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Finally, as the presence of the different inhibitors and the residues involved in their binding produce marked changes in the 1DLO crystal packing of the enzyme, it is worth re-examining the differences between the crystal structures using our flexible model. The binding of NVP and EFV to the polymerase domain of HIV-1 RT is known to affect the conformation of the RNaseH primer grip binding site, which is observed in a closed conformation in the apo structure (Figure 9). The residues of this ligand binding site which are important in the three crystal structures analysed are shown in Figure 9. Binding of NVP or EFV causes minor rearrangements in the RNaseH primer grip binding site in each crystal structure, but the nature of the rearrangement and the extent of the movement required to induce these rearrangements are very different. Analysis of the differences in flexibility between the polymerase domain of the apo and the NVP and EFV bound structures shows that the extent of the movement required to induce these rearrangements in the apo structures is greater than that observed in the inhibitor bound structures. In both inhibitor bound structures the dominant rearrangement observed is a flip of the p51 palm domain of the p66 subunit. However in the case of the apo structure, the movement of the RNaseH primer grip induced by this rearrangement is much greater. In the apo structure, the p51 palm domain moves approximately 8 Å away from the p66 thumb domain, whereas in the NVP bound and EFV bound structures the movement of this domain is only 5 Å in NVP and 4 Å in EFV respectively. The movement of p51 in the apo structure is on the same scale as the movement required in the NNRTI bound structures to accommodate the NNRTI and the movement of the RNaseH primer grip is in the same range as that needed to accommodate the template/primer in the clefts of the RNaseH active site. We thus show that the differences in flexibility observed between the crystal structures are a function of the particular crystal packing of the enzyme rather than the particular inhibitor bound.

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