Minkyu Kim

Interests

Teaching

Synthetic and biological Materials (MSE/BME 461/561), Biomaterial-Tissue Interactions (BME/ABE 486/586),Research Methods in Biomedical Research (BME 597G)

Research

Functional proteins, artificial protein design, polymer networks, polymer gels, self-assembly, bioinspired/biomimetic materials

Courses

Scholarly Contributions

Journals/Publications

• Kim, S., Cathey, M., Bounds, B. C., Scholl, Z., Marszalek, P. E., & Kim, M. (2024). Ligand-Mediated Mechanical Enhancement in Protein Complexes at Nano- and Macro-Scale. ACS Applied Materials & Interfaces, 16(1), 272-280.
• Doole, F. T., Camp, C. P., & Kim, M. (2023). Tailoring the formation and stability of self-assembled structures from precisely engineered intrinsically disordered protein polymers: A comprehensive review. Giant, 14, 100158.
• Knoff, D. S., Kim, S., Fajardo, C., Rivera, J., Cathey, M., Altamirano, D., Camp, C., & Kim, M. (2022). Non-Covalently Associated Streptavidin Multi-Arm Nanohubs Exhibit Mechanical and Thermal Stability in Cross-Linked Protein-Network Materials. Biomacromolecules, 23(10), 4130-4140.
• Lee, T., Camp, C. P., Kim, B., & Kim, M. (2022). Environmentally Friendly Methylcellulose Blend Binder for Hydrophobic Dust Control. ACS Applied Polymer Materials, 4(2), 1512-1522.
• Wang, Y., Kegel, L. L., Knoff, D. S., Deodhar, B. S., Astashkin, A. V., Kim, M., & Pemberton, J. E. (2022). Layered supramolecular hydrogels from thioglycosides. Journal of Materials Chemistry B, 10(20), 3861-3875.
• Ghandi, J., Heinlich, L., Knoff, D. S., Kim, M., & Marmorstein, A. D. (2021). Alteration of Fibrin Hydrogel Gelation and Degradation Kinetics through Addition of Azo Dyes. Journal of Biomedical Materials Research: Part A.
• Camp, C. P., Peterson, I. L., Knoff, D. S., Melcher, L. G., Maxwell, C. J., Cohen, A. T., Wertheimer, A. M., & Kim, M. (2020). Non-cytotoxic Dityrosine Photocrosslinked Polymeric Materials With Targeted Elastic Moduli. Frontiers in Chemistry, 8, 173.
• Knoff, D. S., Szczublewski, H., Altamirano, D., Fajardo, C., & Kim, M. (2020). Cytoskeleton-Inspired Artificial Protein Design to Enhance Polymer Network Elasticity. Macromolecules, 53(9), 3464-3471.
• Lee, T., Kim, S., Kim, S., Kwon, N., Rho, S., Hwang, D. S., & Kim, M. (2020). Environmentally Friendly Methylcellulose-Based Binders for Active and Passive Dust Control. ACS Applied Materials & Interfaces, 12(45), 50860-50869.
• Lee, T., Park, J., Knoff, D. S., Kim, K., & Kim, M. (2019). Liquid amphiphilic polymer for effective airborne dust suppression. RSC ADVANCES, 9(68), 40146-40151.
• Park, J., Kim, K., Lee, T., & Kim, M. (2019). Tailings Storage Facilities (TSFs) Dust Control Using Biocompatible Polymers. MINING METALLURGY & EXPLORATION, 36(4), 785-795.
• Kim, M., Chen, W. G., Souza, B. S., & Olsen, B. D. (2017). Selective Biomolecular Separation System Inspired by the Nuclear Pore Complex and Nuclear Transport. Molecular Systems Design & Engineering, 2, 149-158. doi:10.1039/C7ME00006E
• Wang, R., Sing, M. K., Avery, R. K., Souza, B. S., Kim, M., & Olsen, B. D. (2016). Classical Challenges in the Physical Chemistry of Polymer Networks and the Design of New Materials. ACCOUNTS OF CHEMICAL RESEARCH, 49(12), 2786-2795.
• 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.
• Kim, M., Gkikas, M., Huang, A., Kang, J. W., Suthiwangcharoen, N., Nagarajan, R., & Olsen, B. D. (2014). Enhanced activity and stability of organophosphorus hydrolase via interaction with an amphiphilic polymer. Chemical communications (Cambridge, England), 50(40), 5345-8.
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  A simple approach to enhancing the activity and stability of organophosphorus hydrolase (OPH) is developed based on interactions between the hydrophobic poly(propylene oxide) (PPO) block of amphiphilic Pluronics and the enzyme. This strategy provides an efficient route to new formulations for decontaminating organophosphate neurotoxins.
• 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.
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  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., Tang, S., & Olsen, B. D. (2013). Physics of Engineered Protein Hydrogels. JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 51(7), 587-601.
