title: Theoretical studies on the interaction of proteins and nucleic acid. II. The binding of alpha-helix to B-DNA.
abstract: Interactions between B-DNA and homopolymeric alpha-helices of glycine, alanine, serine, asparagine and aspartic acid have been studied theoretically. The complexation energy has been minimised taking into account the interactions between DNA and the polypeptides as well as the internal energy of the alpha-helix and the interaction energy of counterions with the complex. The results obtained indicate the important role of strong hydrogen bonds between the peptide side chains and nucleic acid phosphate groups, these bonds being much stronger than specific interactions with the base-pairs. The formation of these structural bonds depends on the size of the alpha-helix, which in turn determines whether bridging across the major groove is possible. The steric role of the methyl group of thymine in orienting the peptide helix and the role of DNA screening cations in complex stabilization are also significant.
mesh_terms: D004247:DNA; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010455:Peptides; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D010455:Peptides; D004247:DNA