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Elucidating Allosteric Mechanisms of the AAA+ ClpATPases Using Molecular Dynamics Simulations

Wang, Huan, Ph.D.
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439296238

Abstract Details

2015, PhD, University of Cincinnati, Arts and Sciences: Chemistry.
AAA+ unfolding chaperones play vital function in cells as to maintain its proteasome balance. Misfolded or aggregated proteins could be unfolded and degraded by AAA+ unfolding chaperones through its ATP dependent activities. Structurally AAA+ unfolding chaperones form a oligomeric ring structure and normally binds with a peptidase partner. N or C terminal tagged SP could be recognized by these chaperones and bind to their central pores. During cycles of ATP dependent conformational changes, these unfoldases could remodel SP through large scale paddling motions of flexible loops, with a conserved G-hydrophobic-aromatic-G sequence, and translocate it to peptidase partner for degradation. Provided with abundant information on the general mechanism of how AAA+ unfolding chaperones work, there still remains many questions answered. In this thesis, I am presenting studies based on four aspects regarding this problem: (1) unfolding and translocation of peptides with versatile secondary structures by ClpY using atomistic model (2) Asymmetric processing of peptides in sequential intra-ring allosteric mechanism of ClpY (3) structural analysis of ClpY underlying asymmetric substrate handling (4) repetitive forces assisted unfolding and translocation of model SPs by ClpY. For this purpose, multiple methods including coarse grained simulations, normal mode analysis and implicit solvent model are used in the thesis. Highly cooperative translocation and unfolding have been observed due to preservation of secondary structures in the remodelling process. A maximum number of 4 coordinated subunits is observed in the simulations, in agreement with single molecular experiments. Comparisons of unfolding and translocation timescale of a beta hairpin and helix reveal different unfolding mechanism of secondary structures. Subsequent translocations of unfolded fusion peptides show stochastic stepsize of translocation by coordinated loop motions. I am able to show that central pore loops' TBR mechanism through interplay of van der Waals and electrostatic interactions is responsible for the effective translocation of SP. In a clockwise-sequential intra-ring allostery, the effective torque that central pore loops apply to SPs distributes at more positive value compared to a counter clockwise sequential allostery, indicating a more efficient SP handling. Detailed analysis on interaction between active central loops to peptides shows stronger correlations between successive subunit motions in clockwise fashion allostery, which demonstrates clockwise allostery is more successful in passing SP to next active subunit. The architecture of ClpY ring limits its possible modes of operation. Functional modes are uncovered for ClpY monomer, hexamer and mutant structure, designating important features of intra-subunit and inter-subunit coupling during allosteric motions of ClpY. Repetitive forces unfold and translocate model SPs in similar mechanism as in allosteric simulations. However, I domain's allosteric effect is shown be essential for various SPs to reach extended conformations which manifest I domain's role as assisting unfolding and translocation. For small proteins with strong resistance to mechanical forces, pore loops' 'breathing' motions are shown to rule out the unphysical pathways.
George Stan, Ph.D. (Committee Chair)
Thomas Beck, Ph.D. (Committee Member)
Patrick Limbach, Ph.D. (Committee Member)
131 p.
Physical Chemistry
protein quality control; AAA unfolding chaperone; protein folding; molecular dynamics

Recommended Citations

Citations

  • Wang, H. (2015). Elucidating Allosteric Mechanisms of the AAA+ ClpATPases Using Molecular Dynamics Simulations [Doctoral dissertation, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439296238

    APA Style (7th edition)

  • Wang, Huan. Elucidating Allosteric Mechanisms of the AAA+ ClpATPases Using Molecular Dynamics Simulations. 2015. University of Cincinnati, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439296238.

    MLA Style (8th edition)

  • Wang, Huan. "Elucidating Allosteric Mechanisms of the AAA+ ClpATPases Using Molecular Dynamics Simulations." Doctoral dissertation, University of Cincinnati, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1439296238

    Chicago Manual of Style (17th edition)

ucin1439296238
392
© 2015, some rights reserved.Creative Commons License Elucidating Allosteric Mechanisms of the AAA+ ClpATPases Using Molecular Dynamics Simulations by Huan Wang Ph.D. is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by University of Cincinnati and OhioLINK.