(6kt) Force Response Defines Both Subcellular Architectures and Dynamic Protein Binding

Understanding the dynamics of biological processes is often approached through the lens of biochemical equilibria, wherein a healthy balance of reactants and products is actively maintained within enclosed bioreactors (cells and organelles). However, an equally compelling case can be made that there is also a dynamic and controlled balance of forces (and subsequent motion) within the cell. Altered force response between cytoskeletal elements can result in the stiffest of cellular superstructures or flexible transportation networks that allow for trafficking of organelles. Additionally, physiological processes that alter osmotic pressure or membrane tension can subsequently control phenomena as diverse as subcellular protein-protein phase separation or protein functionalization of organelle surfaces. This balance of forces within the cell is often mediated through intrinsically disordered proteins (IDPs), or proteins that lack a secondary structure and behave as biopolymers.

Through work by myself and others, there has been a growing consensus that IDPs give rise to unique force-responsive structures, combining a template of soft matter principles with sequence-encoded biologically-specific interactions. Exhibiting a dynamic regulation beyond most engineering methods today, these IDPs can be actively reprogrammed via post-translational modifications (much as biochemical equilibria are maintained via enzymatic activity) to alter or instill new functions beyond their naturally encoded state. Additionally, just as an unbalanced biochemical equilibrium is often associated with disease, external insults or internally aberrant perturbations to the homeostatic balance of forces are definitively linked to neuropathologies such as Alzheimer’s and Parkinson’s disease.

Despite the critical role of IDPs in maintaining a balance of forces within a cell, traditional biological and biochemical methods have had little success in bridging emergent mechanical properties afforded by IDPs and the molecular modifications to IDPs that occur in physiology (and disease). Requiring an innovative and multidisciplinary approach, understanding the conformational landscape of these proteins could not only yield insight into possible therapies but allow us to repurpose those emergent functionalities to design a new class of biologically-programmable nanomaterials.

Postdoctoral Project: “Force response defines both subcellular mediated architectures and dynamic protein binding.”

Under supervision of Ka Yee C. Lee, James Franck Institute, Chemistry, and Institute for Biophysical Dynamics, University of Chicago

PhD Dissertation: “Probing forces generated and architectures mediated by Tau on microtubules”

Under supervision of Cyrus R. Safinya, Physics, Materials, and Molecular, Cellular and Developmental Biology, University of California Santa Barbara

Research Experience:

Having found my passion in defining the molecular parameters of neurodegenerative diseases and pursuing biologically-inspired materials, I have taken my formal training in physics and engineering (at UC Berkeley and UC Santa Barbara) and have sought to describe previously intractable biological phenomena through the framework of colloidal and interfacial science. As a graduate student, not only did I train extensively with molecular biologists to express and purify proteins, I developed synchrotron X-ray scattering techniques to investigate the structure and force response of cell-free reconstitutions of microtubules, dynamically-assembly protein nanotubes, and Tau, an intrinsically disordered protein unequivocally linked to Alzheimer’s.

As a Kadanoff-Rice Postdoctoral Fellow at the University of Chicago, I have expanded my biological skillset while developing new experimental platforms and synchrotron-based techniques. In turning my focus to a-synuclein (an intrinsically disordered protein linked to Parkinson’s), I mastered newly developed chemical engineering techniques and molecular cloning to more faithfully represent the healthy and diseased states of the protein. As a-synuclein is known to bind to membrane organelles, I pioneered new membrane-nanoparticles that closely mimicked said organelles to precisely measure protein/membrane interactions. Additionally, this platform allowed for the use of X-ray photon correlation spectroscopy, a technique previously limited to soft matter physics but with which I have validated and advanced for biological studies. My intent has always been to become a complete scientist, undergirded by my belief that only a multidisciplinary approach can unveil physiological function and diseased dysfunction of cellular machinery.

Teaching Interests:

As a graduate student, I had the opportunity to teach three undergraduate-level physics courses, personally delivering 2-3 lectures a week to over 200+ students and supervising 3-5 teaching assistants in associated laboratory courses. As these courses in physics were designed for undergraduates majoring in biology, I understand the need to effectively communicate ideas in a manner most familiar to the audience, not the lecturer. Having taken both undergraduate and graduate engineering courses myself, I am more than capable and happy to teach introductory courses in chemical engineering and also teach (and if necessary, add) advanced courses in colloid/interfacial science, statistical mechanics, advanced X-ray scattering methods, protein expression/purification/modification methods, and soft condensed matter physics – all fundamental tools and knowledge requisite for an advanced training in chemical engineering with a focus in the applied life sciences.

