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| - Closing of the Flaps of HIV-1 Protease Induced by Substrate Binding: A Model ofa Flap Closing Mechanism in Retroviral Aspartic Proteases
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| - The active site of aspartic proteases is covered by one or more flaps, which control access tothe active site and play a significant role in the binding of the substrate. An extensive conformationalchange of the flaps takes place upon binding of substrate to the active site. A long molecular dynamicssimulation was performed on the complex consisting of a peptide (CA-p2) from a natural substrate cleavagesite of the gag/pol polyprotein placed in the active site of HIV-1 protease (PR) with an open flapconformation. During the simulation, the substrate induced the closing of the flaps into the closedconformation in an asymmetrical way through a hydrophobic intermediate state cluster. The nature of theresidues of HIV-1 PR identified to be important in the flap closing mechanism is conserved across knownstructures of retroviral aspartic proteases family. The flap closing mechanism described in HIV-1 PR isproposed to be a general model for flap closing in retroviral aspartic proteases.
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