Molecular thermodynamic model for DNA melting in ionic and crowded solutions.

A molecular thermodynamic model is developed to predict DNA melting in ionic and crowded solutions. Each pair of nucleotides in the double-stranded DNA and each nucleotide in the single-stranded DNA are respectively represented by two types of charged Lennard-Jones spheres. The predicted melting curves and melting temperatures T(m) of the model capture the general feature of DNA melting and match fairly well with the available simulation and experimental results. It is found that the melting curve is steeper and T(m) is higher for DNA with a longer chain. With increasing the fraction of the complementary cytosine-guanine (CG) base pairs, T(m) increases almost linearly as a consequence of the stronger hydrogen bonding of the CG base pair than that of adenine-thymine (AT) base pair. At a greater ionic concentration, T(m) is higher due to the shielding effect of counterions on DNA strands. It is observed that T(m) increases in the presence of crowder because the crowder molecules occupy a substantial amount of system volume and suppress the entropy increase for DNA melting. At a given concentration, a larger crowder exhibits a greater suppression for DNA melting and hence a higher T(m). At the same packing fraction, however, a smaller crowder leads to a higher T(m).

Metal-organic framework MIL-101 for adsorption and effect of terminal water molecules: from quantum mechanics to molecular simulation.

MIL-101 is a chromium terephthalate-based mesoscopic metal-organic framework and one of the most porous materials reported to date. In this study, we investigate the adsorption of CO(2) and CH(4) in dehydrated and hydrated MIL-101 and the effect of terminal water molecules on adsorption. The atomistic structures of MIL-101 are constructed from experimental crystallographic data, energy minimization, and quantum mechanical optimization. The adsorption isotherm of CO(2) predicted from molecular simulation agrees well with experiment and is relatively insensitive to the method (Merz-Kollman or Mulliken) used to estimate the framework charges. Both the united-atom and five-site models of CH(4) predict the isotherm fairly well, though the former overestimates and the latter underestimates. Adsorption first occurs in the microporous supertetrahedra at low pressures and then in the mesoscopic cages with increasing pressure. In the dehydrated MIL-101, more adsorbate molecules are located near the exposed Cr(2) sites than the fluorine saturated Cr(1) sites. The terminal water molecules in the hydrated MIL-101 act as additional interaction sites and enhance adsorption at low pressures. This enhancement is more pronounced for CO(2) than for CH(4), because CO(2) is quadrapolar and interacts more strongly with the terminal water molecules. At high pressures, however, the reverse is observed, as the presence of terminal water molecules reduces free volume and adsorption. For the adsorption of CO(2)/CH(4) mixture, a higher selectivity is found in the hydrated MIL-101.

Thermodynamics and bioenergetics.

Bioenergetics is concerned with the energy conservation and conversion processes in a living cell, particularly in the inner membrane of the mitochondrion. This review summarizes the role of thermodynamics in understanding the coupling between the chemical reactions and the transport of substances in bioenergetics. Thermodynamics has the advantages of identifying possible pathways, providing a measure of the efficiency of energy conversion, and of the coupling between various processes without requiring a detailed knowledge of the underlying mechanisms. In the last five decades, various new approaches in thermodynamics, non-equilibrium thermodynamics and network thermodynamics have been developed to understand the transport and rate processes in physical and biological systems. For systems not far from equilibrium the theory of linear non-equilibrium thermodynamics is used, while extended non-equilibrium thermodynamics is used for systems far away from equilibrium. All these approaches are based on the irreversible character of flows and forces of an open system. Here, linear non-equilibrium thermodynamics is mostly discussed as it is the most advanced. We also review attempts to incorporate the mechanisms of a process into some formulations of non-equilibrium thermodynamics. The formulation of linear non-equilibrium thermodynamics for facilitated transport and active transport, which represent the key processes of coupled phenomena of transport and chemical reactions, is also presented. The purpose of this review is to present an overview of the application of non-equilibrium thermodynamics to bioenergetics, and introduce the basic methods and equations that are used. However, the reader will have to consult the literature reference to see the details of the specific applications.

Correlation between the osmotic second virial coefficient and the solubility of proteins.

