https://scholar.dgist.ac.kr/handle/20.500.11750/743 Fri, 24 Apr 2026 17:05:39 GMT 2026-04-24T17:05:39Z 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). Sat, 31 Jan 2026 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/60291 2026-01-31T15:00:00Z 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. https://scholar.dgist.ac.kr/handle/20.500.11750/59909 https://scholar.dgist.ac.kr/handle/20.500.11750/59037 Title: The N-terminal order-disorder transition is a critical determinant for a metamorphosis of IscU Author(s): Na, Jongbum; Heo, Joongyu; Jeong, Minchan; Kim, Beom Soo; Ji, Sangho; Ko, Young Ho; Shafiei, Alaleh; Baldir, Nilufer; DeMirci, Hasan; Yu, Wookyung; Kim, Jin Hae Abstract: IscU, a key scaffold protein mediating the biogenesis of iron‑sulfur (Fesingle bondS) clusters, exhibits metamorphic characteristics crucial for its versatile and efficient function. Previous studies have demonstrated that IscU has two interconverting conformations: the structured state (S-state) and the disordered state (D-state), each contributing to its distinct functionality and interaction network. Despite its physiological importance, the precise mechanism underpinning the maintenance of IscU's unique structural heterogeneity has remained elusive. In this study, we used computational, spectroscopic, and biochemical approaches to reveal that the N-terminal order-disorder plays a critical role in the metamorphic modulation of Escherichia coli IscU. With computational analysis, we found that the N-terminal region displays greater structural plasticity, which is linked to other regions of IscU through coevolutionary relationships. We also used site-directed mutagenesis, size-exclusion chromatography, circular dichroism, isothermal titration calorimetry, and nuclear magnetic resonance spectroscopic techniques to demonstrate that the degree of orderliness in the N-terminal region correlates positively with the stabilization of IscU's S-state and negatively with its affinity for HscA. Finally, we also showed that the peptide mimicking the N-terminal motif can modulate IscU's metamorphic properties. Our data indicate that the flexibility in the N-terminal region is finely tuned to optimize IscU's physiological efficiency and efficacy. Moreover, our study showcases important evidence suggesting a novel therapeutic potential of the N-terminus-like peptide for related pathogenic processes. Sun, 31 Aug 2025 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/59037 2025-08-31T15:00:00Z https://scholar.dgist.ac.kr/handle/20.500.11750/58929 Title: Protein Microplastic Coronation Complexes Trigger Proteome Changes in Brain-Derived Neuronal and Glial Cells Author(s): Ashim, Janbolat; Ji, Sangho; Kim, Hee-Yeon; Lee, Seoung-Woo; Jang, Soyoung; Kim, Wansoo; Han, Sehyeon; Kim, Choonok; Park, Song; Park, Jin-Kyu; Han, Jee Eun; Choi, Seong-Kyoon; Yu, Wookyung Abstract: The extensive distribution of microplastics (MPs) in the environment and their food chain contamination urgently necessitates a deeper understanding of their molecular-level impact on physiological responses. This study employed a mass spectrometry-based proteomics approach to investigate the potential risks, mechanisms of associated cellular processes, and biological reactions to preformed protein-MPs coronation and intact MPs using brain-derived neuronal and glial cells. Our findings indicate that MPs can adsorb proteins and form a heterogeneous corona layer when interacting with biological fluids such as serum. Proteomics analysis revealed that protein-MP coronation notably alters protein expression levels compared to intact MPs, impacting core cellular biological processes, including protein synthesis machinery and RNA processing pathways, lipid metabolism, and nuclear-cytoplasmic compartmentalization and transport. Notably, the heterogeneous protein adsorption onto MP surfaces perturbs a wide range of cellular signaling pathways through cellular recognition mechanisms, potentially contributing to the challenge of MP accumulation in the brain. Mon, 30 Jun 2025 15:00:00 GMT https://scholar.dgist.ac.kr/handle/20.500.11750/58929 2025-06-30T15:00:00Z