Transition Paths In Folding Reactions

  • Author / Creator
    Hoffer, Noel
  •  Folding is the process by which biomolecules spontaneously self-assemble into specific, complex, three-dimensional structures from simple one-dimensional polypeptide chains. Folding is a critical process in biology as there exists a tight link between the structure and function of biomolecules, and misfolding into the wrong structure often leads to disease. Traditional studies of folding have used ensemble measurements to monitor how the statistics of the folded and unfolded states, respond to perturbations to the stability of the states. Ensemble studies have yielded important results and indeed, are the primary basis for our current understanding of folding reactions. However, due to the asynchronous nature of folding reactions, such studies are incapable of probing transition paths. 
     Transition paths comprise those parts of a folding trajectory where the molecule passes through the high-energy transition states separating the folded and unfolded states. The transition states determine the folding kinetics and mechanism but are difficult to observe because of their brief duration. Single-molecule experiments have in recent years, begun to characterize transition paths in folding reactions, allowing the microscopic conformational dynamics that occur as a molecule traverses the energy barriers, to be probed directly. 
     In this thesis, I present the first direct measurements of transition-path trajectories. I then show how, using single-molecule force spectroscopy, I have been able to make the first-ever measurements of several transition-path properties including: the local velocity along the paths, the path shapes, and the transition state dynamics inferred by them. I discuss how these measurements have been related to theories of folding as diffusion over an energy landscape, to deduce properties such as the diffusion coefficient, and how they further our understanding of folding. The richly detailed information available from transition path measurements holds great promise for an improved understanding of microscopic mechanisms in folding.

  • Subjects / Keywords
  • Graduation date
    Fall 2021
  • Type of Item
  • Degree
    Doctor of Philosophy
  • DOI
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.