https://scholar.dgist.ac.kr/handle/20.500.11750/10015 2026-04-24T14:35:04Z 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/20.500.11750/60065 Title: The disordered N-terminus modulates the conformational metamorphosis of IscU, the Fe-S cluster assembly protein Author(s): 김진해 Abstract: An iron-sulfur (Fe-S) cluster is a ubiquitous and essential cofactor for various proteins, and its imbalance can cause abnormal iron accumulation and lead to fatal diseases, such as ataxia and myopathy. The biosynthesis of Fe-S clusters depends on several critical proteins, among which IscU, the Fe-S cluster assembly protein, plays a pivotal role. IscU shows a ‘metamorphic’ structural feature; it exhibits two interconverting conformations, the structured state (S-state) and the disordered state (D-state), and both conformations have their own functionality and interaction network. However, the detailed mechanism regarding how IscU maintains its structural heterogeneity has remained enigmatic. In this study, we employed interdisciplinary approaches to elucidate that the order-disorder transition in the N-terminal region of IscU is important to modulate its metamorphic feature. We found that the degree of orderliness in the N-terminal region is positively related to the S-state stabilization, while IscU’s affinity for HscA is inversely correlated. This implies that the N-terminal disorder of IscU is maintained on purpose to optimize its physiological efficacy. We propose that this study provides unprecedented insights into the development of novel therapeutic molecules for related pathogenic processes. 2025-02-03T15:00:00Z 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