Time-resolved fluorescence investigation of the human immunodeficiency virus type 1 nucleocapsid protein:: Influence of the binding of nucleic acids

Depending on the HIV-1 isolate, MN or BH10, the nucleocapsid protein, NCp7, corresponds to a 55- or 71-amino acid length product, respectively. The MN NCp7 contains a single Trp residue at position 37 in the distal zinc finger motif, and the BH10 NCp7 contains an additional Trp, at position 61 in the C-terminal chain. The time-resolved intensity decay parameters of the zinc-saturated BH10 NCp7 were determined and compared to those of single-Trp-containing derivatives. The fluorescence decay of BH10 NCp7 could be clearly represented as a linear combination (with respect to both lifetimes and fractional intensities) of the individual emitting Trp residues. This suggested the absence of interactions between the two Trp residues, a feature that was confirmed by molecular modeling and fluorescence energy transfer studies. In the presence of tRNA(Phe), taken as a RNA model, the same conclusions hold true despite the large fluorescence decrease induced by the binding of tRNA(Phe). Indeed, the fluorescence of Trp(37) appears almost fully quenched, in keeping with a stacking of this residue with the bases of tRNA(Phe). Despite the multiple binding sites in tRNA(Phe), the large prevalence of ultrashort lifetimes, associated with the stacking of Trp(37), suggests that this stacking constitutes a major feature in the binding process of NCp7 to nucleic acids. In contrast, Trp(61) only stacked to a small extent with tRNAPhe. Th, behavior of this residue in the tRNA(Phe)-NCp7 complexes appeared to be rather heterogeneous, suggesting that it does not constitute a major determinant in the binding process. Finally, our data suggested that the binding of NCp7 proteins from the two HIV-1 strains to nonspecific nucleic acid sequences was largely similar.