Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins
Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on valu...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Copernicus Publications
2006-01-01
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| Series: | Biogeosciences |
| Online Access: | http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.pdf |
| _version_ | 1819212904544600064 |
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| author | J. M. Dick D. E. LaRowe H. C. Helgeson |
| author_facet | J. M. Dick D. E. LaRowe H. C. Helgeson |
| author_sort | J. M. Dick |
| collection | DOAJ |
| description | Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from <i>Pyrococcus furiosus</i> and <i>Bacillus subtilis</i> was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive chemical potential constraints on the interactions of microbes with their environment. |
| first_indexed | 2024-12-23T06:50:23Z |
| format | Article |
| id | doaj.art-78d88e6f471f42a79d4a303574d23294 |
| institution | Directory Open Access Journal |
| issn | 1726-4170 1726-4189 |
| language | English |
| last_indexed | 2024-12-23T06:50:23Z |
| publishDate | 2006-01-01 |
| publisher | Copernicus Publications |
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| series | Biogeosciences |
| spelling | doaj.art-78d88e6f471f42a79d4a303574d232942022-12-21T17:56:26ZengCopernicus PublicationsBiogeosciences1726-41701726-41892006-01-0133311336Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteinsJ. M. DickD. E. LaRoweH. C. HelgesonThermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from <i>Pyrococcus furiosus</i> and <i>Bacillus subtilis</i> was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive chemical potential constraints on the interactions of microbes with their environment.http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.pdf |
| spellingShingle | J. M. Dick D. E. LaRowe H. C. Helgeson Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins Biogeosciences |
| title | Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins |
| title_full | Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins |
| title_fullStr | Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins |
| title_full_unstemmed | Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins |
| title_short | Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins |
| title_sort | temperature pressure and electrochemical constraints on protein speciation group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins |
| url | http://www.biogeosciences.net/3/311/2006/bg-3-311-2006.pdf |
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