• Callahan, D. J., Liu, W., Li, X., Dreher, M. R., Hassouneh, W., Kim, M., Marszalek, P., & Chilkoti, A. (2012). Triple Stimulus-Responsive Polypeptide Nanoparticles That Enhance Intratumoral Spatial Distribution. NANO LETTERS, 12(4), 2165-2170.
• 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., Wang, C., Benedetti, F., Rabbi, M., Bennett, V., & Marszalek, P. E. (2011). Nanomechanics of Streptavidin Hubs for Molecular Materials. ADVANCED MATERIALS, 23(47), 5684-+.
• Kim, M., Abdi, K., Lee, G., Rabbi, M., Lee, W., Yang, M., Schofield, C. J., Bennett, V., & Marszalek, P. E. (2010). Fast and forceful refolding of stretched alpha-helical solenoid proteins. Biophysical journal, 98(12), 3086-92.
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  Anfinsen's thermodynamic hypothesis implies that proteins can encode for stretching through reversible loss of structure. However, large in vitro extensions of proteins that occur through a progressive unfolding of their domains typically dissipate a significant amount of energy, and therefore are not thermodynamically reversible. Some coiled-coil proteins have been found to stretch nearly reversibly, although their extension is typically limited to 2.5 times their folded length. Here, we report investigations on the mechanical properties of individual molecules of ankyrin-R, beta-catenin, and clathrin, which are representative examples of over 800 predicted human proteins composed of tightly packed alpha-helical repeats (termed ANK, ARM, or HEAT repeats, respectively) that form spiral-shaped protein domains. Using atomic force spectroscopy, we find that these polypeptides possess unprecedented stretch ratios on the order of 10-15, exceeding that of other proteins studied so far, and their extension and relaxation occurs with minimal energy dissipation. Their sequence-encoded elasticity is governed by stepwise unfolding of small repeats, which upon relaxation of the stretching force rapidly and forcefully refold, minimizing the hysteresis between the stretching and relaxing parts of the cycle. Thus, we identify a new class of proteins that behave as highly reversible nanosprings that have the potential to function as mechanosensors in cells and as building blocks in springy nanostructures. Our physical view of the protein component of cells as being comprised of predominantly inextensible structural elements under tension may need revision to incorporate springs.
• 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.
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  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.
• Ke, C., Loksztejn, A., Jiang, Y., Kim, M., Humeniuk, M., Rabbi, M., & Marszalek, P. E. (2009). Detecting solvent-driven transitions of poly(A) to double-stranded conformations by atomic force microscopy. Biophysical journal, 96(7), 2918-25.
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  We report the results of direct measurements by atomic force microscopy of solvent-driven structural transitions within polyadenylic acid (poly(A)). Both atomic force microscopy imaging and pulling measurements reveal complex strand arrangements within poly(A) induced by acidic pH conditions, with a clear fraction of double-stranded molecules that increases as pH decreases. Among these complex structures, force spectroscopy identified molecules that, upon stretching, displayed two distinct plateau features in the force-extension curves. These plateaus exhibit transition forces similar to those previously observed in native double-stranded DNA (dsDNA). However, the width of the first plateau in the force-extension curves of poly(A) varies significantly, and on average is shorter than the canonical 70% of initial length corresponding to the B-S transition of dsDNA. Also, similar to findings in dsDNA, stretching and relaxing elasticity profiles of dspoly(A) at forces below the mechanical melting transition overlap but reveal hysteresis when the molecules are stretched above the mechanical melting transition. These results strongly suggest that under acidic pH conditions, poly(A) can form duplexes that are mechanically stable. We hypothesize that under acidic conditions, similar structures may be formed by the cellular poly(A) tails on mRNA.
• 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.
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  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.

