Jin Ryoun Kim
Source: https://engineering.nyu.edu/faculty/jin-ryoun-kim Parent: https://engineering.nyu.edu/academics/departments/chemical-and-biomolecular-engineering
- Associate Professor
Chemical and Biomolecular Engineering
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Jin Ryoun Kim is performing research in the creation of novel proteins for complex functionality such as the design of a protein sensor for detection of toxic molecules in neurodegenerative diseases and the development of a highly-stable enzyme that can be used in industry. His work has been recognized as significant by prestigious scientific societies and magazines.
He joined the faculty of NYU Tandon in the Department of Chemical and Biological Engineering in 2006.
He earned a Bachelor of Science (with honors) and a Master of Science in Chemical Engineering from Seoul National University in 1997 and 1999, respectively, and a PhD in Chemical and Biological Engineering from the University of Wisconsin-Madison in 2004.
Kim has authored many journal articles and patents and is a member of the American Institute of Chemical Engineering, the American Chemical Society, the Protein Society, and the New York Academy of Sciences.
He is a recipient of the New Investigator Award from the Alzheimer’s Association (2009), the Wechsler Award for Excellence (2009) and the Jacobs Excellence in Education Award (2013).
Research Interests
Data-driven and machine-learning-guided enzyme engineering; Protein mis-assembly in neurodegenerative diseases; Protein folding and stability; Protein-based molecular sensors
Seoul National University, 1997\ \ Bachelor of Science, Chemical Engineering
Seoul National University, 1999\ \ Master of Science, Chemical Engineering
University of Wisconsin-Madison, 2004\ \ Doctor of Philosophy, Chemical and Biological Engineering
Johns Hopkins University, 2006\ \ Postdoctoral Fellow
Journal Articles
- Ali Malli, Denys Vasyutyn, Jin Ryoun Kim, "Advances in machine learning models for predicting enzyme kinetic parameters", Journal of Chemical Information and Modeling, in press (2025)
- Mehmet Emre Erkanli, Yunseok Jang, Ali Malli, Khalid El-Halabi, Chaehyun Ryu, Jin Ryoun Kim, "A three-module machine learning framework for protein sequence- and temperature-dependent kcat/Km prediction in β-glucosidases", ACS Synthetic Biology, 14:3927-3939 (2025)
- Mehet Emre Erkanli, Ryu Hong Park, Jingwei Liu, Gunhyeong Lee, Amulya Hota, Jehyun Lee, Chaehyun Ryu, Ki Jun Jeong, Jin Ryoun Kim, "Enhanced production of hyperthermophilic Pyrococcus furiosus β-glucosidase in Corynebacterium glutamicum by optimization of the promoter, vector backbone, and His-tag location", Enzyme and Microbial Technology, 191:110725 (2025)
- Mehet Emre Erkanli, Ted Kensil Kang, Thorsten Kirsch, Eva A. Turley, Jin Ryoun Kim, Mary Cowman, "The spatial separation of basic amino acids is similar in RHAMM and hyaluronan binding peptide P15-1 despite different sequences and conformations", Proteoglycan Research, 2:e70001 (2024)
- Mehet Emre Erkanli, Khalid El-Halabi, Ted Kensil Kang, Jin Ryoun Kim, "Hotspot Wizard-informed engineering of a hyperthermophilic β-glucosidase for enhanced enzyme activity at low temperatures", Biotechnology and Bioengineering, 121:2079-2090 (2024)
- Mehet Emre Erkanli, Khalid El-Halabi, Jin Ryoun Kim, "Exploring the diversity of β-glucosidase: Classification, catalytic mechanism, molecular characteristics, kinetic models, and applications", Enzyme and Microbial Technology, 173:110363 (2024)
- Jin Ryoun Kim, "Oligomerization by co-assembly of β-amyloid and α-synuclein", Frontiers in Molecular Biosciences, 10:1153839, invited mini review (2023)
- Edward Chau, Jin Ryoun Kim, "α-synuclein-assisted oligomerization of β-amyloid (1-42)", \ Archives of biochemistry and biophysics, 717:109120 (2022)
- Edward Chau, Jin Ryoun Kim, "Engineering of a protein probe with multiple inputs and multiple outputs for evaluation of alpha synuclein aggregation states", Biochemical Engineering Journal, 178: 108292 (2022)
- Edward Chau, Hyunjoo Kim, Jineun Shin, Alberto Martinez, Jin Ryoun Kim, "Inhibition of alpha-synuclein aggregation by AM17, a synthetic resveratrol derivative", Biochemical and Biophysical Research Communications, 574:85-90 (2021).
