Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

Nature Structural Biology volume 7, pages 336–342 (2000)Cite this article

Abstract

A lattice model with side chains was used to investigate protein folding with computer simulations. In this model, we rigorously demonstrate the existence of a specific folding nucleus. This nucleus contains specific interactions not present in the native state that, when weakened, slow folding but do not change protein stability. Such a decoupling of folding kinetics from thermodynamics has been observed experimentally for real proteins. From our results, we conclude that specific non-native interactions in the transition state would give rise to φ-values that are negative or larger than unity. Furthermore, we demonstrate that residue Ile 34 in src SH3, which has been shown to be kinetically, but not thermodynamically, important, is universally conserved in proteins with the SH3 fold. This is a clear example of evolution optimizing the folding rate of a protein independent of its stability and function.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Native state and wild type sequence of the protein model.
Figure 2: Nucleus and control conformation of model protein.
Figure 3: The log(MFPT) of nucleus (circles), control (triangles) and random coil (dotted line).
Figure 4: Contact frequencies for non-local native contacts among post-critical (black bars) and pre-critical (gray bars) states.
Figure 5: Structural alignment of families containing the SH3 fold.
Figure 6: Conserved residues in SH3.

Similar content being viewed by others

References

  1. Creighton, T.E. Proteins: structures and molecular properties, 2nd edition (W.H. Freeman and Company, New York; 1993).

    Google Scholar 

  2. Li, A. & Daggett, V. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275, 677–694 (1998).

    Article  CAS  Google Scholar 

  3. Duan, Y. & Kollman, P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282, 740–744 ( 1998).

    Article  CAS  Google Scholar 

  4. Lazaridis, T. & Karplus, M. ‘New view’ of protein folding reconciled with the old through multiple unfolding simulations. Science 278, 1928–1931 ( 1997).

    Article  CAS  Google Scholar 

  5. Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. Specific nucleus as the transition state for protein folding: evidence from lattice model. Biochemistry 33, 10026–10036 (1994).

    Article  CAS  Google Scholar 

  6. Klimov, D.K. & Thirumalai, D. Cooperativity in protein folding, from lattice models with sidechains to real proteins. Folding Design 3, 127–139 ( 1998).

    Article  CAS  Google Scholar 

  7. Socci, N.D., Onuchic, J.N. & Wolynes, P.G. Protein folding mechanisms and the multidimensional folding funnel. Proteins 32, 136– 158 (1998).

    Article  CAS  Google Scholar 

  8. Hao, M-H & Scheraga, H.A. Molecular mechanisms for cooperative folding of proteins. J. Mol. Biol. 277, 973–983 (1998).

    Article  CAS  Google Scholar 

  9. Kolinski, A. & Skolnick, J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18, 338–352 (1994).

    Article  CAS  Google Scholar 

  10. Berriz, G.F., Gutin, A.M. & Shakhnovich, E.I. Cooperativity and stability in a Langevin model of proteinlike folding. J. Chem. Phys. 106, 9276–9285 (1997).

    Article  CAS  Google Scholar 

  11. Guo, Z. & Brooks III, C.L. Thermodynamics of protein folding: a statistical mechanical study of a small all-β protein . Biopolymers 42, 745–757 (1997).

    Article  CAS  Google Scholar 

  12. Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E. & Shakhnovich, E.I. Identifying the protein folding nucleus using molecular dynamics. J. Mol. Biol. 296, 1183–1188 (2000).

    Article  CAS  Google Scholar 

  13. Itzhaki, L.S., Otzen, D.E. & Fersht, A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260–288 (1995).

    Article  CAS  Google Scholar 

  14. López-Hernández, E. & Serrano, L. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Folding Design 1, 43–55 (1996).

    Article  Google Scholar 

  15. Martinez, J.C., Pisabarro, M.T. & Serrano, L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nature Struct. Biol. 5, 721–729 (1998).

    Article  CAS  Google Scholar 

  16. Martinez, J.C. & Serrano, L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nature Struct.Biol. 6, 1010– 1015 (1999).

    Article  CAS  Google Scholar 

  17. Grantcharova, V.P., Riddle, D.S., Santiago, J.V. & Baker, D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature Struct. Biol. 5, 714–720 (1998).

    Article  CAS  Google Scholar 

  18. Riddle, D.S. et al. Experiment and theory highlight role of native state topology in SH3 folding. Nature Struct. Biol. 6, 1016–1024 (1999).

