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Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

ABSTRACT: We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the "flap" structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied. These analogue enzymes were further studied by X-ray crystallography, NMR relaxation, and pulse-EPR methods, in conjunction with molecular dynamics simulations. We show that conformational isomerization in the flaps is correlated with structural reorganization of residues in the active site, and that it is preorganization of the active site that is a rate-limiting factor in catalysis.

SUBMITTER: Torbeev VY

PROVIDER: S-EPMC3248522 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

Torbeev Vladimir Yu VY Raghuraman H H Hamelberg Donald D Tonelli Marco M Westler William M WM Perozo Eduardo E Kent Stephen B H SB

Proceedings of the National Academy of Sciences of the United States of America 20111208 52

We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the "flap" structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied. These analogue enzymes were further stud ...[more]

PMID: 22158985

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