title: Theoretical studies on alpha-helix--DNA interactions.
abstract: The interaction energies between (Ala)10 and alpha-helix fragment and different nucleotide sequences in right-handed B-form have been optimized using semi-empirical potential energy functions. The energies are calculated for two different orientations of the alpha-helix, viz., when the alpha-helix axis taken in the N----C direction is (i) parallel and (ii) antiparallel to the 5'-3' ascending strand of DNA, proximal to it. When both the DNA molecule as well as the alpha-helix are treated as rigid molecules it is found that a polyalanine alpha-helix has slightly more favourable contacts when it is in the proximity of a four nucleotide sequence of 5'-(N-A-T-N)-3' type, where N is either a purine or a pyrimidine. However, when the two interacting molecules are allowed to undergo local structural variations then the interaction energy appears to be independent of the base sequence confirming the non-specific nature of these interactions.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
authors.forename: B
authors.initials: B
authors.lastname: Gopalakrishnan
authors.forename: M
authors.initials: M
authors.lastname: Bansal
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000378:metabolism*; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D010455:Peptides; C019529:polyalanine; D004247:DNA