- Maayan Hemed-Shaked, Mary K Cowman, Jin Ryoun Kim, Xiayun Huang, Edward Chau, Haim Ovadia, Keren-Or Amar, Lora Eshkar-Sebban, Michal Melamed, Libat Bar Lev, Eli Kedar, Jordi Armengol, Jorge Alemany, Shaul Beyth, Eli Okon, Darja Kanduc, Sharona Elgavish, Shulamit B Wallach-Dayan, Shmuel Jaffe Cohen, David Naor, "MTADV 5-MER peptide suppresses chronic inflammations as well as autoimmune pathologies and unveils a new potential target-Serum Amyloid A", Journal of Autoimmunity, 124:102713 (2021).
- Jaemin Kong, Yongwoo Shin, Jason A Röhr, Hang Wang, Juan Meng, Yueshen Wu, Adlai Katzenberg, Geunjin Kim, Dong Young Kim, Tai-De Li, Edward Chau, Francisco Antonio, Tana Siboonruang, Sooncheol Kwon, Kwanghee Lee, Jin Ryoun Kim, Miguel A Modestino, Hailiang Wang, André D Taylor, "CO2 doping of organic interlayers for perovskite solar cells", Nature, 594:51-56 (2021).
- Jason Candreva, Edward Chau, Margaret E Rice, Jin Ryoun Kim, "Interactions between soluble species of β-amyloid and α-synuclein promote oligomerization while inhibiting fibrillization", Biochemistry, 59:425-435 (2020).
- Amy Wood, Edward Chau, Yanxi Yang, Jin Ryoun Kim, "A KLVFFAE-derived peptide probe for detection of alpha-synuclein fibrils", Applied Biochemistry and Biotechnology, 190:1411-1424 (2020).
- Timothy Charlton, Vandan Shah, Tonniana Lynch, Jason Candreva, Edward Chau, Yanxi Yang, Hyunjoo Kim, Amy Wood, Jin Ryoun Kim, “Amyloid aggregation of Bacillus circulans xylanase under native conditions and its modulation by β-amyloid-derived peptide fragments”, Chembiochem, 19:2566-2574 (2018).
- Anthony J Finch, Jin Ryoun Kim, “Thermophilic proteins as versatile scaffolds for protein engineering”, Microorganisms (invited contribution), 6: E97 (2018).
- Jason Candreva, Edward Chau, Edwin Aoraha, Vikas Nanda, Jin Ryoun Kim, "Hetero-assembly of a dual beta-amyloid variant peptide system", Chemical Communications, 54:6380-6383 (2018).
- Vandan Shah, Timothy Charlton, Jin Ryoun Kim, "Laboratory Evolution of Bacillus circulans Xylanase Inserted into Pyrococcus furiosus Maltodextrin-Binding Protein for Increased Xylanase Activity and Thermal Stability Toward Alkaline pH", Applied Biochemistry and Biotechnology, 184:1232-1246 (2018)
- Vandan Shah, Brennal Pierre, Tamari Kirtadze, Seung Shin, Jin Ryoun Kim, "Stabilization of Bacillus circulans xylanase by combinatorial insertional fusionto a thermophilic host protein", Protein Engineering, Design & Selection, 30:281-290 (2017)
- Abhijit N. Shirke, An Su, J. Andrew Jones, Glenn L. Butterfoss, Mattheos A.G. Koffas, Jin Ryoun Kim, Richard A. Gross, "Comparative thermal inactivation analysis of Aspergillus oryzae and Thiellavia terrestris cutinase: Role of glycosylation.", Biotechnology Bioengineering, 114:63-73 (2017)
- Vandan Shah, Jin Ryoun Kim, "Transposon for protein engineering", Mobile Genetic Elements, 6:6 (2016)
- Brennal Pierre, Jason W. Labonte, Tina Xiong, Edwin Aoraha, Asher Williams, Vandan Shah, Edward Chau, Kazi Yasin Helal, Jeffrey Gray, Jin Ryoun Kim, "Molecular determinants for protein stabilization by insertional-fusion to a thermophilic host protein", ChemBioChem, 16:2392-2402 (2015)
- Edwin Aoraha, Jason Candreva and Jin Ryoun Kim, "Engineering of a peptide probe for β-amyloid aggregates", Molecular Biosystems, 11:2281-2289 (2015)
- Brennal Pierre, Vandan Shah, Jenny Xiao and Jin Ryoun Kim, "Construction of a random circular permutation library using an engineered transposon", Analytical Biochemistry, 474:16-24 (2015)
- Keeshan Williams, Chung-Sei Kim, Jin Ryoun Kim and Rastislav Levicky, "Multimodal electrochemical sensing of transcription factor-operator complexes.", Analyst, 139:1463-71 (2014)
