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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

Transcript of CHNOSZ session to calculate thermodynamic properties of proteins and reactions. Commands at the prompt (>) were entered to calculate (a) the standard molal thermodynamic properties at 25°C and 1 bar and equations of state parameters of nonionized chicken lysozyme (LYSC_CHICK), (b) the standard molal thermodynamic properties of lysozyme as a function of temperature at PSAT and (c) the standard molal properties of the nonionized counterpart to Reaction 1 as a function of temperature at PSAT.
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Figure 2: Transcript of CHNOSZ session to calculate thermodynamic properties of proteins and reactions. Commands at the prompt (>) were entered to calculate (a) the standard molal thermodynamic properties at 25°C and 1 bar and equations of state parameters of nonionized chicken lysozyme (LYSC_CHICK), (b) the standard molal thermodynamic properties of lysozyme as a function of temperature at PSAT and (c) the standard molal properties of the nonionized counterpart to Reaction 1 as a function of temperature at PSAT.

Mentions: Examples of the usage of the info and subcrt functions are shown in the program transcript in Fig. 2. The standard molal thermodynamic properties at 25°C and 1 bar and the equations of state parameters of chicken lysozyme (LYSC_CHICK, accession no. P00698 in the Swiss-Prot database [37]) can be retrieved using the code shown in Fig. 2a. The properties and parameters whose values appear in the example are standard molal Gibbs energy (ΔG°) and enthalpy (ΔH°) of formation from the elements (cal mol-1), standard molal entropy (S°), heat capacity () and c1 (cal K-1 mol-1), standard molar volume (V°) (cm3 mol-1), a1 (cal bar-1 mol-1), a2 and ω (cal mol-1), a3 (cal K bar-1 mol-1), and a4 and c2 (cal K mol-1). The parameters a1, a2, a3, a4, c1, c2 and ω are species-dependent coefficients in the revised HKF equations of state. Note that the properties and parameters of proteins returned by info are those of nonionized proteins; the ionization contributions to thermodynamic properties of proteins are calculated using a separate function. Sample code for calculating the standard molal thermodynamic properties of LYSC_CHICK as a function of temperature at PSAT is shown in Fig. 2b, where the units are °C (T), bar (P), g cm-3 (ρ, density of water) and those listed above for the standard molal properties. The reaction-balancing feature of subcrt is demonstrated in Fig. 2c for Reaction 1 (below). In this mode, all the user has to do is identify the basis species in the system and the reaction coefficients of the proteins, and the program finds the correct quantities of basis species to add to the reaction.


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

Dick JM - Geochem. Trans. (2008)

Transcript of CHNOSZ session to calculate thermodynamic properties of proteins and reactions. Commands at the prompt (>) were entered to calculate (a) the standard molal thermodynamic properties at 25°C and 1 bar and equations of state parameters of nonionized chicken lysozyme (LYSC_CHICK), (b) the standard molal thermodynamic properties of lysozyme as a function of temperature at PSAT and (c) the standard molal properties of the nonionized counterpart to Reaction 1 as a function of temperature at PSAT.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Transcript of CHNOSZ session to calculate thermodynamic properties of proteins and reactions. Commands at the prompt (>) were entered to calculate (a) the standard molal thermodynamic properties at 25°C and 1 bar and equations of state parameters of nonionized chicken lysozyme (LYSC_CHICK), (b) the standard molal thermodynamic properties of lysozyme as a function of temperature at PSAT and (c) the standard molal properties of the nonionized counterpart to Reaction 1 as a function of temperature at PSAT.
Mentions: Examples of the usage of the info and subcrt functions are shown in the program transcript in Fig. 2. The standard molal thermodynamic properties at 25°C and 1 bar and the equations of state parameters of chicken lysozyme (LYSC_CHICK, accession no. P00698 in the Swiss-Prot database [37]) can be retrieved using the code shown in Fig. 2a. The properties and parameters whose values appear in the example are standard molal Gibbs energy (ΔG°) and enthalpy (ΔH°) of formation from the elements (cal mol-1), standard molal entropy (S°), heat capacity () and c1 (cal K-1 mol-1), standard molar volume (V°) (cm3 mol-1), a1 (cal bar-1 mol-1), a2 and ω (cal mol-1), a3 (cal K bar-1 mol-1), and a4 and c2 (cal K mol-1). The parameters a1, a2, a3, a4, c1, c2 and ω are species-dependent coefficients in the revised HKF equations of state. Note that the properties and parameters of proteins returned by info are those of nonionized proteins; the ionization contributions to thermodynamic properties of proteins are calculated using a separate function. Sample code for calculating the standard molal thermodynamic properties of LYSC_CHICK as a function of temperature at PSAT is shown in Fig. 2b, where the units are °C (T), bar (P), g cm-3 (ρ, density of water) and those listed above for the standard molal properties. The reaction-balancing feature of subcrt is demonstrated in Fig. 2c for Reaction 1 (below). In this mode, all the user has to do is identify the basis species in the system and the reaction coefficients of the proteins, and the program finds the correct quantities of basis species to add to the reaction.

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