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
. 2000 Apr;9(4):627–636. doi: 10.1110/ps.9.4.627

A helix-turn motif in the C-terminal domain of histone H1.

R Vila 1, I Ponte 1, M A Jiménez 1, M Rico 1, P Suau 1
PMCID: PMC2144612  PMID: 10794405

Abstract

The structural study of peptides belonging to the terminal domains of histone H1 can be considered as a step toward the understanding of the function of H1 in chromatin. The conformational properties of the peptide Ac-EPKRSVAFKKTKKEVKKVATPKK (CH-1), which belongs to the C-terminal domain of histone H1(o) (residues 99-121) and is adjacent to the central globular domain of the protein, were examined by means of 1H-NMR and circular dichroism. In aqueous solution, CH-1 behaved as a mainly unstructured peptide, although turn-like conformations in rapid equilibrium with the unfolded state could be present. Addition of trifluoroethanol resulted in a substantial increase of the helical content. The helical limits, as indicated by (i,i + 3) nuclear Overhauser effect (NOE) cross correlations and significant up-field conformational shifts of the C(alpha) protons, span from Pro100 to Val116, with Glu99 and Ala117 as N- and C-caps. A structure calculation performed on the basis of distance constraints derived from NOE cross peaks in 90% trifluoroethanol confirmed the helical structure of this region. The helical region has a marked amphipathic character, due to the location of all positively charged residues on one face of the helix and all the hydrophobic residues on the opposite face. The peptide has a TPKK motif at the C-terminus, following the alpha-helical region. The observed NOE connectivities suggest that the TPKK sequence adopts a type (I) beta-turn conformation, a sigma-turn conformation or a combination of both, in fast equilibrium with unfolded states. Sequences of the kind (S/T)P(K/R)(K/R) have been proposed as DNA binding motifs. The CH-1 peptide, thus, combines a positively charged amphipathic helix and a turn as potential DNA-binding motifs.

Full Text

The Full Text of this article is available as a PDF (1.1 MB).

Selected References

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

  1. Bouvet P., Dimitrov S., Wolffe A. P. Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1. Genes Dev. 1994 May 15;8(10):1147–1159. doi: 10.1101/gad.8.10.1147. [DOI] [PubMed] [Google Scholar]
  2. Buck M. Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins. Q Rev Biophys. 1998 Aug;31(3):297–355. doi: 10.1017/s003358359800345x. [DOI] [PubMed] [Google Scholar]
  3. Cerf C., Lippens G., Muyldermans S., Segers A., Ramakrishnan V., Wodak S. J., Hallenga K., Wyns L. Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: sequential assignment and secondary structure. Biochemistry. 1993 Oct 26;32(42):11345–11351. doi: 10.1021/bi00093a011. [DOI] [PubMed] [Google Scholar]
  4. Chen Y. H., Yang J. T., Chau K. H. Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry. 1974 Jul 30;13(16):3350–3359. doi: 10.1021/bi00713a027. [DOI] [PubMed] [Google Scholar]
  5. Chou P. Y., Fasman G. D. Prediction of protein conformation. Biochemistry. 1974 Jan 15;13(2):222–245. doi: 10.1021/bi00699a002. [DOI] [PubMed] [Google Scholar]
  6. Clark D. J., Hill C. S., Martin S. R., Thomas J. O. Alpha-helix in the carboxy-terminal domains of histones H1 and H5. EMBO J. 1988 Jan;7(1):69–75. doi: 10.1002/j.1460-2075.1988.tb02784.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Clore G. M., Gronenborn A. M., Nilges M., Sukumaran D. K., Zarbock J. The polypeptide fold of the globular domain of histone H5 in solution. A study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 1987 Jun;6(6):1833–1842. doi: 10.1002/j.1460-2075.1987.tb02438.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dasso M., Dimitrov S., Wolffe A. P. Nuclear assembly is independent of linker histones. Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12477–12481. doi: 10.1073/pnas.91.26.12477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dou Y., Mizzen C. A., Abrams M., Allis C. D., Gorovsky M. A. Phosphorylation of linker histone H1 regulates gene expression in vivo by mimicking H1 removal. Mol Cell. 1999 Oct;4(4):641–647. doi: 10.1016/s1097-2765(00)80215-4. [DOI] [PubMed] [Google Scholar]
  10. Dyson H. J., Rance M., Houghten R. A., Wright P. E., Lerner R. A. Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix. J Mol Biol. 1988 May 5;201(1):201–217. doi: 10.1016/0022-2836(88)90447-0. [DOI] [PubMed] [Google Scholar]
  11. Erard M., Lakhdar-Ghazal F., Amalric F. Repeat peptide motifs which contain beta-turns and modulate DNA condensation in chromatin. Eur J Biochem. 1990 Jul 20;191(1):19–26. doi: 10.1111/j.1432-1033.1990.tb19088.x. [DOI] [PubMed] [Google Scholar]
  12. Güntert P., Wüthrich K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR. 1991 Nov;1(4):447–456. doi: 10.1007/BF02192866. [DOI] [PubMed] [Google Scholar]
  13. Harper E. T., Rose G. D. Helix stop signals in proteins and peptides: the capping box. Biochemistry. 1993 Aug 3;32(30):7605–7609. doi: 10.1021/bi00081a001. [DOI] [PubMed] [Google Scholar]
  14. Hartman P. G., Chapman G. E., Moss T., Bradbury E. M. Studies on the role and mode of operation of the very-lysine-rich histone H1 in eukaryote chromatin. The three structural regions of the histone H1 molecule. Eur J Biochem. 1977 Jul 1;77(1):45–51. doi: 10.1111/j.1432-1033.1977.tb11639.x. [DOI] [PubMed] [Google Scholar]
  15. Hill C. S., Martin S. R., Thomas J. O. A stable alpha-helical element in the carboxy-terminal domain of free and chromatin-bound histone H1 from sea urchin sperm. EMBO J. 1989 Sep;8(9):2591–2599. doi: 10.1002/j.1460-2075.1989.tb08398.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hinck A. P., Eberhardt E. S., Markley J. L. NMR strategy for determining Xaa-Pro peptide bond configurations in proteins: mutants of staphylococcal nuclease with altered configuration at proline-117. Biochemistry. 1993 Nov 9;32(44):11810–11818. doi: 10.1021/bi00095a009. [DOI] [PubMed] [Google Scholar]
  17. Jimenez M. A., Bruix M., Gonzalez C., Blanco F. J., Nieto J. L., Herranz J., Rico M. CD and 1H-NMR studies on the conformational properties of peptide fragments from the C-terminal domain of thermolysin. Eur J Biochem. 1993 Feb 1;211(3):569–581. doi: 10.1111/j.1432-1033.1993.tb17584.x. [DOI] [PubMed] [Google Scholar]
  18. Jiménez M. A., Muñoz V., Rico M., Serrano L. Helix stop and start signals in peptides and proteins. The capping box does not necessarily prevent helix elongation. J Mol Biol. 1994 Sep 30;242(4):487–496. doi: 10.1006/jmbi.1994.1596. [DOI] [PubMed] [Google Scholar]
