Export citation

Export citation

Choose format for download:

Download Citation
  • Access by Xinjiang University

Entropy reduction effect imposed by hydrogen bond formation on protein folding cooperativity: Evidence from a hydrophobic minimalist model

Marco Aurélio A. Barbosa1,2, Leandro G. Garcia1, and Antônio F. Pereira de Araújo1,*

  • 1Laboratório de Biologia Teórica, Departamento de Biologia Celular, Universidade de Brasília, Brasília-DF 70910-900, Brazil
  • 2Instituto de Física, Departamento de Física Geral, Universidade de São Paulo, São Paulo-SP 05508-900, Brazil

  • *Electronic address: aaraujo@unb.br

Phys. Rev. E 72, 051903 – Published 1 November, 2005

DOI: https://doi.org/10.1103/PhysRevE.72.051903

Abstract

Conformational restrictions imposed by hydrogen bond formation during protein folding are investigated by Monte Carlo simulations of a non-native-centric, two-dimensional, hydrophobic model in which the formation of favorable contacts is coupled to an effective reduction in lattice coordination. This scheme is intended to mimic the requirement that polar backbone groups of real proteins must form hydrogen bonds concomitantly to their burial inside the apolar protein core. In addition to the square lattice, with z=3 conformations per monomer, we use extensions in which diagonal step vectors are allowed, resulting in z=5 and z=7. Thermodynamics are governed by the hydrophobic energy function, according to which hydrophobic monomers tend to make contacts unspecifically while the reverse is true for hydrophilic monomers, with the additional restriction that only contacts between monomers adopting one of zh<z local conformations contribute to the energy, where zh is the number of local conformations assumed to be compatible with hydrogen bond formation. The folding transition abruptness and van’t Hoff-to-calorimetric-enthalpy ratio are found to increase dramatically by this simple and physically motivated mechanism. The observed increase in folding cooperativity is correlated to an increase in the convexity of the underlying microcanonical conformational entropy as a function of energy. Preliminary simulations in three dimensions, even though using a smaller relative reduction in lattice effective coordination zhz=45, display a slight increase in cooperativity for a hydrophobic model of 40 monomers and a more pronounced increase in cooperativity for a native-centric Go-model with the same native conformation, suggesting that this purely entropic effect is not an artifact of dimensionality and is likely to be of fundamental importance in the theoretical understanding of folding cooperativity.

Article Text

References (25)

  1. P. L. Privalov, Protein Folding, edited by T. E. Creighton, (Freeman, New York, 1992).
  2. M. Karplus and E. I. Shakhnovich, in Protein Folding, edited by T. E. Creighton (Freeman, New York, 1992).
  3. A. F. Pereira de Araújo, Protein & Peptide Letters 12, 223 (2005).
  4. A. F. Pereira de Araújo and T. C. Pochapsky, Folding Des. 1, 299 (1996).
  5. K. A. Dill, S. Bronberg, K. Yue, K. M. Fiebig, D. Yee, P. D. Thomas, and H. S. Chan, Protein Sci. 4, 561 (1995).
  6. E. I. Shakhnovich, Curr. Opin. Struct. Biol. 7, 29 (1997).
  7. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545 (1997).
  8. M. Hao and H. A. Scheraga, J. Mol. Biol. 277, 973 (1998).
  9. H. Kaya and H. S. Chan, Proteins 40, 637 (2000).
  10. H. S. Chan, Proteins 40, 543 (2000).
  11. H. S. Chan, S. Shimizu, and H. Kaya, Methods Enzymol. 380, 350 (2004).
  12. H. Kaya and H. S. Chan, Phys. Rev. Lett. 85, 4823 (2000).
  13. S. Miller, J. Janin, A. M. Lesk, and C. Chotia, J. Mol. Biol. 196, 641 (1987).
  14. A. F. Pereira de Araújo, Proc. Natl. Acad. Sci. U.S.A. 96, 12482 (1999).
  15. L. G. Garcia, W. L. Treptow, and A. F. Pereira de Araújo, Phys. Rev. E 64, 011912 (2001).
  16. Marco Aurélio A. Barbosa and A. F. Pereira de Araújo, Phys. Rev. E 67, 051919 (2003).
  17. W. L. Treptow, M. A. A. Barbosa, L. G. Garcia, and A. F. Pereira de Araújo, Proteins 49, 167 (2002).
  18. N. D. Socci and J. N. Onuchic, J. Chem. Phys. 103, 4732 (1995).
  19. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
  20. D. K. Klimov and D. Thirumalai, Folding Des. 3, 127 (1998).
  21. L. G. Garcia and A. F. Pereira de Araújo, Proteins (to be published).
  22. J. Borg, M. H. Jensen, K. Sneppen, and G. Tiana, Phys. Rev. Lett. 86, 1031 (2001).
  23. E. Freire and K. P. Murphy, J. Mol. Biol. 222, 687 (1991).
  24. A. F. Pereira de Araújo, J. Chem. Phys. 114, 570 (2001).
  25. H. Kaya and H. S. Chan, Proteins 52, 510 (2003).

Outline

Information

Sign In to Your Journals Account

Filter

Filter

Article Lookup

Enter a citation