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Calculation of the relative stabilit...

Dick, Jeffrey Michael.

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Calculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Calculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments./
Author:	Dick, Jeffrey Michael.
Description:	177 p.
Notes:	Adviser: Harold C. Helgeson.
Contained By:	Dissertation Abstracts International68-08B.
Subject:	Biogeochemistry. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3275393
ISBN:	9780549168942

Calculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments.
Dick, Jeffrey Michael.

Calculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments. - 177 p.

Adviser: Harold C. Helgeson.

Thesis (Ph.D.)--University of California, Berkeley, 2007.

Microbial adaptation to changing environments depends on maintaining specific assemblages of proteins essential for cellular processes. To characterize energetic constraints on the chemical compositions of proteins in organisms adapted to different environments, the relative stabilities of representative proteins were assessed by locating Gibbs energy minima on theoretical chemical activity diagrams. Standard molal Gibbs free energies of ionized proteins as a function of temperature and pressure were calculated using modified group additivity algorithms for crystalline and aqueous proteins and updated values of the revised Helgeson-Kirkham-Flowers (HKF) equations of state parameters for aqueous sidechain and backbone groups. This approach incorporates experimental calorimetric and volumetric data for reference model amino acids and tripeptides and accounts for ionization contributions to protein charge and other thermodynamic properties. The "speciate" computer software package was developed to automate calculations of the chemical affinity of formation reactions of proteins, and to generate predominance and speciation metastable equilibrium diagrams as a function of temperature, pressure, and chemical potentials such as those represented by pH, Eh, or oxygen fugacity. Comparison of calculated protein metastabilities with subcellular chemistry indicates that the oxidation and hydration states of the cytoplasm, nucleus, mitochondria and other compartments of Saccharomyces cerevisiae (yeast) favor formation of the different proteins found there, and that a hierarchy of metastability levels accounts for proteins in each subcellular localization. Thermodynamic constraints also account for overall changes in the proteomes of S. cerevisiae and Escherichia coli during heat and cold shock stress response experiments, and are consistent with buffering of oxidation states by glutathione or other redox species. Finally, comparison of orthologous extracellular and surface-layer proteins from mesophilic, thermophilic and hyperthermophilic organisms reveals evidence for progress toward a metastable Gibbs energy minimum during microbial adaptation to the temperature, oxidation state and pH of hydrothermal solutions and other biogeochemical systems. These predictions afford a quantitative assessment of the relative chemical metastabilities of different proteins and contribute to understanding the physical chemical basis for other biomacromolecular interactions of significance in biogeochemistry, biotechnology, and medicine.

ISBN: 9780549168942Subjects--Topical Terms:

545717
Biogeochemistry.

Calculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments.
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100 1 $a Dick, Jeffrey Michael. $3 1285804
245 1 0 $a Calculation of the relative stabilities of proteins as a function of temperature, pressure, and chemical potentials in subcellular and geochemical environments.
300 $a 177 p.
500 $a Adviser: Harold C. Helgeson.
500 $a Source: Dissertation Abstracts International, Volume: 68-08, Section: B, page: 5081.
502 $a Thesis (Ph.D.)--University of California, Berkeley, 2007.
520 $a Microbial adaptation to changing environments depends on maintaining specific assemblages of proteins essential for cellular processes. To characterize energetic constraints on the chemical compositions of proteins in organisms adapted to different environments, the relative stabilities of representative proteins were assessed by locating Gibbs energy minima on theoretical chemical activity diagrams. Standard molal Gibbs free energies of ionized proteins as a function of temperature and pressure were calculated using modified group additivity algorithms for crystalline and aqueous proteins and updated values of the revised Helgeson-Kirkham-Flowers (HKF) equations of state parameters for aqueous sidechain and backbone groups. This approach incorporates experimental calorimetric and volumetric data for reference model amino acids and tripeptides and accounts for ionization contributions to protein charge and other thermodynamic properties. The "speciate" computer software package was developed to automate calculations of the chemical affinity of formation reactions of proteins, and to generate predominance and speciation metastable equilibrium diagrams as a function of temperature, pressure, and chemical potentials such as those represented by pH, Eh, or oxygen fugacity. Comparison of calculated protein metastabilities with subcellular chemistry indicates that the oxidation and hydration states of the cytoplasm, nucleus, mitochondria and other compartments of Saccharomyces cerevisiae (yeast) favor formation of the different proteins found there, and that a hierarchy of metastability levels accounts for proteins in each subcellular localization. Thermodynamic constraints also account for overall changes in the proteomes of S. cerevisiae and Escherichia coli during heat and cold shock stress response experiments, and are consistent with buffering of oxidation states by glutathione or other redox species. Finally, comparison of orthologous extracellular and surface-layer proteins from mesophilic, thermophilic and hyperthermophilic organisms reveals evidence for progress toward a metastable Gibbs energy minimum during microbial adaptation to the temperature, oxidation state and pH of hydrothermal solutions and other biogeochemical systems. These predictions afford a quantitative assessment of the relative chemical metastabilities of different proteins and contribute to understanding the physical chemical basis for other biomacromolecular interactions of significance in biogeochemistry, biotechnology, and medicine.
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650 4 $a Chemistry, Biochemistry. $3 1017722
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791 $a Ph.D.
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856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3275393