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- W2222413817 startingPage "e1004675" @default.
- W2222413817 abstract "Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP) through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation." @default.
- W2222413817 created "2016-06-24" @default.
- W2222413817 creator A5036826591 @default.
- W2222413817 creator A5039580290 @default.
- W2222413817 creator A5057942364 @default.
- W2222413817 date "2016-01-06" @default.
- W2222413817 modified "2023-10-03" @default.
- W2222413817 title "Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines" @default.
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- W2222413817 doi "https://doi.org/10.1371/journal.pcbi.1004675" @default.
- W2222413817 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4703411" @default.
- W2222413817 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/26734937" @default.
- W2222413817 hasPublicationYear "2016" @default.
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