STRUCTURE OF THE COMPLEX BETWEEN THE HIV-1 NUCLEOCAPSID PROTEIN NCP7 AND THE SINGLE-STRANDED PENTANUCLEOTIDE D(ACGCC)

The nucleocapsid protein NCp7 of HIV-1 Mal contains two successive Zn knuckles of the CX2CX4HX4C type and plays a major role in virion morph ogenesis, genomic RNA packaging and viral infectivity, mainly through single-stranded nucleic acid binding. We report here the study by H-1 2D NMR of the complex formed between the (12-53)NCp7, encompassing the two Zn knuckles, and d(ACGCC), a deoxynucleotide sequence analog corr esponding to the shortest NCp7 binding site. Ten structures of the (12 -53)NCp7/d(ACGCC) complex have been obtained from 607 NOE-derived dist ance constraints, 28 of which are intermolecular, and from molecular d ynamics studies. The oligonucleotide is almost perpendicular to the se quence linking the two Zn knuckles. The Trp37 indole ring is inserted between the C2 and G3 bases and stacked on the latter. The complex is stabilized by hydrophobic interactions and hydrogen bonds, and account s for the observed loss of virus infectivity induced by mutations in t he Zn knuckle domain. Thus, the interaction between d(ACGCC) and the i nactive mutant Cys23 (12-53)NCp7 was found by NMR to be completely dif ferent from that observed with the wild-type peptide. A mechanism of a ction for NCp7 in virus morphogenesis and replication is proposed from these results, which could facilitate the design of possible antivira l agents acting by a new mechanism. (C) 1998 Academic Press.