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

Dick JM - Geochem. Trans. (2008)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA. jedick@berkeley.edu

ABSTRACT

Background: 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.

Results: 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.

Conclusion: 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.

No MeSH data available.


Related in: MedlinePlus

Relative metastabilities of proteins. log -pH diagrams at 25°C and 1 bar were constructed using activities of the basis species given in the Methods. Predominance field boundaries correspond to metastable equilibrium activities of proteins equal to 10-3. The diagrams were made for (a) all of the proteins listed in Table 1 and (b) the proteins listed in Table 1 except for those appearing in the first diagram. The dashed line appearing in each diagram represents the lower (reducing) stability limit of H2O.
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Figure 3: Relative metastabilities of proteins. log -pH diagrams at 25°C and 1 bar were constructed using activities of the basis species given in the Methods. Predominance field boundaries correspond to metastable equilibrium activities of proteins equal to 10-3. The diagrams were made for (a) all of the proteins listed in Table 1 and (b) the proteins listed in Table 1 except for those appearing in the first diagram. The dashed line appearing in each diagram represents the lower (reducing) stability limit of H2O.

Mentions: The equal-activity boundary shown in Fig. 3a between CSG_METVO and CSG_METJA is consistent with metastable equilibrium between the proteins, or A1 = 0. The location of the boundary can be calculated by combining Eqn. (2) with A1 = 0, the equilibrium constant of the reaction, and the reference activities of the basis species and proteins. In this study, the reference activities of the proteins were set to 10-3 and those of the basis species set to the values listed in the Methods.


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

Dick JM - Geochem. Trans. (2008)

Relative metastabilities of proteins. log -pH diagrams at 25°C and 1 bar were constructed using activities of the basis species given in the Methods. Predominance field boundaries correspond to metastable equilibrium activities of proteins equal to 10-3. The diagrams were made for (a) all of the proteins listed in Table 1 and (b) the proteins listed in Table 1 except for those appearing in the first diagram. The dashed line appearing in each diagram represents the lower (reducing) stability limit of H2O.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654789&req=5

Figure 3: Relative metastabilities of proteins. log -pH diagrams at 25°C and 1 bar were constructed using activities of the basis species given in the Methods. Predominance field boundaries correspond to metastable equilibrium activities of proteins equal to 10-3. The diagrams were made for (a) all of the proteins listed in Table 1 and (b) the proteins listed in Table 1 except for those appearing in the first diagram. The dashed line appearing in each diagram represents the lower (reducing) stability limit of H2O.
Mentions: The equal-activity boundary shown in Fig. 3a between CSG_METVO and CSG_METJA is consistent with metastable equilibrium between the proteins, or A1 = 0. The location of the boundary can be calculated by combining Eqn. (2) with A1 = 0, the equilibrium constant of the reaction, and the reference activities of the basis species and proteins. In this study, the reference activities of the proteins were set to 10-3 and those of the basis species set to the values listed in the Methods.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA. jedick@berkeley.edu

ABSTRACT

Background: 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.

Results: 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.

Conclusion: 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.

No MeSH data available.


Related in: MedlinePlus