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Thermodynamics of protein unfolding-refolding transition

Year 2014, Volume: 17 Issue: 2, 61 - 69, 31.03.2014
https://doi.org/10.5541/ijot.77025

Abstract

A phenomenological thermodynamic model is developed to investigate, in more detail than usual, the pressure-temperature phase diagram of proteins. Indeed, in the whole of previous studies the specific heat difference deltaCP is treated as pressure and temperature independent. This assumption is wrong, as confirmed by Yamaguchi et al (1995) which reported pressure dependence of deltaCP in the case of ribonuclease A. In this work, assuming that the chemical potential has a Taylor series expansion and having an additional thermodynamic piece of information, the analysis shows that it is possible to obtain a complete description of the unfolding-refolding transition of protein, to deduce the volumes, entropies, enthalpies versus transition temperatures and transition pressures and, for the first time, to deduce the specific heat changes versus transition temperatures and transition pressures. Special attention is given to the elliptical shape of the pressure-temperature phase diagram. A quantitative description of the phase transitions in the protein of Zn-Cytochrome c is given.

References

  • A. Yamaguchi, T.H. Yamada and K. Akasaka, Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR, J. Mol. Bio., 250, 689-694, 1995.
  • C.B Anfinsen. and H.A Schegara, Experimental and theoretical aspects of protein folding, Adv. Prot. Chem., 29, 205-300, 1975.
  • C. Tanford, Theoretical models for the mechanism of denaturation, Adv. Prot. Chem., 24, 1-95, 1970.
  • C. Levinthal, Are there pathways for protein folding?, J. Chem. Phys., 65, 44-45, 1968.
  • D. B. Wetlaufer, Nucleation, rapid folding and globular intrachain regions in proteins, Proc. Natl. Acad. Sci. USA, 70, 697-701, 1973.
  • C. J. Camacho and D. Thirumalai, Kinetics and Thermodynamics of Folding in Model Proteins. Proc. Natl. Acad. Sci. USA, 90, 6369-6372, 1993. Z. Guo and D. Thirumalai, Kinetics and thermodynamics of folding of a de-novo designed 4helix Bundle protein. J.Mol. Biol. 263, 323-243, 1996.
  • S. A. Hawley, Reversible pressure-temperature denaturation of chymotrypsinogen, Biochemistry,10, 2436-2442, 1971.
  • N. A. Clark, Thermodynamics of the re-entrant nematic-bilayer smectic A transition, J. Phys., 40, 345-349, 1979.
  • D. D. Klug and E. Whalley, Elliptic phase boundaries between smectic and nematic phases,. J. Chem. Phys., 71, 1874-877, 1979.
  • L. Smeller, Pressure-temperature phase diagrams of biomolecules,. Biochimica Biophysica Acta, 1595, 1129, 2002.
  • H. Lesch, H. Stadlbauer, J. Friedrich and J.M. Vanderkooi, Stability Diagram and Unfolding of a Modified Cytochrome C: What happens in the transformation regime?, Biophysical Journal, 82, 1644-1653, 2002.
  • H. Lesch, C. Hecht and J. Friedrich, Protein phase diagrams: The physics behind their elliptic shape, J. Chem. Phys., 121, 12671-12675, 2004.
  • M. Sandmann and A. Würflinger, PVT Measurements on 4'-n-Octyl-Biphenyl-4-Carbonitrile (6CB) and 4’n-Heptyl-Biphenyl-4-Carbonitrile (7CB) up to 300 MPa, Z. Naturforsch., 53a, 233-238, 1998. W. Spratte and G.M. Schneider, Smectic Polymorphism of Some Bis-(4,4'-nalkoxybenzylidene) - 1,4-phenylenediamines up to 3 kbars by Differential Thermal Analysis, Liq. Cryst., 51, 101-115, 1979.
  • C. Rein and D. Demus, High pressure differential thermal analysis of nematic compounds with different molecular shapes, Liq. Cryst., 16, 323-331, 1994.
  • G. W. H. Höhne and K. Blankenhorn, High pressure DSC investigations on n-alkanes, n-alkane mixtures and polyethylene, Thermochimica Acta, 238, 351-370, 19 Y. Maeda, H. Furuya and A. Abe, High pressure differential thermal analysis of dimer liquid crystals: α,ω Bis [(4,4'-cyanobiphenylyl) oxy] alkanes, Liq. Cryst., 21, 365-371, 1996.
  • E.A.S Lewis, H.M. Strong and Brown G.H., Volume Measurements and Transitions of MBBA at High Pressure,. Liq. Cryst., 53, 89-99, 1979.
  • A. Anakkar, Etudes thermodynamiques des phases cristallines liquides. Analyse des points multicritiques et modélisation des diagrammes de phase,. Editions Universitaires Européennes, 2010, ISBN 978-613-152043-3, 2012.
  • U. Lucia and G. Maino, Thermodynamical analysis of the dynamics of tumor interaction with the host immune system, Physica A, 313, 569-577, 2002. U. Lucia, Molecular machine as chemicalthermodynamic devices, Chem. Phys. Lett., 556, 242244, 2013.
  • U. Lucia, Irreversible human brain, Medical hypothesis. 80, 112-114, 2013.
  • U. Lucia and G. Maino, Maximum or minimum entropy generation for open sytems?, Physica A, 391, 3392-3398, 2012.
  • U. Lucia, Thermodynamics and cancer stationary states, Physica A, 392, 3648-3653, 2013.
Year 2014, Volume: 17 Issue: 2, 61 - 69, 31.03.2014
https://doi.org/10.5541/ijot.77025