    Article  CAS  Google Scholar 

  19. Fulton, K.F., Main, E.R.G., Daggett, V. & Jackson, S.E. Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J. Mol. Biol. 291, 445– 461 (1999).

    Article  CAS  Google Scholar 

  20. Bromberg, S. & Dill, K.A. Side-chain entropy and packing in proteins. Protein Sci. 3, 997– 1009 (1994).

    Article  CAS  Google Scholar 

  21. Hart, W.E. & Istrail, S. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better the 86% of optimal. J. Comp. Biol. 4, 241– 259 (1997).

    Article  CAS  Google Scholar 

  22. Villegas, V., Martínez, J.C., Avilés, F.X. & Serrano, L. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J. Mol. Biol. 283, 1027–1036 (1998).

    Article  CAS  Google Scholar 

  23. Dobson, C.M. et al. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nature Struct. Biol. 6, 1005–1009 ( 1999).

    Article  Google Scholar 

  24. Daggett, V., Li, A. & Fersht, A.R. Combined molecular dynamics and φ-value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: structural basis of Hammond and anti-Hammond effects. J. Am. Chem. Soc. 120, 12740–12754 (1998).

    Article  CAS  Google Scholar 

  25. Klimov, D.K. & Thirumalai, D. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J. Mol. Biol. 282, 471–492 ( 1998).

    Article  CAS  Google Scholar 

  26. Gutin, A.M., Abkevich, V.I. & Shakhnovich, E.I. A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Folding Design 3, 183–194 ( 1998).

    Article  CAS  Google Scholar 

  27. Matouschek, A., Kellis, J.T., Serrano L. & Fersht, A.R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340, 122–126 ( 1989).

    Article  CAS  Google Scholar 

  28. Fersht, A.R., Itzhaki, L.S., ElMasry, N.F., Matthews, J.M. & Otzen, D.E. Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc. Natl Acad. Sci. USA 91, 10426 –10429 (1994).

    Article  CAS  Google Scholar 

  29. _ali, A., Shakhnovich, E. & Karplus, M. How does a protein fold? Nature 369, 248–251 (1994).

    Article  Google Scholar 

  30. Mirny, L.A., Abkevich, V.I. & Shakhnovich, E.I. How evolution makes proteins fold quickly. Proc. Natl Acad. Sci. USA 95, 4976– 4981 (1998).

    Article  CAS  Google Scholar 

  31. Mirny, L.A. & Shakhnovich, E.I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291, 177– 196 (1999).

    Article  CAS  Google Scholar 

  32. Miyazawa, S. & Jernigan, R. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation . Macromolecules 18, 534– 552 (1985).

    Article  CAS  Google Scholar 

  33. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H. & Teller, E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087–1092 (1953).

    Article  CAS  Google Scholar 

  34. Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. Improved design of stable and fast-folding model proteins . Folding Design 1, 221– 230 (1996).

    Article  CAS  Google Scholar 

  35. Dodge, C., Schneider, R. & Sander, C. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 26, 313–315 (1998).

    Article  CAS  Google Scholar 

  36. Holm, L. & Sander, C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24, 206–209 ( 1996).

    Article  CAS  Google Scholar 

  37. Shakhnovich, E.I. Folding nucleus: specific or multiple? Insights from lattice models and experiments . Folding Design 3, R108– R111 (1998).

    Article  CAS  Google Scholar 

  38. Per, J.K. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. App. Crystallogr. 24, 946 –950 (1991).

    Article  Google Scholar 

  39. Merrit, E.A. & Bacon, D.J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505– 524 (1997).

    Article  Google Scholar 

Download references

Acknowledgements

We thank the NSERC of Canada and NIH for financial support. L.L. would like to thank H. Angerman, G. Berriz, S. Choe, N.V. Dokholyan, L. Gutman, A. Ishchenko, E. Kussell, M. Morrissey and J. Shimada for computer assistance and stimulating discussions. He is particularly grateful to O. Clement for encouragement at a crucial point in this research.

Author information

Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138 , Massachusetts, USA

    Lewyn Li, Leonid A. Mirny & Eugene I. Shakhnovich

Authors
  1. Lewyn Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Leonid A. Mirny
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Eugene I. Shakhnovich
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eugene I. Shakhnovich.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, L., Mirny, L. & Shakhnovich, E. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Mol Biol 7, 336–342 (2000). https://doi.org/10.1038/74111

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/74111

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing