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Domain flexibility in retroviral proteases: structural implications for drug resistant mutations
R B Rose1, C S Craik, R M Stroud
1Department of Biochemistry and Biophysics, University of California in San Francisco, San Francisco, California 94143-0448, USA.
Biochemistry
|March 28, 1998
Summary
Mutations in HIV protease drug resistance arise from domain movements, not just binding site changes. These rigid body rotations at interfaces explain how resistance develops, impacting inhibitor efficacy.
Area of Science:
- Biochemistry
- Structural Biology
- Virology
Background:
- HIV-1 and SIV proteases are critical targets for antiretroviral therapy.
- Drug resistance in HIV often involves mutations distant from the active site, the mechanism of which is not fully understood.
Purpose of the Study:
- To investigate the structural basis of domain movements in HIV and SIV proteases during substrate binding.
- To elucidate the role of these domain motions in the development of drug resistance.
Main Methods:
- X-ray crystallography of unliganded SIV protease at 2.0 A resolution.
- Comparison of unliganded and liganded protease structures using difference distance matrixes.
- Identification and characterization of rigid body domain movements.
Main Results:
- Identified five distinct domains (terminal, core, flap) in the protease dimer that move as rigid bodies.
- Observed ~6-7 degree rotations at hydrophobic interfaces, in addition to flap closure, upon substrate binding.
- The SIV protease structure revealed an exceptionally open conformation.
Conclusions:
- Rigid body domain rotations at interdomain interfaces are a key feature of protease function.
- Mutations at these interfaces can favor the unliganded state, increasing inhibitor off-rate and conferring resistance.
- This provides a mechanism for resistance to competitive inhibitors, particularly when enzyme catalysis is rapid.