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Cotranslational Pulling Forces Alter Outcomes of Protein Synthesis


Zimmer, Matthew Holden (2022) Cotranslational Pulling Forces Alter Outcomes of Protein Synthesis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/p7vk-cf03.


As nascent proteins are synthesized by the ribosome, interactions between the nascent protein and its environment can create pulling forces that are transmitted to the ribosome's catalytic center. These forces can affect the rate and outcomes of translation. We use atomistic and coarse-grained simulation to characterize the origins of pulling forces, the propagation of force to catalytic center of the ribosome, and the effects of force on synthetic outcomes. We uncover a novel form of pulling force-mediated regulation in which the forces generated by the integration of a transmembrane helix induce frameshifting in a viral polyprotein. Computational force measurements of hundreds of mutant viral sequences in combination with deep mutational scanning experiments reveal the structural and sequence-level features that enable this powerful regulatory mechanism. Force measurements are also used to provide a molecular picture for complex pulling force experiments on multispanning membrane proteins. In particular, we identify signatures of cotranslational helix packing interactions and the translocation of surface helices. To understand how forces are propagated through the nascent protein in the ribosomal exit tunnel, we ran and analyzed hundreds of microseconds of atomistic molecular dynamics with an applied pulling force on the nascent protein. The simulations reveal how the secondary structure of nascent proteins and their interactions with the ribosome control force propagation. The inhibition of force transduction by nascent protein-ribosome interactions explains how amino acids tens of angstroms away from the catalytic center of the ribosome can still influence the force-induced restart of stalled ribosomes.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Frameshifting; Cotranslational;Membrane protein;Biophysics
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Biochemistry and Molecular Biophysics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Miller, Thomas F.
Thesis Committee:
  • Clemons, William M. (chair)
  • Voorhees, Rebecca M.
  • Wang, Zhen-Gang
  • Miller, Thomas F.
Defense Date:21 July 2021
Record Number:CaltechTHESIS:07232021-171251780
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Chapter 2 adapted for Chapter 3 adapted for Chapter 4 adapted for Chapter 5
Zimmer, Matthew Holden0000-0002-1437-2636
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14312
Deposited By: Matthew Zimmer
Deposited On:19 Aug 2021 21:15
Last Modified:26 Aug 2021 16:20

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