Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA.
Geochem Trans. 2008 Oct 3;9:10. doi: 10.1186/1467-4866-9-10.
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.
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.
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.
生活在不同环境中的生物体需要各种成分的蛋白质。蛋白质形成所需的能量取决于蛋白质的组成以及地球化学变量，包括温度、压力、氧逸度和 pH 值。本研究的目的是探索蛋白质系统的亚稳平衡状态对地球化学变量变化的依赖关系。
开发了一个名为 CHNOSZ 的软件包，该软件包实现了修订后的 Helgeson-Kirkham-Flowers（HKF）状态方程和离子化展开水溶液蛋白质的基团加和性。该程序可用于计算反应的标准摩尔 Gibbs 能量和其他热力学性质，并制作表示蛋白质亚稳平衡分布的化学分类和优势图。该方法考虑了开放系统中反应的化学亲和力，该系统的特征是基础物质的化学势。该软件包中包含的热力学数据库允许将其应用于矿物和其他无机系统以及蛋白质或其他生物分子系统。
为适应不同温度和化学条件生长的古菌和细菌的模型细胞表面蛋白质生成了亚稳平衡活性图。可以将预测的蛋白质亚稳平衡分布与生物体的最佳生长温度和地球化学变量进行比较。结果表明，蛋白质亚稳性的热力学评估可能有助于整合生物和地球化学观测结果。
