Retrovirus integrase: identification of a potential leucine zipper motif

The secondary structure of the retrovirus integration protein(IN) was predicted from seven inferred retrovirus IN sequences.The IN sequences were aligned by computer and the phylogeneticrelationships between them were determined. The secondary structureof the aligned IN sequences was predicted by two consensus predictionmethods. The predicted secondary structural patterns from thetwo consensus prediction schemes were compared with and superimposedon a composite structural profile of hydropathic/chain flexibility/amphipathicindexes with each index profile being calculated independentlyfor the aligned IN sequences. The use of this composite structuralprofile not only enhanced the prediction accuracy but also helpedin defining the surface loop regions which would be otherwiseunpredictable by the use of consensus prediction methods alone.An amphipathic helix was identified by these united structuralprediction-chain property profiles. Helical wheel analysis gavethe amphipathic helix a coiled-coil like pattern which was similarto the leucine zipper discovered for some eukaryotic gene regulatoryproteins. The proposed amphipathic helix may play an essentialrole in defining the biological properties of IN.