Abstract

References

  • A. Yamaguchi, T.H. Yamada and K. Akasaka, Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR, J. Mol. Bio., 250, 689-694, 1995.
  • C.B Anfinsen. and H.A Schegara, Experimental and theoretical aspects of protein folding, Adv. Prot. Chem., 29, 205-300, 1975.
  • C. Tanford, Theoretical models for the mechanism of denaturation, Adv. Prot. Chem., 24, 1-95, 1970.
  • C. Levinthal, Are there pathways for protein folding?, J. Chem. Phys., 65, 44-45, 1968.
  • D. B. Wetlaufer, Nucleation, rapid folding and globular intrachain regions in proteins, Proc. Natl. Acad. Sci. USA, 70, 697-701, 1973.
  • C. J. Camacho and D. Thirumalai, Kinetics and Thermodynamics of Folding in Model Proteins. Proc. Natl. Acad. Sci. USA, 90, 6369-6372, 1993. Z. Guo and D. Thirumalai, Kinetics and thermodynamics of folding of a de-novo designed 4helix Bundle protein. J.Mol. Biol. 263, 323-243, 1996.
  • S. A. Hawley, Reversible pressure-temperature denaturation of chymotrypsinogen, Biochemistry,10, 2436-2442, 1971.
  • N. A. Clark, Thermodynamics of the re-entrant nematic-bilayer smectic A transition, J. Phys., 40, 345-349, 1979.
  • D. D. Klug and E. Whalley, Elliptic phase boundaries between smectic and nematic phases,. J. Chem. Phys., 71, 1874-877, 1979.
  • L. Smeller, Pressure-temperature phase diagrams of biomolecules,. Biochimica Biophysica Acta, 1595, 1129, 2002.
  • H. Lesch, H. Stadlbauer, J. Friedrich and J.M. Vanderkooi, Stability Diagram and Unfolding of a Modified Cytochrome C: What happens in the transformation regime?, Biophysical Journal, 82, 1644-1653, 2002.
  • H. Lesch, C. Hecht and J. Friedrich, Protein phase diagrams: The physics behind their elliptic shape, J. Chem. Phys., 121, 12671-12675, 2004.
  • M. Sandmann and A. Würflinger, PVT Measurements on 4'-n-Octyl-Biphenyl-4-Carbonitrile (6CB) and 4’n-Heptyl-Biphenyl-4-Carbonitrile (7CB) up to 300 MPa, Z. Naturforsch., 53a, 233-238, 1998. W. Spratte and G.M. Schneider, Smectic Polymorphism of Some Bis-(4,4'-nalkoxybenzylidene) - 1,4-phenylenediamines up to 3 kbars by Differential Thermal Analysis, Liq. Cryst., 51, 101-115, 1979.
  • C. Rein and D. Demus, High pressure differential thermal analysis of nematic compounds with different molecular shapes, Liq. Cryst., 16, 323-331, 1994.
  • G. W. H. Höhne and K. Blankenhorn, High pressure DSC investigations on n-alkanes, n-alkane mixtures and polyethylene, Thermochimica Acta, 238, 351-370, 19 Y. Maeda, H. Furuya and A. Abe, High pressure differential thermal analysis of dimer liquid crystals: α,ω Bis [(4,4'-cyanobiphenylyl) oxy] alkanes, Liq. Cryst., 21, 365-371, 1996.
  • E.A.S Lewis, H.M. Strong and Brown G.H., Volume Measurements and Transitions of MBBA at High Pressure,. Liq. Cryst., 53, 89-99, 1979.
  • A. Anakkar, Etudes thermodynamiques des phases cristallines liquides. Analyse des points multicritiques et modélisation des diagrammes de phase,. Editions Universitaires Européennes, 2010, ISBN 978-613-152043-3, 2012.
  • U. Lucia and G. Maino, Thermodynamical analysis of the dynamics of tumor interaction with the host immune system, Physica A, 313, 569-577, 2002. U. Lucia, Molecular machine as chemicalthermodynamic devices, Chem. Phys. Lett., 556, 242244, 2013.
  • U. Lucia, Irreversible human brain, Medical hypothesis. 80, 112-114, 2013.
  • U. Lucia and G. Maino, Maximum or minimum entropy generation for open sytems?, Physica A, 391, 3392-3398, 2012.
  • U. Lucia, Thermodynamics and cancer stationary states, Physica A, 392, 3648-3653, 2013.
There are 21 citations in total.

