Secondary structural analysis of retrovirus integrase: Characterization by circular dichroism and empirical prediction methods

Abstract

The retrovirus integrase (IN) protein is essentialfor integration of viral DNA into host DNA. The secondary structure of thepurified IN protein from avian myeloblastosis virus was investigated by bothcircular dichroism (CD) spectroscopy and five empirical prediction methods. The secondary structures determined from the resolving of CD spectra through a least‐squares curve fitting procedure were compared with those predicted from four statistical methods, e.g., the Chou–Fasman, arnier–Osguthorpe–Robson, Nishikawa–Ooi, and a JOINT scheme which combined all three of these methods, plus a pure a priori one, the Ptitsyn–Finkelstein method. Among all of the methods used, the Nishikawa–Ooiprediction gave the closest match in the composition of secondary structureto the CD result, although the other methods each correctly predictedoneor more secondary structural group. Most of the α‐helix and β‐sheet states predicted by the Ptitsyn–Finkelstein methodwere in accord with the Nishikawa–Ooi method. Secondary structural predictions by the Nishikawa–Ooi method were extended further toinclude IN proteins from four phylogenetic distinct retroviruses. The structuralrelationships between the four most conserved amino acid blocks of these IN proteins were compared using sequence homology and secondary structure predictions.