Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations
Chromatin phase separation is dynamically regulated by many factors, such as post-translational modifications and effector proteins, and plays a critical role in genomic activities. The liquid-liquid phase separation (LLPS) of chromatin and/or effector proteins has been observed both in vitro and in...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2025
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| Online Access: | https://hdl.handle.net/10356/182262 |
| _version_ | 1826115946929979392 |
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| author | Chin, Sze Yuet Chen, Yinglu Zhao, Lei Liu, Xinyi Chng, Choon-Peng Soman, Aghil Nordenskiöld, Lars Huang, Changjin Shi, Xiangyan Xue, Kai |
| author2 | School of Physical and Mathematical Sciences |
| author_facet | School of Physical and Mathematical Sciences Chin, Sze Yuet Chen, Yinglu Zhao, Lei Liu, Xinyi Chng, Choon-Peng Soman, Aghil Nordenskiöld, Lars Huang, Changjin Shi, Xiangyan Xue, Kai |
| author_sort | Chin, Sze Yuet |
| collection | NTU |
| description | Chromatin phase separation is dynamically regulated by many factors, such as post-translational modifications and effector proteins, and plays a critical role in genomic activities. The liquid-liquid phase separation (LLPS) of chromatin and/or effector proteins has been observed both in vitro and in vivo. However, the underlying mechanisms are largely unknown, and elucidating the physicochemical properties of the phase-separated complexes remains technically challenging. In this study, we detected dynamic, viscous, and intermediate components within the phosphorylated heterochromatin protein 1α (pHP1α) phase-separated system by using modified solid-state NMR (SSNMR) pulse sequences. The basis of these sequences relies on the different time scale of motion detected by heteronuclear Overhauser effect (hetNOE), scalar coupling-based, and dipolar coupling-based transfer schemes in NMR. In comparison to commonly utilized scalar coupling-based methods for studying the dynamic components in phase-separated systems, hetNOE offers more direct insight into molecular dynamics. NMR signals from the three different states in the protein gel were selectively excited and individually studied. Combined with molecular dynamics (MD) simulations, our findings indicate that at low KCl concentration (30 mM), the protein gel displays reduced molecular motion. Conversely, an increase in molecular motion was observed at a high KCl concentration (150 mM), which we attribute to the resultant intermolecular electrostatic interactions regulated by KCl. |
| first_indexed | 2025-03-09T11:31:17Z |
| format | Journal Article |
| id | ntu-10356/182262 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-03-09T11:31:17Z |
| publishDate | 2025 |
| record_format | dspace |
| spelling | ntu-10356/1822622025-01-20T02:16:56Z Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations Chin, Sze Yuet Chen, Yinglu Zhao, Lei Liu, Xinyi Chng, Choon-Peng Soman, Aghil Nordenskiöld, Lars Huang, Changjin Shi, Xiangyan Xue, Kai School of Physical and Mathematical Sciences School of Mechanical and Aerospace Engineering School of Biological Sciences Centre of High Field NMR Spectroscopy and Imaging Chemistry Molecular docking Nuclear magnetic resonance Chromatin phase separation is dynamically regulated by many factors, such as post-translational modifications and effector proteins, and plays a critical role in genomic activities. The liquid-liquid phase separation (LLPS) of chromatin and/or effector proteins has been observed both in vitro and in vivo. However, the underlying mechanisms are largely unknown, and elucidating the physicochemical properties of the phase-separated complexes remains technically challenging. In this study, we detected dynamic, viscous, and intermediate components within the phosphorylated heterochromatin protein 1α (pHP1α) phase-separated system by using modified solid-state NMR (SSNMR) pulse sequences. The basis of these sequences relies on the different time scale of motion detected by heteronuclear Overhauser effect (hetNOE), scalar coupling-based, and dipolar coupling-based transfer schemes in NMR. In comparison to commonly utilized scalar coupling-based methods for studying the dynamic components in phase-separated systems, hetNOE offers more direct insight into molecular dynamics. NMR signals from the three different states in the protein gel were selectively excited and individually studied. Combined with molecular dynamics (MD) simulations, our findings indicate that at low KCl concentration (30 mM), the protein gel displays reduced molecular motion. Conversely, an increase in molecular motion was observed at a high KCl concentration (150 mM), which we attribute to the resultant intermolecular electrostatic interactions regulated by KCl. Agency for Science, Technology and Research (A*STAR) Ministry of Education (MOE) Nanyang Technological University National Supercomputing Centre (NSCC) Singapore We would like to thank Nanyang Technological University for the funding of NMR measurements at NTU Centre of High-Field NMR Spectroscopy and Imaging, as well as A*STAR for their support to Dr. Kai Xue (I23PGE0003). We acknowledge the National Natural Science Foundation of China (grant number: 32201006), Guangdong Province (grant numbers: 2021QN02Y103, 2022ZDZX2061), and 2023 Stable Support Plan Program of Shenzhen Colleges and Universities Fund for the financial support. We thank the support from the Ministry of Education (MOE), Singapore Academic Research Fund Tier 3 Grant (MOE2019-T3-1-012) to Prof. Lars Nordenskiöld. The computational work for this article was partially performed on resources of the National Supercomputing Centre, Singapore (https://www.nscc.sg) and supported by Ministry of Education (MOE), Singapore, under its Academic Research Fund Tier 1 (RG135/22). 2025-01-20T02:16:56Z 2025-01-20T02:16:56Z 2024 Journal Article Chin, S. Y., Chen, Y., Zhao, L., Liu, X., Chng, C., Soman, A., Nordenskiöld, L., Huang, C., Shi, X. & Xue, K. (2024). Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations. Journal of Physical Chemistry B, 128(42), 10451-10459. https://dx.doi.org/10.1021/acs.jpcb.4c03749 1520-6106 https://hdl.handle.net/10356/182262 10.1021/acs.jpcb.4c03749 39387162 2-s2.0-85207144002 42 128 10451 10459 en I23PGE0003 MOE2019-T3-1-012 RG135/22 Journal of Physical Chemistry B © 2024 American Chemical Society. All rights reserved. |
| spellingShingle | Chemistry Molecular docking Nuclear magnetic resonance Chin, Sze Yuet Chen, Yinglu Zhao, Lei Liu, Xinyi Chng, Choon-Peng Soman, Aghil Nordenskiöld, Lars Huang, Changjin Shi, Xiangyan Xue, Kai Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations |
| title | Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations |
| title_full | Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations |
| title_fullStr | Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations |
| title_full_unstemmed | Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations |
| title_short | Investigating different dynamic pHP1α states in their KCl-mediated liquid-liquid phase separation (LLPS) using solid-state NMR (SSNMR) and molecular dynamic (MD) simulations |
| title_sort | investigating different dynamic php1α states in their kcl mediated liquid liquid phase separation llps using solid state nmr ssnmr and molecular dynamic md simulations |
| topic | Chemistry Molecular docking Nuclear magnetic resonance |
| url | https://hdl.handle.net/10356/182262 |
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