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An essential step of the reverse transcription of the HIV-1 genome is the first strand transfer that requires the annealing of the TAR RNA hairpin to the cTAR DNA hairpin. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. Using nuclear magnetic resonance and gel retardation assays, we investigated the interaction between NC and the top half of the cTAR DNA (mini-cTAR). We show that NC(11-55) binds the TGG sequence in the lower stem that is destabilized by the adjacent internal loop. The 5' thymine interacts with residues of the N-terminal zinc knuckle and the 3' guanine is inserted in the hydrophobic plateau of the C-terminal zinc knuckle. The TGG sequence is preferred relative to the apical and internal loops containing unpaired guanines. Investigation of the DNA-protein contacts shows the major role of hydrophobic interactions involving nucleobases and deoxyribose sugars. A similar network of hydrophobic contacts is observed in the published NC:DNA complexes, whereas NC contacts ribose differently in NC:RNA complexes. We propose that the binding polarity of NC is related to these contacts that could be responsible for the preferential binding to single-stranded nucleic acids.
Pubmed ID: 21227929
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THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AANT, the Amino Acid-Nucleotide Interaction Database, contains information derived from all of the protein/nucleic acid complexes with experimentally determined structures in the Protein Data Bank. You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures. The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters.
View all literature mentionsSoftware for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images.
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