Minkyu Kim
Assistant Professor, BIO5 Institute
Assistant Professor, Biomedical / Materials Science Engineer
Assistant Professor, Biomedical Engineering
Primary Department
Department Affiliations
(520) 621-6070
Work Summary
Minkyu Kim's research interests are in the areas of biopolymers and biomaterials for advanced national defense and healthcare. He is currently working to develop functional biopolymer materials for the treatment of antimicrobial-resistance diseases and atherosclerosis.
Research Interest
Minkyu Kim, Ph.D., is an Assistant Professor in the Department of Materials Science and Engineering and the Department of Biomedical Engineering at the University of Arizona. He received a M.S. (2006) in Biomedical Engineering and a Ph.D. (2011) in Mechanical engineering and Materials Science at Duke University. During his Ph.D., he worked in the Single-Molecule Force Spectroscopy group led by Prof. Marszalek. He was a postdoc at MIT from 2012 to 2016, and worked in the Bioinspired and Biofunctional Polymers group led by Prof. Olsen. Dr. Kim’s research is focused on the design and development of biopolymer-based functional materials for targeted applications in healthcare and for national defense. Based on his diverse research experiences in the areas of biopolymer nanomechanics, polymer physics and self-assembly, biomolecular engineering and soft materials, his group is currently developing (a) mechanically responsive soft materials that mimic reversible deformability of red blood cell and that can be utilized as targeted drug delivery vehicles for the early treatment of atherosclerosis and (b) nuclear membrane inspired biopolymer materials that selectively filter and neutralize a broad range of bacteria, fungi and viruses for pharmaceutical, food safety, water decontamination and defense applications. In addition to biomaterial development to mitigate atherosclerosis and infectious diseases, Dr. Kim is also interested in addressing how bioinspired design and biosynthesis can be used for the preparation of novel functional materials, how the nanomechanics of folded biopolymers and artificially engineered hyperbranched biopolymer structures can be translated into the mechanics of macromolecular materials that provide new insight into polymer science, and how protein sequences can control parameters that regulate the functional properties of polymeric materials. Lab Website: http://kim.lab.arizona.edu

Publications

Lam, C. N., Kim, M., Thomas, C. S., Chang, D., Sanoja, G. E., Okwara, C. U., & Olsen, B. D. (2014). The nature of protein interactions governing globular protein-polymer block copolymer self-assembly. Biomacromolecules, 15(4), 1248-58.

The effects of protein surface potential on the self-assembly of protein-polymer block copolymers are investigated in globular proteins with controlled shape through two approaches: comparison of self-assembly of mCherry-poly(N-isopropylacrylamide) (PNIPAM) bioconjugates with structurally homologous enhanced green fluorescent protein (EGFP)-PNIPAM bioconjugates, and mutants of mCherry with altered electrostatic patchiness. Despite large changes in amino acid sequence, the temperature-concentration phase diagrams of EGFP-PNIPAM and mCherry-PNIPAM conjugates have similar phase transition concentrations. Both materials form identical phases at two different coil fractions below the PNIPAM thermal transition temperature and in the bulk. However, at temperatures above the thermoresponsive transition, mCherry conjugates form hexagonal phases at high concentrations while EGFP conjugates form a disordered micellar phase. At lower concentration, mCherry shows a two-phase region while EGFP forms homogeneous disordered micellar structures, reflecting the effect of changes in micellar stability. Conjugates of four mCherry variants with changes to their electrostatic surface patchiness also showed minimal change in phase behavior, suggesting that surface patchiness has only a small effect on the self-assembly process. Measurements of protein/polymer miscibility, second virial coefficients, and zeta potential show that these coarse-grained interactions are similar between mCherry and EGFP, indicating that coarse-grained interactions largely capture the relevant physics for soluble, monomeric globular protein-polymer conjugate self-assembly.

Kim, M., Wang, C., Benedetti, F., & Marszalek, P. E. (2012). A nanoscale force probe for gauging intermolecular interactions. Angewandte Chemie (International ed. in English), 51(8), 1903-6.
Kim, M., Chen, W. G., Kang, J. W., Glassman, M. J., Ribbeck, K., & Olsen, B. D. (2015). Artificially Engineered Protein Hydrogels Adapted from the Nucleoporin Nsp1 for Selective Biomolecular Transport. Advanced materials (Deerfield Beach, Fla.), 27(28), 4207-12.
Jiang, Y., Rabbi, M., Kim, M., Ke, C., Lee, W., Clark, R. L., Mieczkowski, P. A., & Marszalek, P. E. (2009). UVA generates pyrimidine dimers in DNA directly. Biophysical journal, 96(3), 1151-8.

There is increasing evidence that UVA radiation, which makes up approximately 95% of the solar UV light reaching the Earth's surface and is also commonly used for cosmetic purposes, is genotoxic. However, in contrast to UVC and UVB, the mechanisms by which UVA produces various DNA lesions are still unclear. In addition, the relative amounts of various types of UVA lesions and their mutagenic significance are also a subject of debate. Here, we exploit atomic force microscopy (AFM) imaging of individual DNA molecules, alone and in complexes with a suite of DNA repair enzymes and antibodies, to directly quantify UVA damage and reexamine its basic mechanisms at a single-molecule level. By combining the activity of endonuclease IV and T4 endonuclease V on highly purified and UVA-irradiated pUC18 plasmids, we show by direct AFM imaging that UVA produces a significant amount of abasic sites and cyclobutane pyrimidine dimers (CPDs). However, we find that only approximately 60% of the T4 endonuclease V-sensitive sites, which are commonly counted as CPDs, are true CPDs; the other 40% are abasic sites. Most importantly, our results obtained by AFM imaging of highly purified native and synthetic DNA using T4 endonuclease V, photolyase, and anti-CPD antibodies strongly suggest that CPDs are produced by UVA directly. Thus, our observations contradict the predominant view that as-yet-unidentified photosensitizers are required to transfer the energy of UVA to DNA to produce CPDs. Our results may help to resolve the long-standing controversy about the origin of UVA-produced CPDs in DNA.

Kim, D., Novak, M. T., Wilkins, J., Kim, M., Sawyer, A., & Reichert, W. M. (2007). Response of monocytes exposed to phagocytosable particles and discs of comparable surface roughness. Biomaterials, 28(29), 4231-9.

This in vitro study characterized the temporal cytokine expression profile from human monocytes exposed to phagocytosable Ti particles (0.78+/-0.12 microm) and to Ti discs of comparable surface roughness. Human THP-1 monocytes were cultured in six well tissue culture polystyrene (TCPS) plates. Each well was either bare, contained Ti particles (the particles were clearly engulfed by the monocytes), or contained a Ti disc. Half of the wells were treated with 1 microg/mL lipopolysaccharide (LPS), while the other half were left unstimulated. Unstimulated and LPS-stimulated cells in bare wells were the negative and positive controls, respectively. Supernatant was sampled from each well at 1, 6, 24, 48, and 72 h and assayed for the expression of nine different cytokines using a Luminex system. Three cytokines (IL-1beta, GM-CSF and IL-13) gave little to no response under all conditions, while six cytokines (TNF-alpha, IL-6, MIP-1alpha, MCP-1, VEGF, and IL-1ra) were clearly detectable. Expression levels generally increased with culture time, particle concentration, and LPS stimulation. Most significantly, it was found that cells treated by Ti discs produced in many instances a higher cytokine expression than did particles.