Open AccessBinding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies.
Author(s) -
Jan Brzeski,
Tomasz Grycuk,
Andrzej W. Lipkowski,
Witold R. Rudnicki,
Bogdan Lesyng,
Andrzej Jerzmanowski
Publication year - 1998
Publication title -
acta biochimica polonica
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.452
H-Index - 78
eISSN - 1734-154X
pISSN - 0001-527X
DOI - 10.18388/abp.1998_4304
Subject(s) - dna , serine , alanine , binding site , chemistry , biochemistry , structural motif , dna binding site , peptide , biophysics , biology , stereochemistry , amino acid , gene , enzyme , gene expression , promoter
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.