(2gd) Engineering Spatial Organization in Biological Systems

Biological systems leverage spatiotemporal control as a critical feature to enable a variety of functions, from carbon fixation to infection. While engineering biology efforts have yielded remarkable progress towards addressing emerging societal challenges in areas from sustainability to human health, many of these efforts largely overlook the potential opportunities afforded by the spatiotemporal control that is central to many biological processes. This, in turn, limits the potential of engineering biology efforts. Combining my expertise in protein and polymer materials and phase behavior gained during my PhD in Prof. Bradley Olsen’s lab with expertise in protein assemblies and synthetic biology gained during my postdoctoral work in Prof. Danielle Tullman-Ercek’s lab, I will address this critical gap to understand how we can apply protein engineering and synthetic biology tools to manipulate and understand protein-driven spatial organization in biological systems. These principles have the potential for application in nearly every area in which we have seen advances in synthetic biology, as well as areas that have previously been intractable with existing approaches.

Specifically, my research program will be centered around three main areas. First, I will create a microbial system for decentralized plastic composting by developing a suite of tools that pair polymer/protein interaction optimization with cellular reprogramming to enable efficient microbial upcycling of ubiquitous, persistent plastics into valuable soil amendments. My second research area will focus on investigating strategies for protein particle delivery by probiotic vehicles, where the use of a probiotic chassis for delivery will minimize manufacturing cost and thus improve availability of these therapeutic assemblies. Finally, my third research area will explore the mechanism of protein liquid-liquid phase separation (LLPS) using cell-free systems to provide controllable complexity of local environment, with a focus on understanding how changes to local environment stimulate or hinder protein LLPS. Combined, the output of these projects will not only produce tangible bioengineered products for addressing challenges like plastic waste, but also build a fundamental set of knowledge surrounding spatiotemporal organization in biology.

Research Experience

My work as a faculty member will build on the scientific expertise I have accrued in my PhD and postdoctoral work. My PhD work investigated the phase behavior of protein/polymer, fusion protein, and disordered protein materials, drawing connections between polymer thermodynamics/physical chemistry and protein material behaviors. Several key accomplishments in this area include:

• Encapsulation of enzymes in complex coacervate micelles to improve enzyme stability in organic solvents
• Evidence that charge asymmetry in fusion protein materials drives microphase separation in fusion protein materials similarly to block copolymer materials
• Discovery of a cononsolvency-driven phase separation in elastin-like polypeptides (a widely used and studied protein material)
• Application of this discovered cononsolvency phenomenon towards a scalable, low-cost method for protein purification and desalting

My postdoctoral work in Prof. Danielle Tullman-Ercek’s lab at Northwestern has focused on applying recent advances in synthetic biology and protein engineering to studying multi-protein assemblies. In this space, I have:

• Identified the unique roles of two different proteins in the assembly process of complex, multi-component protein compartments.
• Coordinated a team of interdisciplinary collaborators with expertise in molecular dynamics simulations and kinetic reaction modeling for a deeper understanding of this assembly process and its implications in metabolic pathway organization
• Developed a high-throughput assay for assessing the assembly of these complex protein compartments.

Combined, the expertise I have gained through this work uniquely positions me to pursue research in the spaces described above—in plastic biodegradation, protein-polymer interactions like those studied in my PhD play a key role in enzymatic efficiencies; expertise in protein particle assembly and engineering is necessary to develop probiotic therapeutics capable of particle delivery; understanding the polymer physical chemistry that underlies polymeric phase behavior is essential in contextualizing phase separations in complex biological milieus.

Teaching Interests

As a graduate student at the Massachusetts Institute of Technology (MIT), I worked as a teaching assistant for the graduate level statistical mechanics and thermodynamics course. This included weekly preparation of supplemental lectures for office hours and design/writing of problems for both homework and exams. I also independently prepared guest lectures for both undergraduate and graduate courses in polymer science and protein engineering, often with a focus on bringing interdisciplinarity into the classroom—when guest lecturing in polymer courses, I focused on discussion of biopolymers like proteins; when guest lecturing in protein engineering courses, I focused on how protein-based materials present unique opportunities and challenges in the protein-engineering space. I hope to bring this perspective to all courses I teach. Beyond the formal classroom, I have provided mentorship in science to students at many levels, including high school, undergraduate, master’s, and PhD.

