Integration of the human immunodeficiency virus (HIV‐1) DNA into the host genome is catalysed by a virus‐encoded protein integrase. Here, we report some of the structural and functional properties of two synthetic peptides: integrase‐(147–175)‐peptide reproducing the residues 147–175 (SQGVVESMNKELK159KIIGQVRDQAEHLKTAY) of the HIV‐1 integrase, and [Pro159] integrase‐(147–175)‐peptide where the lysine 159 is substituted for a proline. Circular dichroism revealed that both peptides are mostly under unordered conformation in aqueous solution, contrasting with the α‐helix exhibited by residues 147–175 in the protein crystal structure. In a weak α‐helix‐promoting environment, integrase‐(147–175)‐peptide self‐associated into stable coiled‐coil oligomers, while [Pro159] integrase‐(147–175)‐peptide did not. This property was further confirmed by cross‐linking experiments. In our in vitro experiments, only integrase‐(147–175)‐peptide was able to reduce the integration activity of the enzyme. We propose that the inhibitory activity shown by integrase‐(147–175)‐peptide is dependent on its ability to bind to its counterpart in integrase through a peptide‐protein coiled‐coil structure disturbing the catalytic properties of the enzyme.

Results are presented on a peptide fragment (1013-1056) from human DNA topoisomerase II alpha. This was selected using the procedure of Lupas et al. (Lupas, A., Van Dyke, M., and Stock, J. (1991) Science 252, 1162-1164) for its potential to adopt a stable coiled-coil structure. The same theoretical treatment rejected the segment 994-1021 proposed by Zwelling and Perry (Zwelling, L. A., and Perry, W. M. (1989) Mol. Endocrinol. 3, 603-604) as a possible core for leucine-zipper formation. Our experimental studies combine cross-linking and CD analysis. Cross-linking establishes that the 1013-1056 fragment forms a stable homodimer in solution. Effects of increasing peptide concentration on CD spectra confirm that only the 1013-1056 fragment can undergo a coiled-coil stabilization from an isolated alpha-helix. Unfolding experiments further show that the coiled-coil is more stable in guanidium chloride than in urea. Values of -6.8 and -7.4 kcal/mol for the dimerization free energy are determined by thermal and urea unfolding, respectively. These are strikingly similar to the value recently found for the dissociation/reassociation of the entire yeast topoisomerase II from sedimentation equilibrium experiments (Lamhasni, S., Larsen, A. K., Barray, M., Monnot, M., Delain, E., and Fermandjian, S. (1995) Biochemistry 34, 3632-3639), although their significance relatively to topoisomerase II undoubtedly requires further analysis.