https://scholar.dgist.ac.kr/handle/20.500.11750/10032 2026-04-24T15:58:40Z https://scholar.dgist.ac.kr/handle/20.500.11750/60291 Title: Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts Author(s): Jeon, Juhyeong; Yang, Wonjin; Park, Sangmin; Kim, Jin Hae; Lee, Young-Ho; Yu, Wookyung Abstract: Intrinsically disordered proteins and protein regions (IDRs) underpin a wide range of vital biological processes but exhibit dynamic and heterogeneous conformations. Currently, many computational efforts seek to elucidate the conformational ensembles of these disordered proteins, yet most methods still struggle to fully capture their structural diversity. Here, we integrate structural libraries of various IDRs—derived from coarse-grained molecular dynamics (MD) simulations and machine learning models—with experimental chemical shifts obtained from NMR spectroscopy. Through a maximum entropy reweighting approach, we obtain reliable ensembles that more accurately reflect observed chemical shifts and reveal transient states. Our results highlight the importance of comprehensive sampling strategies for capturing diverse conformational states. Furthermore, we show that these weighted ensembles faithfully track conformational rearrangements under various conditions such as temperature, mutational effects, and environment, which are not fully captured by experiments alone. This approach provides a dataset encompassing each IDR’s specific structures along with their weights, offering a foundation for systematically exploring IDR structural landscapes, refining our understanding of their functional roles, and shedding light on processes related to misfolding and aggregation. Copyright © 2026 the Author(s). 2026-01-31T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/59922 Title: Structural and dynamic basis of Ssp4-mediated DNA protection in foodborne bacterial spores Author(s): Seo, Minseok; Kim, Bokyung; Shin, Hyogyung; Kim, Jinwoo; Lee, Jong-bong; Ko, Young-ho; Kim, Jin Hae; Kim, Yoori Abstract: Clostridium perfringens forms metabolically dormant endospores that withstand extreme environmental conditions. Small acid-soluble proteins (SASPs) are ubiquitous DNA-binding proteins in endospores that promote resistance. While their protective role has been previously characterized, we aimed to provide further biophysical insight into the nature of these interactions, focusing on variant-specific structural dynamics through novel single-molecule and NMR approaches. Here, we characterize the DNA-binding properties and structural features of two Ssp4 variants using single-molecule fluorescence imaging and NMR spectroscopy along with electrophoretic mobility shift assays (EMSA). Both Ssp4 variants bind DNA cooperatively, but single-molecule analysis revealed preferential binding to GC-rich regions and significantly increased residence time in the presence of dipicolinic acid (DPA). NMR analysis reveals that an aspartic acid residue at position 36 (D36) stabilizes the Ssp4 structure, and its removal induces local structural perturbations without altering DNA affinity. Our findings provide molecular insights into how Ssp4 variants protect DNA in substantially dehydrated endospores and promote spore survival. © 2025 Elsevier B.V., All rights reserved. 2025-09-30T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/59914 Title: Recent advances in biomolecular 19F-NMR: applications to structural characterization of Hsp90 Author(s): Kim, Jin Hae Abstract: Hsp90 is a dynamic chaperone protein whose ATP-driven conformational cycle plays critical roles in the maturation and regulation of client proteins. Due to its large size and multi-domain architecture, however, conventional structural methods provide only limited insight into its dynamic features and related functionalities. Recent advances in 19F NMR spectroscopy have enabled residue-specific and background-free monitoring of Hsp90 dynamics across multiple structural scales. This mini-review highlights three representative studies that employed 19F NMR to dissect Hsp90’s mechanistic cycle. These studies demonstrate the unique power of 19F NMR to probe conformational populations, exchange kinetics, and allosteric regulation in large protein systems. 2025-11-30T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/59909 Title: Erythropoietin-derived Non-erythropoietic Peptides Conferring Oxidative Stress Resistance to Keratinocytes and Fibroblasts Author(s): Han, Min Ae; Ashim, Janbolat; Ji, Youngheum; Kang, Eunho; Jeong, Minchan; Kim, Sung Jae; Yu, Wookyung; Kim, Jin Hae; Moon, Cheil; Lee, Chang-Hun Abstract: Erythropoietin (EPO) exerts tissue-protective effects; however, its erythropoietic activity limits broader use. Three EPO-derived peptides (ML1-C1/C2/C3) were designed from the C-helix of EPO to remove erythropoietic activity while retaining cell-protective activity. Circular dichroism and nuclear magnetic resonance spectroscopies were used to assess the solution structures of ML1-C1/C2/C3 peptides. The peptide activities for cytoprotection and growth support were assessed using skin-relevant cells, HaCaT cells and 3T3-L1 cells, which proposes an effect on skin epithelial keratinocytes and pre-adipocytic fibroblasts, respectively. Also, an erythroid-precursor cell line, TF-1, was used to evaluate the erythropoietic function of the three peptides. Spectroscopic analyses of ML1-C1/C2/C3 peptides revealed similar secondary structures and different flexibilities between the peptides. While ML1-C1 and ML1-C3 had highly flexible loop-like structures, ML1-C2 had less flexible loop-like structures. Also, their cellular effects vary in a cell type-dependent manner. The EPO-derived peptides can attenuate H2O2-induced loss of viability in HaCaT cells and 3T3-L1 cells. Under low-serum conditions, the three peptides promoted HaCaT proliferation, whereas only ML1-C1 improved 3T3-L1 proliferation. In TF-1 cells, none of the peptides increased cell viability or hemoglobin staining, whereas recombinant human EPO did, indicating the lack of erythropoietic activity of the peptides under experimental conditions. These findings support the potential of EPO-derived peptides as skin-protective agents and motivate future work for skin therapeutics or cosmetic purposes.