- Michael Hernandez, Yang Hu and Jin Ryoun Kim, "A conformation-switching fluoresent protein probe for detection of alpha synuclein oligomers", Chemical Communications, 49:10712-4 (2013)
- Han Yuan, Mihir Tank, Abeer Alsofyani, Naman Shah, Nishant Talati, Jaclyn C LoBello, Jin Ryoun Kim, Yoji Oonuki, Carol A de la Motte and Mary K Cowman, "Molecular mass dependence of hyaluronan detection by sandwich ELISA-like assay and membrane blotting using biotinylated hyaluronan binding protein, Glycobiology, 23:1270-80 (2013)
- Vandan Shah, Brennal Pierre and Jin Ryoun Kim, "Facile construction of a random protein domain insertion library using an engineered transposon", Analytical Biochemistry, 432:97-102 (2013)
- Ahra Ko and Jin Ryoun Kim, "Effects of intramolecular distance between amyloidogenic domains on amyloid aggregation", International Journal of Molecular Sciences, 13: 12169-12181 (invited contribution) (2012)
- Mary K Cowman, Michael Hernandez, Jin Ryoun Kim, Han Yuan and Yang Hu, "Macromolecular Crowding in the Biomatrix", Structure and Function of Biomatrix: Control of Cell Function and Gene Expression, edited by E.A. Balazs and M. Hargittai, Matrix Biology Institute in Edgewater, NJ, in press (2012)
- Yang Hu, Baihao Su, HeQiu Zheng and Jin Ryoun Kim, "A peptide probe for detection of various beta-amyloid oligomers", Molecular BioSystems, 8:2741-2752 (2012)
- Yang Hu, HeQiu Zheng, Baihao Su and Jin Ryoun Kim, "Modulation of beta-amyloid aggregation by engineering the sequence connecting beta-strand forming domains", Biochimica et Biophysica Acta - Proteins and Proteomics, 1824:1069-1079 (2012)
- Michael Hernandez, Sofia Golbert, Li Guo Zhang and Jin Ryoun Kim, "Creation of aggregation-defective alpha synuclein variants by engineering the sequence connecting beta strand forming domains", ChemBioChem, 12:2630-2639 (2011)
- Joon Ho Ahn, Yang Hu, Michael Hernandez and Jin Ryoun Kim, "Crocetin inhibits beta-amyloid fibrillization and stabilizes beta-amyloid oligomers", Biochemical and Biophysical Research Communications, 414:79-83 (2011)
- Jung-Eun Cho and Jin Ryoun Kim, "Recent approaches targeting beta-amyloid for therapeutic intervention of Alzheimer's disease", Recent Patents on CNS Drug Discovery (invited review), 6:222-233 (2011)
- Brennal Pierre, Jin Ryoun Kim, “Stabilizing proteins while preserving primary sequences”, Research Advances in Protein Engineering Design & Selection (invited contribution), Global Research Network, Kerala, India (2011).
- Brennal Pierre, Tina Xiong, Leonie Hayles, Visweswara Reddy Guntaka, and Jin Ryoun Kim, "Stability of a guest protein depends on stability of a host protein in insertional fusion", Biotechnology & Bioengineering, 108(5):1011-1020 (2011)
- Yang Hu, Baihao Su, Chung-Sei Kim, Michael Hernandez, Agueda Rostagno, Jorge Ghiso, and Jin Ryoun Kim, "A strategy for designing a peptide probe for detection of beta-amyloid oligomers", ChemBioChem,11: 2409-2418 (2010)
- Chung-Sei Kim, Brennal Pierre, Marc Ostermeier, Loren L. Looger and Jin Ryoun Kim, "Enzyme stabilization by domain insertion into a thermophilic protein", Protein Engineering, Design & Selection, 22:615-623 (2009)
- Sachin Khapli, Jin Ryoun Kim, Jin Kim Montclare, Rastislav Levicky, Maurizio Porfiri and Stavroula Sofou, "Frozen Cyclohexane-in-Water Emulsion as a Sacrificial Template for the Synthesis of Multilayered Polyelectrolyte Microcapsules", Langmuir, 25: 9728?733 (2009)
- Jing Liang, Jin Ryoun Kim, James T. Boock, Thomas, J. Mansell, Marc Ostermeier, "Ligand binding and allostery can emerge simultaneously", Protein Sci. 16: 929-937 (2007).