With my background in chemical engineering, I am equipped to teach any core course at the undergraduate or graduate level. Further, my research experience in bioengineering paired with my graduate coursework prepared me to teach courses in bioproduction, a growing area that requires chemical engineering expertise in industry. I am interested in developing a graduate-level course focused on protein engineering, highlighting spaces in which fundamental chemical engineering concepts have advanced protein engineering efforts. Finally, in all classes I teach, I will incorporate principles of local community impact, diversity, equity and inclusion into my problem sets to emphasize early and often that as engineers, we must optimize around these considerations in additional to more traditional goals like yield and process profitability. As one part of my work with at Northwestern University with the Chemical and Biological Engineering Department’s Anti-Racism, Diversity, Equity and Inclusion (ChBE ARDEI) Committee, I have participated in and subsequently hosted workshops on incorporating these concepts into problems in chemical engineering courses like kinetics, fluid dynamics, and mass/energy balances. I thus hope to expand this practice beyond my own classrooms and into those of interested colleagues at my faculty institution.

Selected Publications (11 of 19)

Mills, C. E.; Waltmann, C.; Archer, A. G.; Kennedy, N. W.; Abrahamson, C. H.; Jackson, A. D.; Roth, E. W.; Shirman, S.; Jewett, M. C.; Mangan, N. M.; Olvera de la Cruz, M.; Tullman-Ercek, D. Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology. Accepted at Nat. Comm. Preprint DOI: 10.1101/2021.10.31.466680

Mills, C. E.*; Kennedy, N. W.*; Abrahamson, C. H.; Archer, A. G.; Shirman, S.; Jewett, M. C.; Mangan, N. M.; Tullman-Ercek, D. Linking the Salmonella enterica 1,2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB. J. Bact. 2022

Waltmann, C.; Mills, C. E.; Wang, J.; Qiao, B.; Torkelson, J. M.; Tullman-Ercek, D.; Olvera de la Cruz, M. Functional enzyme-polymer complexes. Proc. Natl. Acad. Sci. U.S.A. 2022, 119, e2119509119

Mills, C. E.*; Kennedy, N. W.*; Nichols, T. M.; Abrahamson, C. H.; Tullman-Ercek, D. Bacterial microcompartments: tiny organelles with big potential. Curr. Opin. Microbiol. 2021, 63, 36-42

Li, Y.*; Kennedy, N. W.*; Li, S.; Mills, C. E.; Tullman-Ercek, D.; Olvera de la Cruz, M. Computational and experimental approaches to controlling bacterial microcompartment assembly. ACS Cent. Sci. 2021, 4, 658-670

Mills, C. E.*; Ding. E.*; Olsen, B.D. Protein Purification by Ethanol-Induced Phase Transitions of the Elastin-Like Polypeptide (ELP). Ind. Eng. Chem. Res. 2019, 58, 11698-11709

Mills, C. E.; Ding, E.; Olsen, B.D. Cononsolvency of elastin-like polypeptides (ELPs) in water/alcohol solutions. Biomacromolecules 2019, 20, 2167-2173

Mills, C. E.; Michaud, Z.; Olsen, B. D. Elastin-like Polypeptide (ELP) Charge Influences Self-Assembly of ELP-mCherry Fusion Proteins. Biomacromolecules 2018, 19, 2517-2525

Mills, C.E.; Obermeyer, A. C.; Dong, X. H.; Walker, J.; Olsen, B. D. Complex coacervate core micelles for the dispersion and stabilization of organophosphate hydrolase in organic solvents. Langmuir 2016, 32, 13367-13376

Obermeyer, A. C.; Mills, C. E.; Dong, X. H.; Flores, R. J.; Olsen, B. D. Complex coacervation of supercharged proteins with polyelectrolytes. Soft Matter 2016, 12, 3570-3581

Jeon, J.; Mills, C. E.; Shell, M. S. Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization. J. Phys. Chem. B. 2013, 117, 3935-3943

Selected Awards

Synthetic Biology Young Speaker Series (SynBYSS), Invited Speaker (2022)

Distinguished Postdoc Service Award, Northwestern University Dept. Chemical and Biological Engineering (2022)

Rising Star in Chemical Engineering, MIT (2020)

Excellence in Graduate Polymer Research Finalist, AIChE National Meeting (2018)

Graduate Woman of Excellence, Office of Graduate Education, MIT (2017)

National Science Foundation Graduate Research Fellowship (2013-2019)

Beckman Scholar (2012-2013)