(6is) Proteins Nanoparticles with Control of Shape, Size, and Valency for Therapeutics

Research
Interests:

Protein therapeutics, especially
antibodies, have revolutionized medicine in the last 30 years. These molecules perform
exquisite functions that are not yet found in synthetic molecules—protein
therapeutics feature molecular recognition and catalytic rate enhancement
activities that specifically interact amongst a sea of molecules that are found
in the body and in cells. However, the engineering of these proteins is
currently limited to mutations to the amino acid sequence and chemical
modification. By treating protein materials as nanoparticles, my future work
will create new protein therapeutics that have improved pharmacokinetics and
pharmacodynamics. In analogy to nanoparticles, the size, shape, surface
chemistry, valency, and functionality of proteins
will be chemically controlled to tune serum half-life, improve tissue- and
cell-specific targeting, and control the function of binding and catalytic
domains. To create these new protein materials, functional protein domains are scaffolded by fibrous protein domains, such that the
properties of the functional and scaffold domains are varied independently. By
decoupling the scaffold from function, protein nanoparticles are built from the
bottom up with chemically tailorable properties. My work will seek to answer
three questions:

1. How do material properties of a
protein scaffold affect activity?

2. What is the effect of multi- and
hyper-valency on antibody binding to cells?

3. Can antibody binding and enzyme
activity be tuned by changing the local chemical environment in a protein
material?

Successful Proposals

American Cancer Society Postdoctoral
Fellowship

National Science Foundation Graduate
Research Fellowship

Past Research

Proteins materials are made by
crosslinking individual protein molecules. As a postdoctoral fellow with
Professor Milan Mrksich at Northwestern University, I used a site-specific crosslinking
method to create megamolecules, protein structure
notable for their giant size, homogenous chemical composition, and tunable
shapes. I used energy transfer to measure the end-to-end distance of megamolecules and found that linear megamolecules
are relatively rigid and can be varied in size from 5–20 nm. These megamolecules served as a scaffold for antibody and enzyme
domains, and the binding affinity of antibody megamolecules
was increased by orders-of-magnitude by varying size and valency.
This work impacts the development of next-generation therapeutic proteins such
as bispecific antibodies.

Many proteins with interesting material
properties, such as spider silk, are difficult to produce in bacteria due to toxicity
to or degradation by the bacteria as they accumulate in the cell. As a graduate
student with Professor Danielle Tullman-Ercek at the University of California,
Berkeley, I improved production of these proteins by engineering a bacterial
protein secretion system to accumulate protein outside of the cell. Proteins
are unfolded during secretion, and I showed that proteins spontaneously refold
and achieve post-translational modification after secretion. I also controlled
expression of the secretion system gene cluster to increase the titer by
10-fold and enable macroscopic hydrogels to be made from secreted proteins.
This work impacts the biotechnology industry, where therapeutic proteins are
still produced and harvested from inside bacteria.

Teaching
Interests:

I
am interested in teaching courses in chemical kinetics, biochemical engineering,
process design, thermodynamics, and introductory chemical engineering. Further,
I am interested in creating an upper-division course in synthetic biology that
will analyze academic and industrial efforts through case studies.

Teaching
Experience and Philosophy

My
goal as a teacher is for my students to build a physical intuition for
molecular phenomena, and I do this through analogies and small-group problem
solving. I have served as a graduate student instructor for courses in process
design and biochemical engineering, for which I was awarded an outstanding
instructor award. In addition, I seek additional teaching opportunities by
giving guest lectures in courses on protein engineering and biosensors. I am
also interested in teaching lay audiences through science outreach and I work
with middle-school students in Chicago on science projects.

Mentorship
Experience

My
teaching extends to the laboratory, where I have mentored 11 students. As a
mentor, my goal is to give students the tools to develop into independent
researchers. My focuses are on designing good experiments and presenting their
work. I run a journal club with students and colleagues where the focus is on
the experimental design from high quality publications. To work on their
writing skills, I give feedback on research reports, with particular focus on
the introduction and motivation of their work. Finally, I support students to
present their work at national conferences, where they have presented 16 posters
and oral presentations.

Selected
Publications

1.         *Taylor, E.L., *Metcalf, K.J., Carlotti, B., Lai, C.-T., Modica, J.,
Schatz, G., Mrksich, M., Goodson, T. “Long-Range Energy Transfer in Protein Megamolecules,” Submitted
and available upon request.

2.         *Zhou, S., *Metcalf, K.J., Bugga, P., Grant, J., Mrksich, M. “A photoactivable reaction for nanoscale patterning of
multiple proteins,” Submitted and
available upon request.

3.         Metcalf,
K.J., Slininger Lee, M., Jakobson, C.M., Tullman-Ercek, D. “An Estimate
Is Worth About a Thousand Experiments: Using Order-of-Magnitude Estimates to
Identify Cellular Engineering Targets,” Submitted
and available upon request.

4.         Metcalf,
K.J., Bevington, J.L., Rosales, S., Burdette,
L.A., Valdivia, E., Tullman-Ercek, D. “Proteins adopt functionally active
conformations after type III secretion," Microbial Cell Factories,
2016. DOI: 10.1186/s12934-016-0606-4

5.         Azam, A., Li,
C., Metcalf, K.J.,
Tullman-Ercek, D. "Type III Secretion as a Generalizable Strategy for the
Production of Full-Length Biopolymer-Forming Proteins," Biotechnology
and Bioengineering, 2015. DOI: 10.1002/bit.25656

6.         Metcalf,
K.J., Finnerty, C., Azam,
A., Valdivia, E., Tullman-Ercek, D. "Using Transcriptional Control to
Increase Titers of Secreted Heterologous Proteins by the Type III Secretion
System," Applied and Environmental Microbiology, 2014. DOI:
10.1128/AEM.01330-14