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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

Properties of archaeal surface-layer proteins. Shown are calculated values of the net charge per residue (a) and standard molal Gibbs energy of formation from the elements (b) at 25°C and 1 bar for surface-layer proteins from archaeal species listed in Table 1. The computed charges per residue of CSG_METFE and CSG_METSC are indistinguishable from one another in (a).
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Figure 4: Properties of archaeal surface-layer proteins. Shown are calculated values of the net charge per residue (a) and standard molal Gibbs energy of formation from the elements (b) at 25°C and 1 bar for surface-layer proteins from archaeal species listed in Table 1. The computed charges per residue of CSG_METFE and CSG_METSC are indistinguishable from one another in (a).

Mentions: In Reaction 1 it can be noted that O2(g) appears on the same side of the reaction as ; hence, the metastability of this protein is increased relative to that of by decreasing log , which can be seen in Fig. 3a. It is also apparent from Fig. 3a that at pH 7, the formation of CSG_METJA is predicted to be favored by increasing pH. However, at pHs less than ~6, increasing pH favors formation of CSG_METVO. This observation is consistent with the variation in the charges of the proteins as a function of pH, which are shown normalized to the lengths of the proteins in Fig. 4a. For example, at pH 2, the charge per residue of CSG_METJA is greater than that of CSG_METVO, and a statement of Reaction 1 written for the proteins in their calculated ionization states at this pH would have H+ as a reactant instead of a product. The standard molal Gibbs energies of the ionized proteins which were used to calculate log K1 are depicted in Fig. 4b per residue of protein.


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

Dick JM - Geochem. Trans. (2008)

Properties of archaeal surface-layer proteins. Shown are calculated values of the net charge per residue (a) and standard molal Gibbs energy of formation from the elements (b) at 25°C and 1 bar for surface-layer proteins from archaeal species listed in Table 1. The computed charges per residue of CSG_METFE and CSG_METSC are indistinguishable from one another in (a).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Properties of archaeal surface-layer proteins. Shown are calculated values of the net charge per residue (a) and standard molal Gibbs energy of formation from the elements (b) at 25°C and 1 bar for surface-layer proteins from archaeal species listed in Table 1. The computed charges per residue of CSG_METFE and CSG_METSC are indistinguishable from one another in (a).
Mentions: In Reaction 1 it can be noted that O2(g) appears on the same side of the reaction as ; hence, the metastability of this protein is increased relative to that of by decreasing log , which can be seen in Fig. 3a. It is also apparent from Fig. 3a that at pH 7, the formation of CSG_METJA is predicted to be favored by increasing pH. However, at pHs less than ~6, increasing pH favors formation of CSG_METVO. This observation is consistent with the variation in the charges of the proteins as a function of pH, which are shown normalized to the lengths of the proteins in Fig. 4a. For example, at pH 2, the charge per residue of CSG_METJA is greater than that of CSG_METVO, and a statement of Reaction 1 written for the proteins in their calculated ionization states at this pH would have H+ as a reactant instead of a product. The standard molal Gibbs energies of the ionized proteins which were used to calculate log K1 are depicted in Fig. 4b per residue of protein.

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