Skip to main content
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 2000 Oct;9(10):1993–2000. doi: 10.1110/ps.9.10.1993

Role of a solvent-exposed aromatic cluster in the folding of Escherichia coli CspA.

H M Rodriguez 1, D M Vu 1, L M Gregoret 1
PMCID: PMC2144470  PMID: 11106173

Abstract

Escherichia coli CspA is a member of the cold shock protein family. All cold shock proteins studied to date fold rapidly by an apparent two-state mechanism. CspA contains an unusual cluster of aromatic amino acids on its surface that is necessary for nucleic acid binding and also provides stability to CspA (Hillier et al., 1998). To elucidate the role this aromatic cluster plays in the determining the folding rate and pathway of CspA, we have studied the folding kinetics of mutants containing either leucine or serine substituted for Phe 18, Phe20, and/or Phe31. The leucine substitutions are found to accelerate folding and the serine substitutions to decelerate folding. Because these residues exert effects on the free energy of the folding transition state, they may be necessary for nucleating folding. They are not responsible, however, for the very compact, native-like transition state ensemble seen in the cold shock proteins, as the refolding rates of the mutants all show a similar, weak dependence of unfolding rate on denaturant concentration. Using mutant cycle analysis, we show that there is energetic coupling among the three residues between the unfolded and transition states, suggesting that the cooperative nature of these interactions helps to determine the unfolding rate. Overall, our results suggest that separate evolutionary pressures can act simultaneously on the same group of residues to maintain function, stability, and folding rate.

