(3cf) Proteins Repurposed: Augmenting Biocatalyst and Biomaterial Function with Noncanonical Amino Acids

The genetic code has been deciphered, and researchers are now developing genetic methods to outfit proteins, nature’s flagship polymers, with an expanded set of noncanonical amino acids (NCAAs). Despite these advances, the unique mapping of a given amino acid sequence to a specific protein function – the “protein code” – remains mysterious. Poor understanding of the protein sequence-to-function relationship limits our ability to rationally design new proteins with predictable characteristics. What if we could use designer NCAAs to bypass this limitation, and decide for ourselves what a given amino acid sequence should do? My research program will undertake a new approach to biocatalyst and biomaterials design that uses genetically encoded chemofunctional NCAAs to predictably augment and transform proteins for specific, user-defined applications.

Chemofunctional NCAAs integrate design features drawn from small molecule chemocatalysts into their reactive side chains, enabling them to catalyze chemical reactions independent of (but ultimately enhanced by) their sequence background. These cofactor-like amino acids map an input sequence to a specific functional output by biasing the sequence towards certain reactivity modes. Installation of a genetically encoded chemofunctional NCAA effectively generates a new reactivity “hotspot” on the protein sequence landscape that can then be explored by directed evolution (see figure). I intend to evaluate this protein design paradigm in several ways, including: (1) repurposing extant sulfur group transfer enzymes, (2) expanding the types of genetically encodable chemofunctional NCAAs through aminoacyl-tRNA synthetase engineering to enable diverse modes of enzyme augmentation and (3) harnessing NCAAs to build photoresponsive protein networks.

Teaching Interests

I have been shaped as a student and teacher by years of rich scientific dialogue; because of this, I am a dedicated educator with a track-record of obtaining strong classroom results. As an undergraduate and graduate student, I have been a teaching assistant in six chemical engineering classes. When I teach, I aim to create a lively learning environment that breaks outs of the traditional performance-based lecture format. Active learning strategies that I find useful in my teaching include Pair-And-Share, Live Classroom Polling (“clicker questions”), 1-Minute Papers, Group Brainstorming, and Flipped Classroom. As evidence of my strong communication skills, I delivered one of the 2015 Caltech Everhart Lectures.

I would consider it a privilege to teach any aspect of the standard chemical engineering, especially Thermodynamics, Transport Phenomena, and Polymer Chemistry/Physics. As a possible addition to standard departmental offerings, with my unique training in chemistry and chemical engineering I am interested in developing an interdisciplinary course for upper-level students that bridges a knowledge gap between these two disciplines. Principles of Industrial Catalysis would provide a comprehensive overview of the major catalytic industrial processes used today, including their reaction mechanisms and the process design considerations necessary for their scale-up. After completing the class, students would be able to (1) describe these processes in depth and (2) evaluate what new catalysts could offer meaningful improvements. I have prepared a sample syllabus for this class, and can provide it upon request.

Qualifications

I have comprehensive research training in two key areas relevant to the implementation of my proposed research program. During graduate work with David A. Tirrell (Caltech ChemE), I engineered proteins with structural NCAAs to elucidate the mechanisms of polymer transport in reversible macromolecular networks. During postdoctoral work with Scott J. Miller (Yale Chemistry), I developed reactive NCAAs for applications in asymmetric synthesis, and discovered the first catalytic method for activating S(VI) sulfamates. This new method represents the first organocatalytic approach to site-selective alcohol sulfamoylation, and is currently under industry consideration (Takeda Pharmaceuticals) in an alternate process route to an immuno-oncology drug.

Peer-Reviewed Manuscripts

1. Rapp, P.B.; Murai, K.; Ichiishi, N.; Leahy, D.K.; Miller, S.J. Catalytic sulfamoylation of alcohols with activated aryl sulfamates. Org. Lett. 2020, 22 (1), 168–174.
2. Rapp, P.B.; Omar, A.K.; Silverman, B.R.; Wang, Z.G.; Tirrell, D.A. Mechanisms of diffusion in associative polymer networks: evidence for chain hopping. J. Am. Chem. Soc. 2018, 140 (43), 14185–14194.
3. Rapp, P.B., Omar, A.K.; Shen, J.J.; Buck, M.E.; Wang, Z.G.; Tirrell, D.A. Analysis and control of chain mobility in protein hydrogels. J. Am. Chem. Soc., 2017, 139 (10), 3796–3804.

Selected Honors and Awards

• Yale FAS Postdoctoral Travel Award. Competitive funding for conference travel. 2019.
• ARCS Foundation Scholar. ARCS Foundation, Los Angeles Chapter. 2015 – 2017.
• Caltech Everhart Lecturer. Graduate student speaking and research award. 2015.
• UIUC Bronze Tablet. University Honors Scholar (top 3% of graduating class). 2011.
• Donald E. Eisele Award. Excellence in Chemical Engineering Scholarship. 2011.
• Robert S. Frye Award. Outstanding Scholarship in Chemical Engineering. 2010.
• Northrop Grumman Scholarship. Endowed Engineering Scholarship, 2009.