Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1996 Sep;5(9):1942–1946. doi: 10.1002/pro.5560050924

A fragment of staphylococcal nuclease with an OB-fold structure shows hydrogen-exchange protection factors in the range reported for "molten globules".

A T Alexandrescu 1, S A Dames 1, R Wiltscheck 1
PMCID: PMC2143544  PMID: 8880922

Abstract

Hydrogen-exchange rates for an OB-fold subdomain fragment of staphylococcal nuclease have been measured at pH 4.7 and 4 degrees C, conditions close to the minimum of acid/base catalyzed exchange. The strongest protection from solvent exchange is observed for residues from a five-stranded beta-barrel in the NMR structure of the protein. Protection factors, calculated from the experimental hydrogen-exchange rates, range between 1 and 190. Similarly small protection factors have in many cases been attributed to "molten globule" conformations that are supposed to lack a specific tertiary structure. The present results suggest that marginal protection from solvent exchange does not exclude well-defined structure.

Full Text

The Full Text of this article is available as a PDF (1.3 MB).

Selected References

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

  1. Alexandrescu A. T., Gittis A. G., Abeygunawardana C., Shortle D. NMR structure of a stable "OB-fold" sub-domain isolated from staphylococcal nuclease. J Mol Biol. 1995 Jul 7;250(2):134–143. doi: 10.1006/jmbi.1995.0365. [DOI] [PubMed] [Google Scholar]
  2. Bai Y., Sosnick T. R., Mayne L., Englander S. W. Protein folding intermediates: native-state hydrogen exchange. Science. 1995 Jul 14;269(5221):192–197. doi: 10.1126/science.7618079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baldwin R. L. The nature of protein folding pathways: the classical versus the new view. J Biomol NMR. 1995 Feb;5(2):103–109. doi: 10.1007/BF00208801. [DOI] [PubMed] [Google Scholar]
  4. Buck M., Radford S. E., Dobson C. M. Amide hydrogen exchange in a highly denatured state. Hen egg-white lysozyme in urea. J Mol Biol. 1994 Apr 1;237(3):247–254. doi: 10.1006/jmbi.1994.1228. [DOI] [PubMed] [Google Scholar]
  5. Guijarro J. I., Jackson M., Chaffotte A. F., Delepierre M., Mantsch H. H., Goldberg M. E. Protein folding intermediates with rapidly exchangeable amide protons contain authentic hydrogen-bonded secondary structures. Biochemistry. 1995 Mar 7;34(9):2998–3008. doi: 10.1021/bi00009a031. [DOI] [PubMed] [Google Scholar]
  6. Jacobs M. D., Fox R. O. Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy. Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):449–453. doi: 10.1073/pnas.91.2.449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Kalnin N. N., Kuwajima K. Kinetic folding and unfolding of staphylococcal nuclease and its six mutants studied by stopped-flow circular dichroism. Proteins. 1995 Oct;23(2):163–176. doi: 10.1002/prot.340230206. [DOI] [PubMed] [Google Scholar]
  8. Koide S., Jahnke W., Wright P. E. Measurement of intrinsic exchange rates of amide protons in a 15N-labeled peptide. J Biomol NMR. 1995 Nov;6(3):306–312. doi: 10.1007/BF00197811. [DOI] [PubMed] [Google Scholar]
  9. Kuboniwa H., Tjandra N., Grzesiek S., Ren H., Klee C. B., Bax A. Solution structure of calcium-free calmodulin. Nat Struct Biol. 1995 Sep;2(9):768–776. doi: 10.1038/nsb0995-768. [DOI] [PubMed] [Google Scholar]
  10. Lu J., Dahlquist F. W. Detection and characterization of an early folding intermediate of T4 lysozyme using pulsed hydrogen exchange and two-dimensional NMR. Biochemistry. 1992 May 26;31(20):4749–4756. doi: 10.1021/bi00135a002. [DOI] [PubMed] [Google Scholar]
  11. Miranker A., Radford S. E., Karplus M., Dobson C. M. Demonstration by NMR of folding domains in lysozyme. Nature. 1991 Feb 14;349(6310):633–636. doi: 10.1038/349633a0. [DOI] [PubMed] [Google Scholar]
  12. Murzin A. G. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 1993 Mar;12(3):861–867. doi: 10.1002/j.1460-2075.1993.tb05726.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Neri D., Billeter M., Wider G., Wüthrich K. NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science. 1992 Sep 11;257(5076):1559–1563. doi: 10.1126/science.1523410. [DOI] [PubMed] [Google Scholar]
  14. Ohgushi M., Wada A. 'Molten-globule state': a compact form of globular proteins with mobile side-chains. FEBS Lett. 1983 Nov 28;164(1):21–24. doi: 10.1016/0014-5793(83)80010-6. [DOI] [PubMed] [Google Scholar]
  15. Pedersen T. G., Thomsen N. K., Andersen K. V., Madsen J. C., Poulsen F. M. Determination of the rate constants k1 and k2 of the Linderström-Lang model for protein amide hydrogen exchange. A study of the individual amides in hen egg-white lysozyme. J Mol Biol. 1993 Mar 20;230(2):651–660. doi: 10.1006/jmbi.1993.1176. [DOI] [PubMed] [Google Scholar]
  16. Radford S. E., Dobson C. M., Evans P. A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature. 1992 Jul 23;358(6384):302–307. doi: 10.1038/358302a0. [DOI] [PubMed] [Google Scholar]
  17. Robinson C. V., Gross M., Eyles S. J., Ewbank J. J., Mayhew M., Hartl F. U., Dobson C. M., Radford S. E. Conformation of GroEL-bound alpha-lactalbumin probed by mass spectrometry. Nature. 1994 Dec 15;372(6507):646–651. doi: 10.1038/372646a0. [DOI] [PubMed] [Google Scholar]
  18. Roder H., Elöve G. A., Englander S. W. Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature. 1988 Oct 20;335(6192):700–704. doi: 10.1038/335700a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Shortle D., Meeker A. K. Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation. Proteins. 1986 Sep;1(1):81–89. doi: 10.1002/prot.340010113. [DOI] [PubMed] [Google Scholar]
  20. Shortle D., Meeker A. K. Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry. 1989 Feb 7;28(3):936–944. doi: 10.1021/bi00429a003. [DOI] [PubMed] [Google Scholar]
  21. Udgaonkar J. B., Baldwin R. L. NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature. 1988 Oct 20;335(6192):694–699. doi: 10.1038/335694a0. [DOI] [PubMed] [Google Scholar]
  22. Zahn R., Spitzfaden C., Ottiger M., Wüthrich K., Plückthun A. Destabilization of the complete protein secondary structure on binding to the chaperone GroEL. Nature. 1994 Mar 17;368(6468):261–265. doi: 10.1038/368261a0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES