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1998 | 45 | 1 |

Tytuł artykułu

Binding of SPXK- and APXK-peptide motifs to At-rich DNA. Experimental and theoretical studies

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK- type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

Wydawca

-

Rocznik

Tom

45

Numer

1

Opis fizyczny

p.221-231

Twórcy

autor
  • Polish Academy of Sciences, A.Pawinskiego 5A, 02-106 Warsaw, Poland
autor
autor
autor

Bibliografia

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  • 8. Omichinski, J.G., Clore, G.M., Schaad, 0., Felsenfeld, G., Trainor, C., Appella, E., Stahl, S.J. & Gronenborn, A.M. (1993) NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science 261, 438-446.
  • 9. Kissinger, C.R., Liu, B., Martin-Blanko, E., Kornberg, T.B. & Pabo, C. (1990) Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: A framework for understanding homeodomain-DNA interac­tions. Cell, 63, 579-590.
  • 10. Suzuki. M. (1989) SPXX, a frequent sequence motif in gene regulatory proteins. J. Mol. Biol. 207, 61-84.
  • 11. Shetty, K.T., Link, W.T. & Pant. C.H. (1993) cdc2-Likc kinase from rat spinal cord specifi­cally phosphorylates KSPXK motifs in neuro- filamental proteins: Isolation and characteri­zation. Proc. Natl. Acad. Sci. U.S.A. 90, 6844- 6848.
  • 12. Tomaszewski, R. & Jerzmanowski, A. (1997) The AT-rich flanks of the oocyte-type 5S RNA gene of Xenopus laevis act as a strong local sig­nal for histone Hl-mediated chromatin reor­ganization in vitro. Nucleic Acids Res. 25,458- 465.
  • 13. Kandolf, M. (1994) The Hla histone variant is the in vivo repressor of oocyte-type 5S gene transcription in Xenopus laevis embryos. Proc. NatL Acad. Sci. U.S.A. 91, 7257-7261.
  • 14. Shen, X. & Gorowski, M. (1996) Linker his­tones are not essential and affect chromatin condensation in vivo. Cell 86, 475-483
  • 15. Prymakowska-Bosak, M., Przewłocka, M.R., Iwkiewicz, J., Egierszdorff, S., Kuraś, M., Chaubet, N., Gigot, C., Spiker, S. & Jerzma­nowski, A. (1996) Histone HI overexpressed to high level in tobacco affects certain develop­mental programs but has limited effect on ba­sal cellular functions. Proc. NatL Acad. Sci, U.S.A 93, 10250-10255.
  • 16. Russel, S.T. & Waishel, A. (1985) Calculations of electrostatic energies in proteins. The ener­getics of ionized groups in bovine pancreatic trypsin inhibitor. J. MvL Biol. 185,389-404.
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  • 20. Lesyng, B. & McCammon, J.A. (1993) Molecu­lar modeling methods. Basic techniques and challenging problems. Pharmac. Ther. 60, 149-167.
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  • 22. Grycuk, T. & lesyng, B. (1996) Studies on macromolecular recognition processes. Appli­cation of a Poisson-Boltzman model to protein- nucleic acids interactions. 3rd European Con­ference on Mathematics Applied to Biology and Medicine, October 6-10, Abstract, p. 29, Hei­delberg.
  • 23. Churchill, M.E.A. & Suzuki, M. (1989) 'SPKK' motifs prefer to bind to DNA at A/T-rich sites. KMBOJ. 8, 4189-4195.
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Typ dokumentu

Bibliografia

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Identyfikator YADDA

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