- Jin Ryoun Kim, Todd J. Gibson, Regina M. Murphy, “Predicting solvent and aggregation effects of peptides using group contribution calculations”, Biotechnoogy Progress, 22:605-608 (2006).
- Jin Ryoun Kim, Marc Ostermeier, “Modulation of effector affinity by hinge region mutations also modulates switching activity in an engineered allosteric TEM1 beta-lactamase”, Archives of Biochemistry and Biophysics, 446:44-51 (2006).
- Gurkan Guntas, Thomas J. Mansell, Jin Ryoun Kim, Marc Ostermeier, “Directed evolution of protein switches and their application to the creation of ligand-binding proteins”, Proc. Natl. Acad. Sci. USA, 102:11224-11229 (2005).
- Jin Ryoun Kim, Adrian Muresan, Ka Yee C. Lee, Regina M. Murphy, “Urea modulation of beta-amyloid fibril growth: Experimental studies and kinetic models”, Protein Science, 13:2888-2898 (2004).
- Jin Ryoun Kim, Regina M. Murphy, “Mechanism of accelerated assembly of beta-amyloid filaments into fibrils by KLVFFK6”, Biophysical Journal, 86:3194-3203 (2004).
- Jin Ryoun Kim, Todd J. Gibson, Regina M. Murphy, “Targeted control of kinetics of beta-amyloid self-association by surface tension-modifying peptides”, Journal of Biological Chemistry, 278:40730-40735 (2003).
- Jin Ryoun Kim, Jihye Yang, Young Je Yoo, “The optimum pH of oxidoreductases: A comparison between experimental and calculated pH optimum”, Journal of the Korean Chemical Society, 46:432-436 (2002).
- Jin Ryoun Kim, Yoo Seoung Choi, Young Je Yoo, “Reactivation of Horseradish peroxidase in organic solvent using extraction”, Biotechnology Letters, 22:485-489 (2000).
- Hyon Joo Lee, Jin Ryoun Kim, Young Je Yoo, “The stabilization of enzyme in organic solvent at low temperature”, Progress in Biotechnology, 15:465-470 (1998).
NIH-NIA, NSF BBBE, NSF Biosensing, NSF MRI, Alzheimer's association, Ines Mandl Foundation
Research News
Biomedical engineers show potential of new peptide for fighting Alzheimer’s disease and COVID-19
NYU Tandon professors Mary Cowman and Jin Ryoun Kim recently published a paper describing a novel peptide with broad therapeutic potential to combat chronic inflammation in multiple diseases. The peptide, called Amilo 5-MER, was discovered by Professor David Naor and his colleague Dr. Shmuel Jaffe Cohen in the Faculty of Medicine at the Hebrew University of Jerusalem in Israel. They showed that Amilo 5-MER has anti-inflammatory effects that reduce pathological and clinical symptoms in mouse models for rheumatoid arthritis, inflammatory bowel disease, and multiple sclerosis.
Based on Naor's finding that the peptide binds to several proteins associated with inflammation, including Serum Amyloid A (SAA), Cowman and Kim proposed a working mechanism for the peptide. In a collaboration between the Israeli and Tandon teams they were able to show that the peptide inhibits aggregation of SAA into more pro-inflammatory and pro-amyloidogenic forms. Amyloid-type aggregation of proteins is associated with many diseases, and the Amilo 5-MER peptide has been found to bind to other aggregating proteins that play key roles in chronic inflammations and neurodegenerative diseases. Thus, the peptide could have significant therapeutic value in many other pathological conditions, such as Alzheimer's Disease, AA amyloidosis, and even COVID-19.
The project was supported by the Ines Mandl Research Foundation (IMRF), which is dedicated to providing research funding in the fight against connective tissue disease. It is the legacy of Dr. Ines Mandl, who was the first woman to graduate from the Polytechnic Institute of Brooklyn (today’s NYU Tandon School of Engineering) with a Ph.D. in chemistry in 1949.
August 26, 2021