Gopalakrishnan, B and Bansal, M (1988) Theoretical studies on alpha-helix--DNA interactions. In: Journal of Biomolecular Structure & Dynamics, 5 (4). 859 -871.
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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.
| Item Type: | Journal Article |
|---|---|
| Publication: | Journal of Biomolecular Structure & Dynamics |
| Publisher: | Adenine Press |
| Additional Information: | Copyright of this article belongs to Adenine Press. |
| Department/Centre: | Division of Biological Sciences > Molecular Biophysics Unit |
| Date Deposited: | 11 Oct 2010 09:21 |
| Last Modified: | 11 Oct 2010 09:21 |
| URI: | http://eprints.iisc.ac.in/id/eprint/33016 |
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