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Expanding the Scope of Metalloprotein Families and Substrate Classes in New-to-Nature Reactions


Knight, Anders Matthew (2021) Expanding the Scope of Metalloprotein Families and Substrate Classes in New-to-Nature Reactions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/7qh5-5130.


Heme proteins, in particular cytochromes P450, have been extensively used in biocatalytic applications due to their high degree of regio-, chemo-, and stereoselectivity in oxene-transfer reactions. In 2013, it was shown for the first time that engineered heme proteins can also catalyze analogous carbene- and nitrene-transfer reactions. Research in this field has since grown dramatically, with emphasis on developing new heme protein variants to increase the scope of biotransformations accessible through these new transfer reactions. This thesis details the expansion of these new-to-nature carbene and nitrene-transfer reactions to include new substrate classes previously unexplored with iron-porphyrin proteins, the use of non-heme metalloproteins for these transformations, and steps toward improving the robustness of the new-to-nature biocatalytic platform. Chapter 1 introduces the steps the field of biocatalysis has taken toward engineering enzymes with new catalytic functions and the process by which these activities are discovered and enhanced. Chapter 2 details the discovery and engineering of heme proteins which catalyze the stereodivergent cyclopropanation of unactivated and electron-deficient alkenes via carbene transfer, expanding the substrate classes beyond styrenyl alkenes. Chapter 3 shows the development of engineered variants of a heme protein (Rhodothermus marinus nitric oxide dioxygenase) for the diastereodivergent synthesis of cyclopropanes functionalized with a pinacolborane moiety, enabling product diversification through standard cross-coupling reactions. In Chapter 4, a collection of non-heme metalloproteins is curated, and a non-heme iron enzyme (Pseudomonas savastanoi ethylene-forming enzyme) is shown to be both amenable to directed evolution and non-native ligand substitution to enhance its nitrene-transfer activity. Chapter 5 describes the expansion of sequence space targeted for screening in the serine-ligated cytochrome P411 from Bacillus megaterium (P411BM3) biocatalytic platform to enhance the mutational robustness of these remarkable enzymes. Overall, this work provides a framework for bringing model new-to-nature reactions to their full potential in synthetic biocatalytic reactions.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Biocatalysis, carbene transfer, nitrene transfer, cyclopropanation, directed evolution, protein engineering
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Arnold, Frances Hamilton
Thesis Committee:
  • Shapiro, Mikhail G. (chair)
  • Arnold, Frances Hamilton
  • Clemons, William M.
  • Reisman, Sarah E.
  • Bois, Justin S.
Defense Date:9 June 2020
Non-Caltech Author Email:andersknight (AT)
Funding AgencyGrant Number
NSF Graduate Research Fellowship ProgramDGE-1144469
Record Number:CaltechTHESIS:06212020-111155395
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Chapter 1. adapted for Chapter 2. adapted for Chapter 3. adapted for Chapter 4. Sequence information for constructs used in this work
Knight, Anders Matthew0000-0001-9665-8197
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:13824
Deposited By: Anders Knight
Deposited On:09 Jul 2020 17:18
Last Modified:08 Nov 2023 00:11

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