Investigations on human immunodeficiency virus type 1 integrase/DNA binding interactions via molecular dynamics and electrostatics calculations

The complete three-dimensional structure of the active site region of the h uman immunodeficiency virus type 1 (HIV-I) integrase (IN) is not unambiguou sly known. This region includes a flexible loop comprising residues 141-148 and the N-terminal portion of the helix alpha-4, which contains E152, the third catalytic residue, and Y143, which plays a secondary role in catalysi s. Relatively high B-factors exist for most of the residues in the aforemen tioned region. The HIV-1 IN belongs to the polynucleotidyl transferase supe rfamily, whose members have been proposed to use two divalent metal ions fo r catalysis. Although only the position of the first metal ion has been det ermined crystallographically for the HIV-1 IN, we recently have proposed a binding site for the second metal ion. Based on this information, we have p erformed two 500-psec molecular dynamics simulations of the catalytic domai n of the HIV-1 IN containing two Mg2+ ions, In one of the simulations, we i ncluded a dianionic phosphate group (HPO42-) in the active site to mimic a portion of the DNA backbone of a substrate for the integration reaction. El ectrostatics calculations and ionization state predictions were carried out on representative structures taken from the molecular dynamics simulations . Different conformational behaviors of the enzyme were observed, depending upon whether two Mg2+ ions were bound or two Mg2+ ions plus phosphate. The electrostatic calculations performed on the dynamical structures provide a further refinement about which regions of the catalytic domain of the HIV- 1 IN may be involved in the DNA binding. (C) 2000 Elsevier Science Inc. All rights reserved.