Analysis of the full-length integrase-DNA complex by a modified approach for DNA docking.
A model of the full-length HIV-1 integrase dimer was constructed assembling the experimentally determined structures of the single domains. Subsequently, the three-domain protein-viral DNA complex was generated for the first time through an automated docking algorithm, obtained modifying the ESCHER program, a well-known method for protein-protein docking. A detailed study of the contacts established with DNA by the enzyme revealed that the predicted model reproduced the results of mutagenesis and cross-linking experiments, confirming the validity of our docking approach in predicting the base specificity in the DNA-protein interaction.
De Luca
Laura
L
Dipartimento Farmaco-Chimico, Università di Messina,Viale Annunziata, I-98168 Messina, Italy.
Pedretti
Alessandro
A
Vistoli
Giulio
G
Barreca
Maria Letizia
ML
Villa
Luigi
L
Monforte
Pietro
P
Chimirri
Alba
A
D001483:Base Sequence; D017931:DNA Primers; D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism*; D019281:Dimerization; D019427:HIV Integrase / Q000378:metabolism*; D008958:Models, Molecular
D017931:DNA Primers; D004279:DNA, Viral; D019427:HIV Integrase