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Hidden Dimensions in Protein Evolution: Stability, Mutational Robustness, and Evolvability


Bloom, Jesse D. (2007) Hidden Dimensions in Protein Evolution: Stability, Mutational Robustness, and Evolvability. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3MNT-7W93.


Proteins are evolvable in the sense that they are readily able to acquire new or improved functions through the process of mutation and selection. Here, I examine what properties influence the ability of proteins to evolve new functions. I show that proteins with similar biochemical properties can differ substantially in their capacities to withstand mutations and evolve new functions. Specifically, more stable proteins are both more mutationally robust and more evolvable, due to improved tolerance for mutations. This fact can be exploited in protein engineering. I then show how evolutionary theory can be modified to describe how a protein's mutational robustness changes during the normal course of neutral genetic drift. One of the main theoretical predictions is that proteins evolving in larger populations will gain excess stability and mutational robustness, a prediction which I confirm experimentally. Finally, I turn to the question of how neutral genetic drift can alter "promiscuous" protein functions that are not under selection. I show that promiscuous functions can change significantly during genetic drift, a phenomenon that may aid in the evolution of beneficial new functions. Overall, this work establishes two mechanisms whereby initially neutral mutations can influence the course of future evolution.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:directed evolution; evolvability; protein evolution
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Awards:Demetriades-Tsafka-Kokkalis Prize in Bioengineering or Related Fields, 2007.
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Arnold, Frances Hamilton
Thesis Committee:
  • Mayo, Stephen L. (chair)
  • Adami, Christoph Carl
  • Rees, Douglas C.
  • Arnold, Frances Hamilton
  • Sternberg, Paul W.
Defense Date:17 May 2007
Non-Caltech Author Email:jesse.bloom (AT)
Record Number:CaltechETD:etd-05232007-094635
Persistent URL:
Bloom, Jesse D.0000-0003-1267-3408
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1984
Deposited By: Imported from ETD-db
Deposited On:29 May 2007
Last Modified:08 Nov 2023 00:11

Thesis Files

PDF (bloom_thesis.pdf) - Final Version
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