A correlation between the osmotic second virial coefficient and the solubility of proteins is derived from classical thermodynamics to support an empirical relation previously found by Wilson and co-workers (1). The model is based on the equality of fugacities of the protein in the equilibrium phases, with the details of the model depending on the standard state used. The parameters in this model have been fitted to data for several systems, mainly with lysozyme as the protein. The model is found to describe experimental data, with variations in protein concentration, salt type and concentration, temperature, and pH, both qualitatively and quantitatively. Agreement between the model and the experimental data is very good for protein solubilities up to 30 mg/mL. Above this value the model underpredicts the experimental data, probably as a result of multibody interactions that are not included in the model here. Variations of the model parameters with protein type, temperature, pH, and salt type are discussed.

Phase equilibria in the lysozyme-ammonium sulfate-water system.

Ternary phase diagrams were measured for lysozyme in ammonium sulfate solutions at pH values of 4 and 8. Lysozyme, ammonium sulfate, and water mass fractions were assayed independently by UV spectroscopy, barium chloride titration, and lyophilization respectively, with mass balances satisfied to within 1%. Protein crystals, flocs, and gels were obtained in different regions of the phase diagrams, and in some cases growth of crystals from the gel phase or from the supernatant after floc removal was observed. These observations, as well as a discontinuity in protein solubility between amorphous floc precipitate and crystal phases, indicate that the crystal phase is the true equilibrium state. The ammonium sulfate was generally found to partition unequally between the supernatant and the dense phase, in disagreement with an assumption often made in protein phase equilibrium studies. The results demonstrate the potential richness of protein phase diagrams as well as the uncertainties resulting from slow equilibration.

On the thermodynamics of microbial growth processes.

In this article, we provide a rigorous thermodynamic analysis of microbial growth process, clarify the role of the generalized degree of reduction concept as it is used in both stoichiometric equations and as a characterizing factor for thermophysical properties, and introduce a classification method to account for errors when using the generalized degree of reduction to estimate the energy and free energy contents of molecules. We maintain the advantages of using the generalized degree of reduction while correcting for the large errors in the principle of energy regularity, especially for small molecules and for nitrogen-source compounds. As a result, we obtain more accurate energy balances (heat loads) and second law constraints, and are able to clarify contradictory statements in the literature as to whether nonphotosynthesis fermentation process can produce oxygen or absorb rather than produce heat. Indeed, the answers to such questions become evident using the classification system introduced here.

Polymer fractionation in aqueous two-phase polymer systems.

We consider the effects of the addition of poly(ethylene glycol) (PEG) of different molecular weights to aqueous two-phase system of PEG 8000 and dextran 500. The first purpose of this study was to determine the molecular weight partitioning of the polymers themselves so that, for example, aqueous two-phase separations using affinity ligands can be improved. The second purpose was to examine whether this molecular weight partitioning could be predicted by using solution thermodynamic models so that it would be possible to optimize affinity partitioning without extensive laboratory work. Experimentally, we find that, by increasing the PEG concentration of any molecular weight in the feed, the high molecular weight PEG concentration in the dextran-rich phase is reduced. This observation can be used to reduce the loss of expensive ligated PEG used in affinity partitioning. Further, there is generally good agreement between our experimental data and the predictions of a solution thermodynamic model.

Vancomycin partitioning in aqueous two-phase systems: effects of pH, salts, and an affinity ligand.

The partitioning of vancomycin in polyethylene glycol (PEG)-dextran and PEG-phosphate aqueous two-phase systems was studied at different pHs, at varying concentrations of neutral salts, and with an affinity ligand attached to methoxy polyethylene glycol (MPEG). Vancomycin is found to partition preferentially into the PEG-rich top phase, and its partition coefficient increases nearly exponentially with the addition of water structure-making salts, such as sodium sulfate and sodium chloride, but is independent of sodium phosphate concentration. In the PEG-dextran system the vancomycin partition coefficient increases 3-fold in acidic and neutral solutions, while in the PEG-phosphate system it increases about 30-fold on the addition of the same amount of sodium chloride (1. 5 mol/kg). In basic solution, above its isoelectric point, the vancomycin partition coefficient increases slightly with NaCI concentration in the PEG-dextran system. We also examined the use of the dipeptide D-ala-D-ala as an affinity ligand on MPEG to extract vancomycin into the PEG-rich phase. The vancomycin partition coefficient increased almost 7-fold upon adding the MPEG-ligand in an amount equal to approximately 3% of the total PEG in the system. Finally, fractionation of the polydisperse phase-forming polymers in the two-phase PEG-dextran system was observed. The effect of this polymer fractionation on the partition coefficient of vancomycin is discussed.