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Theoretical studies on alpha-helix--DNA interactions.

B Gopalakrishnan·M Bansal
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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.

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Base CompositionBase SequenceDNADNA-Binding ProteinsModels, MolecularNucleic Acid ConformationPeptidesProtein ConformationThermodynamicsJournal ArticleResearch Support, Non-U.S. Gov't

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B Gopalakrishnan, M Bansal. 1988. Theoretical studies on alpha-helix--DNA interactions.. https://doi.org/10.1080/07391102.1988.10506431

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