title: Analysis of the full-length integrase-DNA complex by a modified approach for DNA docking.
abstract: 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.
authors.affiliation: Dipartimento Farmaco-Chimico, Università di Messina,Viale Annunziata, I-98168 Messina, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: De Luca
authors.forename: Alessandro
authors.initials: A
authors.lastname: Pedretti
authors.forename: Giulio
authors.initials: G
authors.lastname: Vistoli
authors.forename: Maria Letizia
authors.initials: ML
authors.lastname: Barreca
authors.forename: Luigi
authors.initials: L
authors.lastname: Villa
authors.forename: Pietro
authors.initials: P
authors.lastname: Monforte
authors.forename: Alba
authors.initials: A
authors.lastname: Chimirri
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism*; D019281:Dimerization; D019427:HIV Integrase / Q000378:metabolism*; D008958:Models, Molecular
chemical_list: D017931:DNA Primers; D004279:DNA, Viral; D019427:HIV Integrase