consisting of three discrete functional domains: the N terminal domain ; the catalytic core domain MG-341 , contains three absolutely conserved negatively charged amino acids which coordinate divalent metal ions ; and the C terminal Domain . Several lines of evidence suggest that the integration proceeds through a series of functionally IN–vDNA complexes. It is likely that binding of vDNA substrate impose the proper configuration of domains for the reaction to occur. Therefore, structure based understanding of the mechanism of HIV 1 IN–vDNA interactions is of great importance for realizing the process of vDNA integration and rational design of anti AIDS drugs.
Nevertheless, the elucidation of the structure of HIV 1 IN complexed with vDNA and the inhibition action of HIV 1 IN strand transfer inhibitor raltegravir on the HIV 1 IN–vDNA complex has been proved to be a great challenge, and the absence P-glycoprotein of reliable information on the crystal structure of the full length HIV 1 IN with vDNA substrates has been an important obstacle. Thus, starting from the availability of the experimental fragmental structures, the full length HIV 1 IN models assembled by molecular modeling techniques have been performed during the past years. These studies focus on the active site to try to elucidate the binding mode of INSTI constructed by relationship among retroviruses. These structures are very helpful to understand the binding mode of RAL to HIV 1 IN–vDNA complex and mechanism of HIV 1 IN resistance to RAL.
However, analysis of the detailed structural information of the interaction mechanism and conformational change of the HIV 1 IN and vDNA after RAL binding at the active site is still objectified lacking. Hence, a further study of the molecular interaction mechanism in HIV 1 IN–vDNA complex and the binding mode of RAL to the HIV 1 IN–vDNA complex are urgently needed. In this work, a full length 3D structure of HIV 1 IN was modeled using homology modeling based on the crystal structures of the PFV IN complexed with a short oligonucleotide substrate. Next, the vDNA, Mg2þ ions, and RAL were fitted into the binding site of HIV 1 IN by superposing the homology modeled HIV 1 IN to the Mg2þ ions bound crystal complexes of PFV IN using the Ca positions of the respective catalytic triads as guide.
Following this step, molecular dynamics simulation was performed to obtain the dynamic structural information of the complexes of HIV 1 IN with the vDNA and RAL by using the modeled structures as the initial structures. Based on the obtained molecular dynamics trajectory, molecular mechanics Poisson–Boltzmann surface area and molecular mechanics Generalized Born surface area calculations on the HIV 1 IN–vDNA and HIV 1 IN–vDNA–RAL complexes were carried out to identify the key contact residues of the HIV 1 IN binding to vDNA and the conformation changes of the HIV 1 IN amino acid residues and vDNA nucleotides at the active site with RAL free and RAL bound complexes. Furthermore, by analyzing the binding mode of RAL to the HIV 1 IN–vDNA complex and the constructed structure of HIV 1 IN post catalytic strand transfer complex , a possible INSTI binding and inhibition mechanism was also proposed. Methods Sequence alignment and homology modeling The amino acid sequence .