title: An empirical potential study of the interaction of L-lysine-L-alanine-L-alanine tripeptide with four models of B-DNA with different compositions.
abstract: The empirical potential including the intra- and intermolecular energy terms was used to study the interaction of L-Lysine-L-Alanine-L-Alanine Tripeptide with four models of B-DNA with different compositions. On the basis of a detailed search of the respective potential energy surface, it was found that the peptide is preferentially bounded to the AT-rich sequences. Analysis of the different energy contributions indicated that the electrostatic term is responsible for this preference. The results agree with the experimental data on the selectivity of some DNA--binding proteins and polypeptides to AT-rich DNA.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Praha.
authors.forename: J
authors.initials: J
authors.lastname: Vondrásek
authors.forename: J
authors.initials: J
authors.lastname: Sponar
authors.forename: P
authors.initials: P
authors.lastname: Hobza
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D009842:Oligopeptides; C043367:lysyl-alanyl-alanine; D004247:DNA