Calculation of the relative metastabilities of proteins using the CHNOSZ software package

<p>Abstract</p> <p>Background</p> <p>Proteins of various compositions are required by organisms inhabiting different environments. The energetic demands for protein formation are a function of the compositions of proteins as well as geochemical variables including temperature, pressure, oxygen fugacity and pH. The purpose of this study was to explore the dependence of metastable equilibrium states of protein systems on changes in the geochemical variables.</p> <p>Results</p> <p>A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules.</p> <p>Conclusion</p> <p>Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations.</p

Crossover equation of state models applied to the critical behavior of Xenon

The turbidity ( τ ) measurements of Güttinger and Cannell (Phys Rev A 24:3188–3201, 1981) in the temperature range 28mK≤T−Tc≤29K along the critical isochore of homogeneous xenon are reanalyzed. The singular behaviors of the isothermal compressibility ( κT ) and the correlation length ( ξ ) predicted from the master crossover functions are introduced in the turbidity functional form derived by Puglielli and Ford (Phys Rev Lett 25:143–146, 1970). We show that the turbidity data are thus well represented by the Ornstein–Zernike approximant, within 1 % precision. We also introduce a new crossover master model (CMM) of the parametric equation of state for a simple fluid system with no adjustable parameter. The CMM model and the phenomenological crossover parametric model are compared with the turbidity data and the coexisting liquid–gas density difference ( ΔρLV ). The excellent agreement observed for τ , κT , ξ , and ΔρLV in a finite temperature range well beyond the Ising-like preasymptotic domain confirms that the Ising-like critical crossover behavior of xenon can be described in conformity with the universal features estimated by the renormalization-group methods. Only 4 critical coordinates of the vapor–liquid critical point are needed in the (pressure, temperature, molecular volume) phase surface of xenon