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 tempe...
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| Format: | Article |
| Language: | English |
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BMC
2008-10-01
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| Series: | Geochemical Transactions |
| Online Access: | http://www.geochemicaltransactions.com/content/9/1/10 |
| _version_ | 1818084238852882432 |
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| author | Dick Jeffrey M |
| author_facet | Dick Jeffrey M |
| author_sort | Dick Jeffrey M |
| collection | DOAJ |
| description | <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> |
| first_indexed | 2024-12-10T19:50:43Z |
| format | Article |
| id | doaj.art-761c712cc86e4b4da2169691ec8793f6 |
| institution | Directory Open Access Journal |
| issn | 1467-4866 |
| language | English |
| last_indexed | 2024-12-10T19:50:43Z |
| publishDate | 2008-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Geochemical Transactions |
| spelling | doaj.art-761c712cc86e4b4da2169691ec8793f62022-12-22T01:35:48ZengBMCGeochemical Transactions1467-48662008-10-01911010.1186/1467-4866-9-10Calculation of the relative metastabilities of proteins using the CHNOSZ software packageDick Jeffrey M<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>http://www.geochemicaltransactions.com/content/9/1/10 |
| spellingShingle | Dick Jeffrey M Calculation of the relative metastabilities of proteins using the CHNOSZ software package Geochemical Transactions |
| title | Calculation of the relative metastabilities of proteins using the CHNOSZ software package |
| title_full | Calculation of the relative metastabilities of proteins using the CHNOSZ software package |
| title_fullStr | Calculation of the relative metastabilities of proteins using the CHNOSZ software package |
| title_full_unstemmed | Calculation of the relative metastabilities of proteins using the CHNOSZ software package |
| title_short | Calculation of the relative metastabilities of proteins using the CHNOSZ software package |
| title_sort | calculation of the relative metastabilities of proteins using the chnosz software package |
| url | http://www.geochemicaltransactions.com/content/9/1/10 |
| work_keys_str_mv | AT dickjeffreym calculationoftherelativemetastabilitiesofproteinsusingthechnoszsoftwarepackage |