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

100%

Brzeski J., Grycuk T., Lipkowski A. W., Rudnicki W., Lesyng B., Jerzmanowski A.

Acta Biochimica Polonica

1998

tom 45

nr 1

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.

Interaction of HIV Tat model peptides with tRNA and 5S rRNA

80%

Giel-Pietraszuk M., Barciszewska M. Z., Mucha P., Rekowski P., Kupryszewski G., Barciszewski J.

Acta Biochimica Polonica

1997

tom 44

nr 3

New data are presented on the interaction of model synthetic peptides containing an arginine-rich region of human immunodeficiency virus (HIV-Tat), with native RNA molecules: tRNA Phe of Saccharomyces cerevisiae and 5S rRNA from Lupinas luteus. Both RNA species form complexes with the Tatl (GRKKRRQRRRA) and Tat2 (GRKKRRQRRRAPQDSQTHQASLSKQPA) pep- tides, as shown by electrophoretic gel shift and RNase footprint assays, and CD measurements. The nucleotide sequence UGGG located in the dihydrouridine loop of tRNA Phe as well as in the loop D of 5S rRNA is specifically protected against RNases. Our data indicate direct interactions of guanine of RNA moieties with argininc residues. These interactions seem similar to those observed in DNA-protein complexes, but different from those previously observed in the TAR RNA-Tat complexes.

Ograniczanie wyników

2 Acta Biochimica Polonica

1 Barciszewska M. Z.

1 Barciszewski J.

1 Brzeski J.

1 Giel-Pietraszuk M.

1 Grycuk T.

1 Jerzmanowski A.

1 Kupryszewski G.

1 Lesyng B.

1 Lipkowski A. W.

1 Mucha P.

1 Rekowski P.

1 Rudnicki W.

1 1998

1 1997

Wyniki wyszukiwania

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

Interaction of HIV Tat model peptides with tRNA and 5S rRNA