Full Text

The Full Text of this article is available as a PDF (302.5 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abkevich V. I., Gutin A. M., Shakhnovich E. I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry. 1994 Aug 23;33(33):10026–10036. doi: 10.1021/bi00199a029. [DOI] [PubMed] [Google Scholar]
  2. Blaber M., Lindstrom J. D., Gassner N., Xu J., Heinz D. W., Matthews B. W. Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. Biochemistry. 1993 Oct 26;32(42):11363–11373. doi: 10.1021/bi00093a013. [DOI] [PubMed] [Google Scholar]
  3. Broome B. M., Hecht M. H. Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J Mol Biol. 2000 Mar 3;296(4):961–968. doi: 10.1006/jmbi.2000.3514. [DOI] [PubMed] [Google Scholar]
  4. Chen B. L., Baase W. A., Schellman J. A. Low-temperature unfolding of a mutant of phage T4 lysozyme. 2. Kinetic investigations. Biochemistry. 1989 Jan 24;28(2):691–699. doi: 10.1021/bi00428a042. [DOI] [PubMed] [Google Scholar]
  5. Davidson A. R., Lumb K. J., Sauer R. T. Cooperatively folded proteins in random sequence libraries. Nat Struct Biol. 1995 Oct;2(10):856–864. doi: 10.1038/nsb1095-856. [DOI] [PubMed] [Google Scholar]
  6. Davidson A. R., Sauer R. T. Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2146–2150. doi: 10.1073/pnas.91.6.2146. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fersht A. R. Characterizing transition states in protein folding: an essential step in the puzzle. Curr Opin Struct Biol. 1995 Feb;5(1):79–84. doi: 10.1016/0959-440x(95)80012-p. [DOI] [PubMed] [Google Scholar]
  8. Fersht A. R., Matouschek A., Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol. 1992 Apr 5;224(3):771–782. doi: 10.1016/0022-2836(92)90561-w. [DOI] [PubMed] [Google Scholar]
  9. 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. Nat Struct Biol. 1998 Aug;5(8):714–720. doi: 10.1038/1412. [DOI] [PubMed] [Google Scholar]
  10. Hillier B. J., Rodriguez H. M., Gregoret L. M. Coupling protein stability and protein function in Escherichia coli CspA. Fold Des. 1998;3(2):87–93. doi: 10.1016/S1359-0278(98)00014-5. [DOI] [PubMed] [Google Scholar]
  11. Horovitz A., Fersht A. R. Co-operative interactions during protein folding. J Mol Biol. 1992 Apr 5;224(3):733–740. doi: 10.1016/0022-2836(92)90557-z. [DOI] [PubMed] [Google Scholar]
  12. Hutchinson E. G., Sessions R. B., Thornton J. M., Woolfson D. N. Determinants of strand register in antiparallel beta-sheets of proteins. Protein Sci. 1998 Nov;7(11):2287–2300. doi: 10.1002/pro.5560071106. [DOI] [PMC free article] [PubMed] [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. 1995 Nov 24;254(2):260–288. doi: 10.1006/jmbi.1995.0616. [DOI] [PubMed] [Google Scholar]
  14. Jackson S. E. How do small single-domain proteins fold? Fold Des. 1998;3(4):R81–R91. doi: 10.1016/S1359-0278(98)00033-9. [DOI] [PubMed] [Google Scholar]
  15. Jacob M., Holtermann G., Perl D., Reinstein J., Schindler T., Geeves M. A., Schmid F. X. Microsecond folding of the cold shock protein measured by a pressure-jump technique. Biochemistry. 1999 Mar 9;38(10):2882–2891. doi: 10.1021/bi982487i. [DOI] [PubMed] [Google Scholar]
  16. Kim D. E., Gu H., Baker D. The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4982–4986. doi: 10.1073/pnas.95.9.4982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lim W. A., Farruggio D. C., Sauer R. T. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry. 1992 May 5;31(17):4324–4333. doi: 10.1021/bi00132a025. [DOI] [PubMed] [Google Scholar]
  18. 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. Fold Des. 1996;1(1):43–55. [PubMed] [Google Scholar]
  19. Martinez J. C., Pisabarro M. T., Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol. 1998 Aug;5(8):721–729. doi: 10.1038/1418. [DOI] [PubMed] [Google Scholar]
  20. Martínez J. C., Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol. 1999 Nov;6(11):1010–1016. doi: 10.1038/14896. [DOI] [PubMed] [Google Scholar]
  21. Matouschek A., Otzen D. E., Itzhaki L. S., Jackson S. E., Fersht A. R. Movement of the position of the transition state in protein folding. Biochemistry. 1995 Oct 17;34(41):13656–13662. doi: 10.1021/bi00041a047. [DOI] [PubMed] [Google Scholar]
  22. Minor D. L., Jr, Kim P. S. Context is a major determinant of beta-sheet propensity. Nature. 1994 Sep 15;371(6494):264–267. doi: 10.1038/371264a0. [DOI] [PubMed] [Google Scholar]
  23. Minor D. L., Jr, Kim P. S. Measurement of the beta-sheet-forming propensities of amino acids. Nature. 1994 Feb 17;367(6464):660–663. doi: 10.1038/367660a0. [DOI] [PubMed] [Google Scholar]
  24. Mirny L. A., Abkevich V. I., Shakhnovich E. I. How evolution makes proteins fold quickly. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4976–4981. doi: 10.1073/pnas.95.9.4976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mirny L. A., Shakhnovich E. I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol. 1999 Aug 6;291(1):177–196. doi: 10.1006/jmbi.1999.2911. [DOI] [PubMed] [Google Scholar]
  26. Pace C. N., Vajdos F., Fee L., Grimsley G., Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 1995 Nov;4(11):2411–2423. doi: 10.1002/pro.5560041120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Perl D., Welker C., Schindler T., Schröder K., Marahiel M. A., Jaenicke R., Schmid F. X. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nat Struct Biol. 1998 Mar;5(3):229–235. doi: 10.1038/nsb0398-229. [DOI] [PubMed] [Google Scholar]
  28. Reid K. L., Rodriguez H. M., Hillier B. J., Gregoret L. M. Stability and folding properties of a model beta-sheet protein, Escherichia coli CspA. Protein Sci. 1998 Feb;7(2):470–479. doi: 10.1002/pro.5560070228. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Riddle D. S., Grantcharova V. P., Santiago J. V., Alm E., Ruczinski I., Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol. 1999 Nov;6(11):1016–1024. doi: 10.1038/14901. [DOI] [PubMed] [Google Scholar]
  30. Sali A., Shakhnovich E., Karplus M. How does a protein fold? Nature. 1994 May 19;369(6477):248–251. doi: 10.1038/369248a0. [DOI] [PubMed] [Google Scholar]
  31. Schindelin H., Jiang W., Inouye M., Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5119–5123. doi: 10.1073/pnas.91.11.5119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schindler T., Graumann P. L., Perl D., Ma S., Schmid F. X., Marahiel M. A. The family of cold shock proteins of Bacillus subtilis. Stability and dynamics in vitro and in vivo. J Biol Chem. 1999 Feb 5;274(6):3407–3413. doi: 10.1074/jbc.274.6.3407. [DOI] [PubMed] [Google Scholar]
  33. Schindler T., Herrler M., Marahiel M. A., Schmid F. X. Extremely rapid protein folding in the absence of intermediates. Nat Struct Biol. 1995 Aug;2(8):663–673. doi: 10.1038/nsb0895-663. [DOI] [PubMed] [Google Scholar]
  34. Smith C. K., Regan L. Guidelines for protein design: the energetics of beta sheet side chain interactions. Science. 1995 Nov 10;270(5238):980–982. doi: 10.1126/science.270.5238.980. [DOI] [PubMed] [Google Scholar]
  35. Smith C. K., Withka J. M., Regan L. A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. Biochemistry. 1994 May 10;33(18):5510–5517. doi: 10.1021/bi00184a020. [DOI] [PubMed] [Google Scholar]
  36. Tanford C. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv Protein Chem. 1970;24:1–95. [PubMed] [Google Scholar]
  37. Tisi L. C., Evans P. A. Conserved structural features on protein surfaces: small exterior hydrophobic clusters. J Mol Biol. 1995 Jun 2;249(2):251–258. doi: 10.1006/jmbi.1995.0294. [DOI] [PubMed] [Google Scholar]
  38. Wouters M. A., Curmi P. M. An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs. Proteins. 1995 Jun;22(2):119–131. doi: 10.1002/prot.340220205. [DOI] [PubMed] [Google Scholar]
  39. Zaremba S. M., Gregoret L. M. Context-dependence of amino acid residue pairing in antiparallel beta-sheets. J Mol Biol. 1999 Aug 13;291(2):463–479. doi: 10.1006/jmbi.1999.2961. [DOI] [PubMed] [Google Scholar]
  40. Zhu H., Braun W. Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. Protein Sci. 1999 Feb;8(2):326–342. doi: 10.1110/ps.8.2.326. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES