How the HIV-1 Nucleocapsid Protein Binds and Destabilises the (−)Primer Binding Site During Reverse Transcription

• Published in: Journal of molecular biology Vol. 383; no. 5; pp. 1112 - 1128
• Main Authors: Bourbigot, Sarah, Ramalanjaona, Nick, Boudier, Christian, Salgado, Gilmar F.J., Roques, Bernard P., Mély, Yves, Bouaziz, Serge, Morellet, Nelly
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 28.11.2008; Elsevier
• Subjects: 4-(4′-dimethylaminophenylazo)benzoic acid; 6-carboxyrhodamine; Amino Acid Sequence; Base Sequence; Binding Sites; DABCYL; Dimerization; DNA Primers - chemistry; DNA Primers - genetics; DNA Primers - metabolism; exchange; exchange spectroscopy; EXSY; FCS; fluorescence correlation spectroscopy; gag Gene Products, Human Immunodeficiency Virus - chemistry; gag Gene Products, Human Immunodeficiency Virus - metabolism; HIV-1; HIV-1 - chemistry; Human immunodeficiency virus 1; human immunodeficiency virus type 1; human immunodeficiency virus type 1 (HIV-1); isothermal titration calorimetry; ITC; Magnetic Resonance Spectroscopy; Molecular Sequence Data; NOE; NOESY; nuclear magnetic resonance (NMR); nuclear Overhauser enhancement; nuclear Overhauser enhancement spectroscopy; Nucleic Acid Conformation; nucleocapsid protein (NCp7); Nucleocapsid Proteins - chemistry; Nucleocapsid Proteins - metabolism; PBS; primer binding site (PBS); primer-binding site; Protein Binding; Protein Structure, Secondary; Reverse Transcription; Rh6G; RNA, Transfer - metabolism; ROESY; rotating frame Overhauser effect spectroscopy; Sequence Deletion; Spectrometry, Fluorescence; stem–loop; Titrimetry; TOCSY; total correlated spectroscopy; HIV-1; PBS; Rh6G; NOE; ROESY; human immunodeficiency virus type 1 (HIV-1); TOCSY; DABCYL; primer binding site (PBS); nuclear magnetic resonance (NMR); FCS; ITC; SL; EXSY; nucleocapsid protein (NCp7); NOESY; exchange
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2008.08.046

The human immunodeficiency virus type 1 nucleocapsid protein (NCp7) plays an important role in the second strand transfer during reverse transcription. It promotes annealing of the 18-nucleotide complementary DNA primer-binding site (PBS) sequences at the 3′ ends of (−)DNA and (+)DNA. NMR studies show that NCp7(12–55) and NCp7(1–55) interact at the 5′ end of the loop of ΔP(−)PBS, a (−)PBS derivative without the 3′ protruding sequence, in a slow-exchange equilibrium. This interaction is mediated through the binding of the hydrophobic plateau (Val13, Phe16, Thr24, Ala25, Trp37, and Met46) on the zinc finger domain of both peptides to the 5-CTG-7 sequence of ΔP(−)PBS. The stacking of the Trp37 aromatic ring with the G7 residue likely constitutes the determinant factor of the interaction. Although NCp7(12–55) does not melt the ΔP(−)PBS stem–loop structure, it opens the loop and weakens the C5·G11 base pair next to the loop. Moreover, NCp7(12–55) was also found to bind but with lower affinity to the 10-CGG-12 sequence in an intermediate-exchange equilibrium on the NMR time scale. The loop modifications may favour a kissing interaction with the complementary (+)PBS loop. Moreover, the weakening of the upper base pair of the stem likely promotes the melting of the stem that is required to convert the kissing complex into the final (±)PBS extended duplex.