AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA.
To understand the binding of both viral and human DNA to HIV-1 integrase, fully flexible dinucleotides were docked onto the core domain of integrase. AutoDocking did identify sites on integrase where favorable interactions with nucleotides can occur, and those sites were in agreement with recently published protein fingerprinting data. By analyzing the phosphates of the docked dinucleotides, we developed a model indicating where the viral cDNA and human DNA bind to the integrase core domain.
Perryman
Alexander L
AL
Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365, USA. aperryma@mccammon.ucsd.edu
McCammon
J Andrew
JA
D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004279:DNA, Viral / Q000737:chemistry; D019427:HIV Integrase / Q000737:chemistry*; D015497:HIV-1; D006801:Humans; D008958:Models, Molecular; D009711:Nucleotides / Q000737:chemistry*; D017434:Protein Structure, Tertiary
D004279:DNA, Viral; D009711:Nucleotides; D004247:DNA; D019427:HIV Integrase