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Computer Simulations of Titin I27 and Knotted Protein Remodeling by Clp Biological Nanomachines

Javidialesaadi, Abdolreza
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1523628577990709

Abstract Details

2018, PhD, University of Cincinnati, Arts and Sciences: Chemistry.
Cellular protein quality control comprises a network of chaperones that maintain the proteome viability by performing key cellular tasks such as degrading or remodeling misfolded proteins. Bacterial Caseinolytic proteases (Clp) which are responsible for protein degradation include powerful ring-shaped AAA+ (ATPases Associated with diverse cellular Activities) motors with a central narrow pore that unfold and translocate tagged abnormal proteins. Clp ATPase machines thread substrate proteins (SPs) through their central channel by using repetitive ATP-driven subunit motions coupled with axial mechanical forces exerted onto the SP. The molecular details of unfolding and translocation of SPs by these biomolecules are not fully yet understood. Here I present three studies regarding this issue: (1) I perform Langevin dynamics simulations using a coarse-grained model of SPs, Titin I27 and its V13P variant, threading through the ClpY pore. I probe the effect of ClpY surface heterogeneity and changes in pore width on the SP orientation and the direction of applied force during SP unfolding. I contrast mechanisms of SP unfolding in a restrained geometry, as in single-molecule force spectroscopy experiments, and in an unrestrained geometry, as in the in vivo degradation process. In open pore configurations, unfolding of the unrestrained SPs occurs via an unzipping mechanism which involves force application along a weak mechanical direction. In the partially closed pore, unfolding occurs via a shearing mechanism with force application in a strong mechanical direction. By contrast, unfolding of the restrained I27 is limited to a shearing mechanism due to application of force along the strong mechanical direction. I propose that Clp nanomachine plasticity underlies direction-dependent pulling mechanisms that enable versatile SP remodeling actions. (2) I use an implicit solvent model of ClpY and different I27 tandem constructs as SPs and perform Langevin dynamics simulations of cyclical opening and closing of ClpY to mimic the single molecule experiments, in which the N-terminal of I27 and (I27)_4 are restrained and compare and contrast it with in vivo ClpY action setups in which unrestrained I27, (I27)2 and (I27)4 are used as substrates. I find that ClpY unfolds and translocates unrestrained single domain I27 with higher efficiency compared with other cases. Restraining the N-terminal of SP or the presence of external domains significantly reduces the unfolding yield by restraining the orientation of SP. I propose that Clp ATPase biological nanomachines utilize direction depend pulling mechanisms to unfold their substrates. (3) I perform further simulations of unfolding and translocation of knotted proteins through the central pore of ClpY by using an implicit solvent model of ClpY and three knotted proteins with 3_1, 5_2 and 6_1 knot types. I find that unfolding and translocation process results in knot displacement toward the N-terminal and knot tightening caused by non-native contacts hinders the translocation process.
George Stan, Ph.D. (Committee Chair)
Thomas Beck, Ph.D. (Committee Member)
Laura Sagle, Ph.D. (Committee Member)
111 p.
Physical Chemistry
Clp ATPase; Protein Quality Control; Protein Unfolding; Molecular Simulation; Titin I27; Knotted Protein

Recommended Citations

Citations

  • Javidialesaadi, A. (2018). Computer Simulations of Titin I27 and Knotted Protein Remodeling by Clp Biological Nanomachines [Doctoral dissertation, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1523628577990709

    APA Style (7th edition)

  • Javidialesaadi, Abdolreza. Computer Simulations of Titin I27 and Knotted Protein Remodeling by Clp Biological Nanomachines. 2018. University of Cincinnati, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1523628577990709.

    MLA Style (8th edition)

  • Javidialesaadi, Abdolreza. "Computer Simulations of Titin I27 and Knotted Protein Remodeling by Clp Biological Nanomachines." Doctoral dissertation, University of Cincinnati, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1523628577990709

    Chicago Manual of Style (17th edition)

ucin1523628577990709
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This open access ETD is published by University of Cincinnati and OhioLINK.