Presentations

• Kim, M. (2023, Apr). Design of Artificial Protein Polymers for Healthcare Materials. 2023 MRS Spring Conference. San Francisco, CA: NSF.
• Kim, M. (2023, Feb). Artificial Protein Polymers for Multifunctional Materials. Civil & Architectural Engineering & Mechanics, University of Arizona, Tucson, AZ. Tucson: University of Arizona.
• Kim, M. (2023, Oct). Design of Erythrocyte-Inspired Polymeric Materials for Advanced Healthcare. ASU Biomaterials Day, Society for Biomaterials. Phoenix, AZ.
• Kim, M., Maier, R. M., Lee, T., Rodriguez, C., Martinez, F., Grinnell, D., & Hogan, D. E. (2023). Tailings Dust Control Using Bioinspired Glycolipid Surfactants. Society for Mining, Metallurgy, and Exploration Annual Conference. Denver, CO.
• Kim, M. (2021, April). Design of Mechanosensitive Polymeric Materials Inspired by Red Blood Cell. Department seminar. Online, Tim Taylor Department of Chemical Engineering, Kansas State University.
• Kim, M. (2022, January). Functional Biopolymeric Materials. Seminar. Online - SungKyunKwan University.
• Camp, C. P., Knoff, D. S., Doole, F. T., & Kim, M. (2021, April). Mechanical properties of engineered hydrogel materials modulated by sequence-controlled protein polymers. 2021 ACS spring meeting. Online.
• Doole, F. T., Melcher, L. G., Camp, C. P., Wertheimer, A. M., Singharoy, A., Brown, M. F., & Kim, M. (2021, April). Artificial Protein Design as an Effective Material Platform for Antimicrobial Peptides. 2021 MRS Spring meeting. Online.
• Kim, M. (2021, April). Artificial protein design rules to harness protein tertiary structures for polymeric materials with exotic mechanical behaviors. 2021 MRS Spring meeting. Online.
• Kim, M. (2021, May). Environmentally-Friendly Polymer Formulations for Dust Control in Mining Industry. UA Superfund Colloquium Seminar. Online - University of Arizona.
• Kim, M. (2021, September). Design of Mechanosensitive Polymeric Materials Inspired by Red Blood Cell. Department Seminar. ”, Department of Aerospace and Mechanical Engineering, the University of Arizona.
• Kim, M. (2020, June). Genetically Engineered Biopolymer Materials to Mitigate Infectious Diseases. Yonsei University. Seoul, Korea.
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  This presentation switched to online.
• Kim, M. (2019, Apr). Development of Polymer Formulations to Control (Ultra)Fine Dust in Subway Tunnel. Seminar. Seoul Metro, the City of Seoul, Korea.
• Kim, M. (2019, Nov). Controlling a Dust in a Dry World. College of Engineering. College of Engineering, University of Arizona: Tech Launch Arizona.
• Kim, M. (2019, Nov). Design of Mechanosensitive Polymeric Materials Inspired by Red Blood Cell Mechanics. Seminar. Department of Chemistry and Biochemistry, University of Arizona.
• Kim, M. (2019, Sep). New Concept of Dust Suppressant using Liquid Biocompatible Polymer. Seminar. Korea Electric Power Research Institute, Korea.
• Knoff, D. S., & Kim, M. (2019, Nov). Towards the construction of strong physical hydrogels: Translating single-molecule behaviors to macroscale hydrogel mechanical properties. MRS Fall Meeting. Boston, MA.
• Knoff, D. S., Szczublewski, H., & Kim, M. (2019, Apr). Cytoskeleton-Inspired Biopolymer Design to Reduce Topological Defects in Polymer Networks. MRS Spring meeting. Phoenix, AZ.
• Kim, M. (2018, May). Ligand-Mediated Mechanical Reinforcement of Injectable Protein Hydrogels. Canadian Chemistry Conference and Exhibition. Edmonton, AB, Canada.
• Kim, M. (2018, Sep). Genetically Engineered Biopolymer Materials to Mitigate Infectious Diseases. Nanoscience Seminar, Arizona State University. Phoenix, AZ.
• Kim, M. (2017, Apr). Artificially Engineered Protein Polymer Materials for Selective Biomolecular Separation. MRS Spring Meeting. Phoenix, AZ.
• Kim, M. (2017, Feb). Artificially Engineered Protein Polymers for Next-Generation Functional Materials. Seminar. Department of Environmental and Chemical Engineering, University of Arizona.

