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Coarse grained molecular dynamics simulations of the coupling between the allosteric mechanism of the ClpY nanomachine and threading of a substrate protein

Kravats, Andrea N.
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384849649

Abstract Details

2013, PhD, University of Cincinnati, Arts and Sciences: Chemistry.
Protein quality control is critical in maintaining cell viability. Recognition and degradation of aberrant proteins in the cellular environment is essential, as many neurodegenerative diseases are linked to protein misfolding and aggregation. Powerful AAA+ ATPases, such as ClpY and p97, play a vital role in the degradation pathway of PQC. These nanomachines form hexameric macromolecular assemblies which selectively recognize and thread proteins tagged for degradation through their narrow central pore to be delivered to sequestered protease components for degradation. Flexible loops with a conserved G-hydrophobic-aromatic-G sequence reside within the central pore and undergo a large scale paddling motion resulting from ATP hydrolysis. The loops impart mechanical forces onto substrate proteins (SP) which results in unfolding and translocation. While the overall mechanism of these macromolecular machines is generally understood, molecular details of SP processing have not been established. The focus of this study is on the molecular details of SP processing by the single ring ClpY ATPase, which has been well characterized crystallographically in multiple nucleotide bound states. Here, I am presenting studies based on four aspects regarding this problem : (1) Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase, (2) Asymmetric processing of a substrate protein in sequential allosteric cycles of the ClpY nanomachine, (3) The dependence of SP topology on unfolding and translocation mechanisms by the ClpY nanomachine, and (4) Structure mediated unfolding and translocation pathways of SulA by pulling through non-allosteric AAA+ pores. I used coarse-grained Langevin dynamics simulations to probe the unfolding and translocation of a four-helix bundle model SP using the allosteric transitions of ClpY. My results indicate that unfolding occurs by unraveling from the SP's tagged C-terminus, resulting in a three helix bundle. This minimally unfolded, obligatory unfolding intermediate, is competent for translocation. Translocation occurs through sharp stepped transitions indicating a powerstroke mechanism. To further understand the coupling between intra-ring motions of ClpY and mechanical action applied to the SP, I performed additional simulations of clockwise, counterclockwise and random allosteric mechanisms. My results indicate that the SP unfolding and translocation mechanism is independent of the directional allosteric mechanism. The work provided by single SP-loop interactions allows the SP to sample identical conformational states; However, the rates and yields are affected, with clockwise allostery emerging as the most efficacious due to the favorable torque applied onto the SP. Next, I have probed the dependence of SP topology by examining ClpY processing of a SP with alpha/beta topology. Comparison with the all-alpha SP indicate a well preserved unfolding event by unraveling at the C-terminus and translocation via a powerstroke mechanism. The effective forces for unfolding and the kinetics depend on topology. Last, I have probed the unfolding and translocation of a natural SP of ClpY, SulA, by performing minimalistic simulations pulling through non-allosteric AAA+ pores. The results indicate that initial unfolding near the C-terminus is required for initiation of translocation. Interactions with the surface of the pore facilitate unfolding and translocation by decreasing the energy barriers.
George Stan, Ph.D. (Committee Chair)
Thomas Beck, Ph.D. (Committee Member)
Albert Bobst, Ph.D. (Committee Member)
178 p.
Physical Chemistry
ATPase; protein unfolding; protein translocation; coarse grained simulations

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Citations

  • Kravats, A. N. (2013). Coarse grained molecular dynamics simulations of the coupling between the allosteric mechanism of the ClpY nanomachine and threading of a substrate protein [Doctoral dissertation, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384849649

    APA Style (7th edition)

  • Kravats, Andrea. Coarse grained molecular dynamics simulations of the coupling between the allosteric mechanism of the ClpY nanomachine and threading of a substrate protein. 2013. University of Cincinnati, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384849649.

    MLA Style (8th edition)

  • Kravats, Andrea. "Coarse grained molecular dynamics simulations of the coupling between the allosteric mechanism of the ClpY nanomachine and threading of a substrate protein." Doctoral dissertation, University of Cincinnati, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384849649

    Chicago Manual of Style (17th edition)

ucin1384849649
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© 2013, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.