1dif
From Proteopedia
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HIV-1 PROTEASE IN COMPLEX WITH A DIFLUOROKETONE CONTAINING INHIBITOR A79285
Overview
The structure of the HIV-1 protease in complex with a pseudo-C2 symmetric, inhibitor, which contains a central difluoroketone motif, has been, determined with X-ray diffraction data extending to 1.7 A resolution. The, electron density map clearly indicates that the inhibitor is bound in a, symmetric fashion as the hydrated, or gemdiol, form of the difluoroketone., Refinement of the complex reveals a unique, and almost symmetric, set of, interactions between the geminal hydroxyl groups, the geminal fluorine, atoms, and the active-site aspartate residues. Several hydrogen bonding, patterns are consistent with that conformation. The lowest energy hydrogen, disposition, as determined by semiempirical energy calculations, shows, only one active site aspartate protonated. A comparison between the, corresponding dihedral angles of the difluorodiol core and those of a, hydrated peptide bond analog, calculated ab-initio, shows that the, inhibitor core is a mimic of a hydrated peptide bond in a gauche, conformation. The feasibility of an anti-gauche transition for a peptide, bond after hydration is verified by extensive molecular dynamics, simulations. The simulations suggest that rotation about the C-N scissile, bond would readily occur after hydration and would be driven by the, optimization of the interactions of peptide side-chains with the enzyme., These results, together with the characterization of a transition state, leading to bond breakage via a concerted exchange of two protons, suggest, a proteolysis mechanism whereby only one active site aspartate is, initially protonated. The steps of this mechanism are: asymmetric binding, of the substrate; hydration of the peptidic carbonyl by an active site, water; proton translocation between the active site aspartate residues, simultaneously with carbonyl hydration; optimization of the binding of the, entire substrate facilitated by the flexible structure of the hydrated, peptide bond, which, in turn, forces the hydrated peptide bond to assume a, gauche conformation; simultaneous proton exchange whereby one hydroxyl, donates a proton to the charged aspartate, and, at the same time, the, nitrogen lone pair accepts a proton from the other aspartate; and, bond, breakage and regeneration of the initial protonation state of the, aspartate residues.
About this Structure
1DIF is a Single protein structure of sequence from Human immunodeficiency virus 1 with and as ligands. Full crystallographic information is available from OCA.
Reference
Inhibition and catalytic mechanism of HIV-1 aspartic protease., Silva AM, Cachau RE, Sham HL, Erickson JW, J Mol Biol. 1996 Jan 19;255(2):321-46. PMID:8551523
Page seeded by OCA on Fri Feb 15 15:40:03 2008
