederick A. Stawitcke, and Norman C. Staub.Airway thermal volume in humans and its relation to body size.J. Appl. Physiol. 83(2): 668-676, 1997.The objective of this study was to investigate the influence ofvolume ventilation(E) andcardiac output () on the temperature of the expiredgas at the distal end of the endotracheal tube in anesthetized humans.In 63 mechanically ventilated adults, we used a step decrease in thehumidity of inspired gas to cool the lungs. After change from humid todry gas ventilation, the temperature of the expired gas decreased. Weevaluated the relationship between the inverse monoexponential timeconstant of the temperature fall (1/) and eitherE or . WhenE wasincreased from 5.67 ± 1.28 to 7.14 ± 1.60 (SD) l/min(P = 0.02), 1/ did not changesignificantly [from 1.25 ± 0.38 to 1.21 ± 0.51 min¹,P = 0.81]. In the 11 patients in whom changed during the study period(from 5.07 ± 1.81 to 7.38 ± 2.45 l/min,P = 0.02), 1/ increasedcorrespondingly from 0.89 ± 0.22 to 1.52 ± 0.44 min¹(P = 0.003). We calculated the airwaythermal volume (ATV) as the ratio of the measured values to 1/ and related it to the body height (BH):ATV (liters) = 0.086 BH (cm)  9.55 (r = 0.90).

     

Density functional theory analysis of carbonyl sulfide hydrolysis: effect of solvation and nucleophile variation

The detailed mechanisms of the hydrolysis of carbonyl sulfide (OCS) by nucleophilic water and hydroxide ion in both the gas phase and bulk water solvent have been investigated using density functional theory. Various reaction channels on the potential surface have been identified. The thermodynamic results demonstrate that the hydrolysis of OCS by nucleophilic water and hydroxide ion should proceed more favorably at low temperature. The hydrolysis of OCS by the hydroxide ion is the main reaction channel from thermodynamic and kinetic perspectives, and the bulk solvent can influence the rate-determining step in this channel. However, the solvent barely modifies the activation energy of the rate-determining step. For the hydrolysis of OCS by nucleophilic water, the solvent does not modify the rate-determining step, and the corresponding activation energy of the rate-determining step barely changes. This bulk solvent effect suggests that most of the contribution of the solvent is accounted for by considering one water molecule and a hydroxide ion.     

New developments in first-principles excited-state dynamics simulations: unveiling the solvent specificity of excited anionic cluster relaxation and electron solvation

Charge-transfer-to-solvent excited iodide–polar solvent molecule clusters, [I^? (Solv)_n]^*, have attracted substantial interest over the past 20 years as they can undergo intriguing relaxation processes leading ultimately to the formation of gas-phase molecular analogues of the solvated electron. In this review article, we present a comprehensive overview of the development and application of state-of-the-art first-principles molecular dynamics simulation approaches to understand and interpret the results of femtosecond photoelectron spectroscopy experiments on [I^? (Solv)_n]^* relaxation, which point to a high degree of solvent specificity in the electron solvation dynamics. The intricate molecular details of the [I^? (Solv)_n]^* relaxation process are presented, and by contrasting the relaxation mechanisms of clusters with several different solvents (water, methanol and acetonitrile), the molecular basis of the solvent specificity of electron solvation in [I^? (Solv)_n]^* is uncovered, leading to a more refined view of the manifestation of electron solvation in small gas-phase clusters.