Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase {alpha}4 helix

HIV-1 integrase integrates retroviral DNA through 3'-processing and strand transfer reactions in the presence of a divalent cation (Mg(2+) or Mn(2+)). The alpha4 helix exposed at the catalytic core surface is essential to the specific recognition of viral DNA. To define group determinants of recognition, we used a model composed of a peptide analogue of the alpha4 helix, oligonucleotides mimicking processed and unprocessed U5 LTR end and 5 mM Mg(2+). Circular dichroism, fluorescence and NMR experiments confirmed the implication of the alpha4 helix polar/charged face in specific and non-specific bindings to LTR ends. The specific binding requires unprocessed LTR ends-i.e. an unaltered 3'-processing site CA downward arrowGT3'-and is reinforced by Mg(2+) (K(d) decreases from 2 to 0.8 nM). The latter likely interacts with the ApG and GpT3' steps of the 3'-processing site. With deletion of GT3', only persists non-specific binding (K(d) of 100 microM). Proton chemical shift deviations showed that specific binding need conserved amino acids in the alpha4 helix and conserved nucleotide bases and backbone groups at LTR ends. We suggest a conserved recognition mechanism based on both direct and indirect readout and which is subject to evolutionary pressure.