REACTION-PATH AND FREE-ENERGY CALCULATIONS OF THE TRANSITION BETWEEN ALTERNATE CONFORMATIONS OF HIV-1 PROTEASE

Two different structures of ligand-free HIV protease have been determi ned by X-ray crystallography. These structures differ in the position of two 12 residue, beta-hairpin regions (or ''flaps'') which cap the a ctive site, The movements of the flaps must be involved in the binding of substrates since, in either conformation, the flaps block the bind ing site. One of these structures is similar to structures of the liga nd-bound enzyme; however, the importance of both structures to enzyme function is unclear, This transformation takes place on a time scale t oo long for conventional molecular dynamics simulations, so the proces s was studied by first identifying a reaction path between the two str uctures and then calculating the free energy along this path using umb rella sampling, For the ligand-free enzyme, it is found that the two s tructures are nearly equally stable, with the ligand-bound-type struct ure being less stable, consistent with X-ray crystallography data, The more stable open structure does not have a lower potential energy, bu t is stabilized by entropy, The transition occurs through a collapse a nd reformation of the beta-sheet structure of the conformationally fle xible, glycine-rich flap ends. Additionally, some problems in studying conformational changes in proteins through the use of a single reacti on path are addressed, Proteins 32:7-16, 1998, (C) 1998 Wiley-Liss, In c.