Theoretical studies on alpha-helix--DNA interactions

J Biomol Struct Dyn. 1988 Feb;5(4):859-71. doi: 10.1080/07391102.1988.10506431.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Base Sequence
  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Peptides / metabolism*
  • Protein Conformation
  • Thermodynamics


  • DNA-Binding Proteins
  • Peptides
  • polyalanine
  • DNA