to the binding free Tacrolimus energy shown in Figure 6 indirectly indicated that when RAL was fitted into the binding pocket. There was a conformation change of the nucleotide at the active site, which suggested that RAL can prevent the integration progress of vDNA to hDNA rather than inhibit the vDNA binding to HIV 1 IN. Furthermore, the ligand interactions tool in MOE program was used to show the interactions of the protein residues with the base of vDNA in HIV 1 IN–vDNA complex . Obviously it provides the direct evidence that the T3, G4, C5, G15, C16, and A17 bases of the vDNA end in contact with the HIV 1 IN amino acid residues at the binding interface. These results are consistent well with the experimental results and theoretical models.
The structures of HIV 1 IN in the complex of vDNA obtained DPP-4 in our work are very similar to the constructed model reported in the Refs. In our model, residues within each domain of the HIV 1 IN as well as their linker regions contact the vDNA are shown in Figure 5. In addition, the hydrogen bond analysis presents the key H bonds between the protein residues and the non transferred strand residues at the key contact sites . The free energy decompositions indicated that the residues with positive charges, such as Arg and Lys, can favor the affinity ability of HIV 1 IN and vDNA interface; while the residues with negative charges, such as Asp and Glu, behave in the opposite way . Hydrogen bond analysis. To examine the hydrogen bond required for the HIV 1 IN and vDNA recognition, the hydrogen bond interactions were reported when the occupancy was more than 30% by calculating the percentage of time during simulation that the hydrogen bonds existed.
The obtained data of hydrogen bond occupancy are shown in Supporting Information Table S1 for the HIV 1 IN–vDNA and HIV 1 IN– vDNA–RAL complexes. Stable hydrogen bonds were found at the interface of the HIV 1 IN and vDNA complexes. In particular, the residues Ser147 and Arg263 in HIV 1 IN established hydrogen bond contacts anthropology with nucleotides T3 and G4 of the transferred strand that spends much occupancy times of more than 80% in simulation at CCD and NTD domains, respectively. It also spends more than 36% of its time in the formation of the hydrogen bond between the Ser153 residue and C5 base at the CCD domain.
Moreover, some other hydrogen bonds between the domains of HIV 1 IN and the base of the vDNA have also been identified during the simulation. These consensus interactions Electrostatic interaction analysis. Figure 7 shows the calculated electrostatic surface of the protein residues and vDNA in the binding conformation extracted from MD complexes. Here, we also evaluated the coulombic energy in our model. These results suggested that the electrostatic contribution to the binding was independent from the nature of interacting vDNA. In fact, the interaction between the positively charged core of the protein and the vDNA involved phosphate groups of nucleic acids. The inhibition mechanism of RAL Results of binding free energy calculation. Table 2 summarizes the binding free energies calculated with the MM PBSA and MM GBSA approaches for the RAL binding to HIV 1 IN–vDNA. In the same manner, we did not calculate the entropy contribution and the binding energy .