  19. Johnson N. P., Lindstrom J., Baase W. A., von Hippel P. H. Double-stranded DNA templates can induce alpha-helical conformation in peptides containing lysine and alanine: functional implications for leucine zipper and helix-loop-helix transcription factors. Proc Natl Acad Sci U S A. 1994 May 24;91(11):4840–4844. doi: 10.1073/pnas.91.11.4840. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Khochbin S., Wolffe A. P. Developmentally regulated expression of linker-histone variants in vertebrates. Eur J Biochem. 1994 Oct 15;225(2):501–510. doi: 10.1111/j.1432-1033.1994.00501.x. [DOI] [PubMed] [Google Scholar]
  21. Kumar A., Ernst R. R., Wüthrich K. A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun. 1980 Jul 16;95(1):1–6. doi: 10.1016/0006-291x(80)90695-6. [DOI] [PubMed] [Google Scholar]
  22. Lee H. L., Archer T. K. Prolonged glucocorticoid exposure dephosphorylates histone H1 and inactivates the MMTV promoter. EMBO J. 1998 Mar 2;17(5):1454–1466. doi: 10.1093/emboj/17.5.1454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Marion D., Wüthrich K. Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteins. Biochem Biophys Res Commun. 1983 Jun 29;113(3):967–974. doi: 10.1016/0006-291x(83)91093-8. [DOI] [PubMed] [Google Scholar]
  24. Morán F., Montero F., Azorín F., Suau P. Condensation of DNA by the C-terminal domain of histone H1. A circular dichroism study. Biophys Chem. 1985 Jun;22(1-2):125–129. doi: 10.1016/0301-4622(85)80033-8. [DOI] [PubMed] [Google Scholar]
  25. Muñoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol. 1994 Jun;1(6):399–409. doi: 10.1038/nsb0694-399. [DOI] [PubMed] [Google Scholar]
  26. Muñoz V., Serrano L., Jiménez M. A., Rico M. Structural analysis of peptides encompassing all alpha-helices of three alpha/beta parallel proteins: Che-Y, flavodoxin and P21-ras: implications for alpha-helix stability and the folding of alpha/beta parallel proteins. J Mol Biol. 1995 Apr 7;247(4):648–669. doi: 10.1016/s0022-2836(05)80145-7. [DOI] [PubMed] [Google Scholar]
  27. Ramakrishnan V., Finch J. T., Graziano V., Lee P. L., Sweet R. M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature. 1993 Mar 18;362(6417):219–223. doi: 10.1038/362219a0. [DOI] [PubMed] [Google Scholar]
  28. Reeves R., Nissen M. S. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem. 1990 May 25;265(15):8573–8582. [PubMed] [Google Scholar]
  29. Richardson J. S., Richardson D. C. Amino acid preferences for specific locations at the ends of alpha helices. Science. 1988 Jun 17;240(4859):1648–1652. doi: 10.1126/science.3381086. [DOI] [PubMed] [Google Scholar]
  30. Shen X., Gorovsky M. A. Linker histone H1 regulates specific gene expression but not global transcription in vivo. Cell. 1996 Aug 9;86(3):475–483. doi: 10.1016/s0092-8674(00)80120-8. [DOI] [PubMed] [Google Scholar]
  31. Shen X., Yu L., Weir J. W., Gorovsky M. A. Linker histones are not essential and affect chromatin condensation in vivo. Cell. 1995 Jul 14;82(1):47–56. doi: 10.1016/0092-8674(95)90051-9. [DOI] [PubMed] [Google Scholar]
  32. Suzuki M., Gerstein M., Johnson T. An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA. Protein Eng. 1993 Aug;6(6):565–574. doi: 10.1093/protein/6.6.565. [DOI] [PubMed] [Google Scholar]
  33. Suzuki M. SPKK, a new nucleic acid-binding unit of protein found in histone. EMBO J. 1989 Mar;8(3):797–804. doi: 10.1002/j.1460-2075.1989.tb03440.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Vermaak D., Steinbach O. C., Dimitrov S., Rupp R. A., Wolffe A. P. The globular domain of histone H1 is sufficient to direct specific gene repression in early Xenopus embryos. Curr Biol. 1998 Apr 23;8(9):533–536. doi: 10.1016/s0960-9822(98)70206-4. [DOI] [PubMed] [Google Scholar]
  35. Wishart D. S., Bigam C. G., Holm A., Hodges R. S., Sykes B. D. 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J Biomol NMR. 1995 Jan;5(1):67–81. doi: 10.1007/BF00227471. [DOI] [PubMed] [Google Scholar]
  36. Wishart D. S., Sykes B. D., Richards F. M. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol. 1991 Nov 20;222(2):311–333. doi: 10.1016/0022-2836(91)90214-q. [DOI] [PubMed] [Google Scholar]
  37. Wolffe A. P., Khochbin S., Dimitrov S. What do linker histones do in chromatin? Bioessays. 1997 Mar;19(3):249–255. doi: 10.1002/bies.950190311. [DOI] [PubMed] [Google Scholar]
  38. Wüthrich K., Billeter M., Braun W. Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. J Mol Biol. 1984 Dec 15;180(3):715–740. doi: 10.1016/0022-2836(84)90034-2. [DOI] [PubMed] [Google Scholar]
  39. Zlatanova J., Van Holde K. Histone H1 and transcription: still an enigma? J Cell Sci. 1992 Dec;103(Pt 4):889–895. doi: 10.1242/jcs.103.4.889. [DOI] [PubMed] [Google Scholar]

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

RESOURCES