       Document 0663
 DOCN  M9640663
 TI    Inhibition and catalytic mechanism of HIV-1 aspartic protease.
 DT    9604
 AU    Silva AM; Cachau RE; Sham HL; Erickson JW; Structural Biochemistry
       Program, National Cancer Institute,; Frederick, MD 21702, USA.
 SO    J Mol Biol. 1996 Jan 19;255(2):321-46. Unique Identifier : AIDSLINE
       MED/96150306
 AB    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.
 DE    Binding Sites  Crystallography, X-Ray  Hydrogen Bonding  HIV
       Protease/*METABOLISM  HIV Protease Inhibitors/CHEMISTRY/*METABOLISM
       Methylurea Compounds/CHEMISTRY/*METABOLISM  Models, Molecular  Molecular
       Conformation  Oxidation-Reduction  Protein Conformation  Protons
       Pyridines/CHEMISTRY/*METABOLISM  JOURNAL ARTICLE

       SOURCE: National Library of Medicine.  NOTICE: This material may be
       protected by Copyright Law (Title 17, U.S.Code).

