(2kd) Protein evolution: a bridge between basic discoveries and applications

Enzymes are Nature’s catalysts with tremendous potential for applications in energy, materials, drug manufacturing, and human health. To unlock this potential, we can use directed evolution to reprogram enzymes to perform reactions outside of their natural capabilities. My research has three main components: 1) discover new enzymes, 2) characterize their mechanisms, 3) evolve enzymes for applications in biotechnology. My group will use evolution not only to develop new tools, but also to gain a basic mechanistic understanding of enzymes. My prior research experiences in synthetic biology, enzymology, protein evolution, and gene editing have prepared me to lead a research group that uses protein evolution as a bridge between basic discoveries and applications such as sustainable biocatalysis and human health.

Graduate research:

By exploring biosynthetic pathways in bacteria, we can discover and repurpose natural enzymes for synthetic applications. As an NSF Graduate research fellow in the laboratory of Prof. Michelle Chang at UC Berkeley, I used bioinformatics and comparative metabolomics to discover a new family of enzymes that halogenate unactivated C_sp3-H bonds, a challenging but important synthetic transformation^{1, 2}. By performing biochemistry, X-ray crystallography, and high-throughput screening, I uncovered the mechanistic basis for halogenation within this enzyme family³ and used the resulting insights to engineer new halogenases with promising biocatalytic applications⁴.

1. Marchand, J.A.; Neugebauer, M.E.; Ing, M.C.; Lin, C. -I.; Pelton, J.G.; Chang, M.C.Y. Discovery of a pathway for terminal-alkyne amino acid biosynthesis. Nature 2019, 567, 420–424.
2. Neugebauer, M.E.; Sumida, K. H.; Pelton, J.G.; McMurry, J. L.; Marchand, J. A.; Chang, M.C.Y. A family of radical halogenases for the engineering of amino acid-based products. Nat. Chem. Biol. 2019, 15, 1009–1016.
3. Kissman, E.N.*; Neugebauer, M.E.*; Sumida, K. H.; Swenson, C.V.; Sambold, N.A.; Marchand, J.A.; Chang, M.C.Y. Regioselective control of biocatalytic C-H activation and halogenation. In revision.
4. Neugebauer, M.E.; Kissman, E.N.; Marchand, J. A.; Pelton, J.G.; Sambold, N.A; Millar, D.C.; Chang, M.C.Y. Reaction pathway engineering converts a radical hydroxylase into a halogenase. Nat. Chem. Biol. 2022, 18, 171-179.

Postdoctoral research:

Mutations in genomic DNA can cause genetic diseases. Molecular machines that perform chemistry on DNA, such as base editors, can correct these mutations and potentially cure diseases. Base editors consist of a programmable DNA binding protein, such as catalytically impaired Cas9, fused to a deaminase enzyme, and enable precise nucleotide changes within a target site in the genome. As a Ruth L. Kirschstein NIH Postdoctoral Fellow in the laboratory of David Liu at the Broad Institute, I used continuous protein evolution to develop novel cytosine base editors that perform highly efficient editing of C•G base pairs to T•A base pairs within therapeutically relevant sites and cell types⁵. These newly evolved base editors overcome some limitations of existing cytosine base editors and demonstrate the power of protein evolution for addressing challenges in biotechnology.

5. Neugebauer, M.E., Hsu, A., Arbab, M., Krasnow, N.A., McElroy, A.N., Pandey, S.P., Doman, J.L, Huang, T.P., Raguram, A.R., Banskota, S., Newby, G.A., Tolar, J., Osborn, M.J., Liu, D.R. Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target editing. Nat. Biotechnol., Accepted.

Teaching interests:

I have taught science and engineering in a variety of contexts. In the classroom, I served as a teaching assistant for undergraduate biology, biochemistry, physics, and chemical engineering courses. In the laboratory, I mentored two undergraduate students and three graduate rotation students, many of whom made significant research contributions that led to co-authored manuscripts. As part of an outreach program, I taught three 8-week science courses to 2^nd grade students. Combined with my personal experiences as a student, these experiences have helped to shape my views on effective teaching strategies, which I hope to further develop as a faculty member. I am excited to teach the core chemical engineering curriculum, including kinetics, transport, and thermodynamics, as well as to develop graduate courses related to my research interests of protein engineering and biotechnology.

Commitment to diversity, equity, and inclusion:

The perspectives of scientists from diverse backgrounds and identities are crucial for scientific advancement. I am committed to recruiting and supporting students from groups historically underrepresented in science and fostering a group culture of inclusivity and outreach. I have served as a mentor for outreach programs such as “MIT Women’s Initiative” and “Science Club for Girls,” an organization that emphasizes hands-on exposure to science for K-12 girls from underrepresented groups in the Boston area. In addition to continuing K-12 outreach as a faculty member, I will 1) organize my group’s engagement in outreach 2) recruit and support undergraduate, graduate, and post-doctoral researchers from underrepresented groups, 3) encourage my group to actively participate in drafting our “Lab Values” document, and 4) train my mentees to become supportive and inclusive mentors.