Details

Primary Language English
Journal Section Regular Original Research Article
Authors

Jeanfils Joseph

Anakkar Abdelkader This is me

Buisine Jean-marc This is me

Publication Date March 31, 2014
Published in Issue Year 2014 Volume: 17 Issue: 2

Cite

APA Joseph, J., Abdelkader, A., & Jean-marc, B. (2014). Thermodynamics of protein unfolding-refolding transition. International Journal of Thermodynamics, 17(2), 61-69. https://doi.org/10.5541/ijot.77025
AMA Joseph J, Abdelkader A, Jean-marc B. Thermodynamics of protein unfolding-refolding transition. International Journal of Thermodynamics. March 2014;17(2):61-69. doi:10.5541/ijot.77025
Chicago Joseph, Jeanfils, Anakkar Abdelkader, and Buisine Jean-marc. “Thermodynamics of Protein Unfolding-Refolding Transition”. International Journal of Thermodynamics 17, no. 2 (March 2014): 61-69. https://doi.org/10.5541/ijot.77025.
EndNote Joseph J, Abdelkader A, Jean-marc B (March 1, 2014) Thermodynamics of protein unfolding-refolding transition. International Journal of Thermodynamics 17 2 61–69.
IEEE J. Joseph, A. Abdelkader, and B. Jean-marc, “Thermodynamics of protein unfolding-refolding transition”, International Journal of Thermodynamics, vol. 17, no. 2, pp. 61–69, 2014, doi: 10.5541/ijot.77025.
ISNAD Joseph, Jeanfils et al. “Thermodynamics of Protein Unfolding-Refolding Transition”. International Journal of Thermodynamics 17/2 (March 2014), 61-69. https://doi.org/10.5541/ijot.77025.
JAMA Joseph J, Abdelkader A, Jean-marc B. Thermodynamics of protein unfolding-refolding transition. International Journal of Thermodynamics. 2014;17:61–69.
MLA Joseph, Jeanfils et al. “Thermodynamics of Protein Unfolding-Refolding Transition”. International Journal of Thermodynamics, vol. 17, no. 2, 2014, pp. 61-69, doi:10.5541/ijot.77025.
Vancouver Joseph J, Abdelkader A, Jean-marc B. Thermodynamics of protein unfolding-refolding transition. International Journal of Thermodynamics. 2014;17(2):61-9.