Poster Presentations

• Camp, C. P., & Kim, M. (2023, Apr). Elastic Modulus of Engineered Polymeric Hydrogel Materials Modulated by Sequence-Controlled Protein Polymers. 2023 MRS Spring meeting. San Francisco, CA: NSF.
• Grinnell, D., Pershing, H., Maier, R. M., Hogan, D. E., & Kim, M. (2023). Efficacy of Bioinspired Green Glycolipids as Dust Suppressants in Mine Tailings. NIEHS Superfund Research Program Annual Meeting.
• Kim, S. Y., Cathey, M., Bounds, B., Marszalek, P. E., & Kim, M. (2023, Apr). Biopolymer Design that Translates Single-Molecule Protein Nanomechanics to Macroscale Mechanical Properties of Polymer-Network Materials. 2023 MRS Spring Conference. San Francisco, CA: NSF.
• Lee, S., Kim, B., Grove, T. Z., Van Dyke, M. E., & Kim, M. (2023, Apr). Recombinant Keratins Coating for Enhanced Skin-Implant Interface. 2023 MRS Spring meeting. San Francisco, CA: CDMRP.
• Noh, Y. H., & Kim, M. (2023, Apr). Bioinspired Stiffness-Controlled Protein Filaments based on Understanding Hydrodynamics and Molecular Self-Assembly of Constitutive Proteins. 2023 MRS Spring meeting. San Francisco, CA: NSF.
• Wang, Y., Kegel, L. L., Knoff, D. S., Deodhar, B., Kim, M., & Pemberton, J. (2021, October). Layered Supramolecular Hydrogels from Thioglycosides. 2021 The Rocky Mountain Regional Meeting, ACS. Tucson, AZ.
• Deodhar, B., Knoff, D., Kim, M., & Pemberton, J. (2021, October). Glyonic Liquids: Green Ionic Liquids Manufactured from Sustainable Glycolipids. 2021 The Rocky Mountain Regional Meeting, ACS. Tucson, AZ.
• Doole, F. T., Chan, C. K., Kim, M., Singharoy, A., & Brown, M. F. (2021, Feb). Antimicrobial Peptide-Membrane Interactions: Insights from Molecular Simulations. 65th Annual Meeting of the Biophysical Society. Online.
• Doole, F., Chan, C., Streitwieser, E., Sarkar, D., Kim, M., Struts, A., Singharoy, A., & Brown, M. F. (2021, October). Solid-state NMR spectroscopy and molecular simulations reveal antimicrobial peptide biomembrane interactions. 2021 The Rocky Mountain Regional Meeting, ACS. Tucson, AZ.
• Kim, M. (2021, April). Cytoskeleton-Inspired Biopolymer Design for Reduced Polymer Network Defects Towards Constructing Biomimetic Nonlinear-Elastic Materials. 2021 ACS Spring meeting. Online.
• Doole, F. T., Chan, C. K., Kim, M., Singharoy, A., & Brown, M. F. (2020, Feb). Antimicrobial Peptide Functionalized Biomaterials Investigated by Molecular Dynamics Simulations. 64th Annual Meeting of the Biophysical Society. San Diego, CA.
• Melcher, L. G., Doole, F. T., Camp, C. P., Peterson, I. L., Kim, M., & Wertheimer, A. M. (2020, June). Antimicrobial Properties of Artificial Polypeptide-based Materials. 2020 American Society for Microbiology. Chicago, IL.
• Camp, C. P., Li, Z., Peterson, I., Doole, F. T., Kim, M., & Wertheimer, A. M. (2019, May). Novel Wound Healing Thermoresponsive Biomatrix with Antimicrobial and Anti-Inflammatory Properties. 8th International Symposium on the Diabetic Foot. Hague, Netherlands.
• Lee, T., Knoff, D. S., & Kim, M. (2019, March). Liquid Amphiphilic Polymer for Enhanced Airborne Dust Suppression. ACS Spring Meeting. Orlando, FL.
• Knoff, D. S., & Kim, M. (2018, Apr). Ligand-Mediated Mechanical Reinforcement of Injectable Protein Hydrogels. MRS Spring meeting. Phoenix, AZ.
• Lee, T., Park, J., Kim, K., & Kim, M. (2018, April). Biocompatible Liquid Polymers for Effective Dust Suppression. Material Research Society (MRS)Spring Meeting &Exhibit. Phoenix.
• Park, j., Kim, K., Lee, T., & Kim, M. (2018, February). The Use of Biocompatible Polymer for Mine Tailings Dust Control. Society for Mining, Metallurgy, and Exploration (SME). Minneapolis.