Modelling of the conformational flexibility of human immunodeficiency virus type 1 reverse transcriptase

This study has developed several methods and computational tools to aid the objective comparison of protein conformation, and, through their application to RT, has addressed some of the earliest steps towards this goal. Difference distance matrices were used to study the relative geometry of apo and NNRTI bound RT crystal structures and characterise the regions of the enzyme that possess different degrees of conformational rigidity and flexibility. This technique has the advantage of not requiring superposition of the structures, so enabling an objective interpretation of the backbone movements induced by NNRTI binding to RT. It was observed that, while a significant portion of the enzyme was largely unaffected by complexation with the inhibitors, the thumb subdomain and small segments around the polymerase active site and inhibitor binding site underwent considerable conformational rearrangement. The determination of the structurally invariant regions of RT, by DDM analysis, was subsequently applied to the development of a protocol for the superposition of the RT crystal structures.