Teaching is not just limited to the classroom but also extend to the laboratory and community. Having successfully mentored a total of 15 undergraduate and 4 graduate students during my graduate and postdoctoral work, I have the tools to create a laboratory environment that is both mutually respectful and curiosity driven. I also served as the student coordinator for Research Internships in Science and Engineering from 2013-2015, an undergraduate summer research program that targeted minority-serving institutions. Especially gratifying was the opportunity to work with students who clearly took to science and engineering but had been traditionally marginalized, with over 55% being female and over 40% being underrepresented minority students. Given the interdisciplinary nature of my research and extensive background in outreach programs, I am well equipped to work with students who come from a variety of backgrounds, academic or otherwise.

Proposed Future Research: Leveraging my unique training in soft matter physics and neurobiology, I propose a research program to apply precision force, structural, and dynamics measurements of minimal biological reconstitutions to recover the emergent mechanics conferred by IDPs. In particular, my research will be organized along three thrusts:

• What emergent mechanical and transport properties arise as a function of IDP sequence and cellular conditions? While IDPs are understood to give rise to complex cytoskeletal and subcellular architectures, the biological function of these architectures remains nebulous. While some IDP-mediated architectures seem to facilitate intracellular trafficking (Tau-mediated microtubule networks), others alter spatial localization of organelles and other biomacromolecules (synapsin-1 liquid droplets). Using optical, scattering, and force techniques I have developed, I aim to understand the emergent mechanical and transport properties of these architectures and the IDP sequence motifs/cellular conditions that drive architecture formation.
• How does cellular reprogramming alter IDP functionalization, especially modifications linked to neurodegenerative disease and injury? External insults (mechanical trauma in traumatic brain injury) or aberrant biochemical modifications (hyperphosphorylation of Tau in Alzheimer’s disease) are known to collapse or abrogate function of IDP-mediated architectures. Perturbing the basal state of these architectures both mechanically and biochemically will not only let us understand how diseased states alter architecture function, but examining the biological control of materials properties to affect transport properties may yield insight for other active matter systems that have been of intense, recent interest.
• How can we adapt these emergent properties to design a new class of biologically-programmable materials? Indeed, many of the properties conferred by IDPs can be naively modeled as polymers, ranging from grafted polymer brushes to polymer coacervates. However, that ignores the rich behavior that evolution has granted through biological specificity and reprogramming of IDPs, ranging from polymer brushes that attractively interact with each other to coacervates that specifically recruit certain membrane organelles but not others. By utilizing the principles that drive these properties, we can create new functional and programmable materials through cellular expression as opposed to traditional synthetic approaches.

Biology offers a rich landscape of optimized and actively controlled forces in colloids and fluids. By understanding this landscape, we can elucidate how the homeostatic steady state is perturbed into disease (yielding insights into possible therapies) and potentially repurpose this control for materials development, establishing an experimental framework that extends chemical engineering and soft matter physics into cellular biology.

Selected Publications:

Chung, P.J.*; Zhang, Q.*; Hwang, H.L.; Leong, A.; Dufresne, E.M.; Narayan, S.; Adams, E.J.; Lee, K.Y.C. a-synuclein sterically stabilizes spherical nanoparticle-supported lipid bilayers. ACS Applied Bio Materials, 2 (4), 1413-1419, 2019.

Chung, P.J.; Hwang, H.L.; Dasbiswas K.; Leong, A; Lee, K.Y.C. Osmotic shock-triggered assembly of highly-charged, nanoparticle-supported membranes. Langmuir, 34 (43), 13000-13005, 2018.

Chung, P. J.; Song, C.; Deek, J.; Miller, H. P.; Li, Y.; Choi, M. C.; Wilson, L.; Feinstein, S. C.; Safinya, C. R. Tau Mediates Microtubule Bundle Architectures Mimicking Fascicles of Microtubules Found in the Axon Initial Segment. Nature Communications, 7, 12278, 2016.

Chung, P. J.*; Choi, M. C.*; Miller, H. P.; Feinstein, H. E.; Raviv, U.; Li, Y.; Feinstein, S. C.; Safinya, C. R. Direct Force Measurements Reveal Protein Tau Confers Short-Range Attractions and Isoform-Dependent Steric Stabilization to Microtubules. Proceedings of the National Academy of Sciences, 112 (47), E6416–E6425, 2016.