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Chin SY, Chen Y, Zhao L, Liu X, Chng CP, Soman A, Nordenskiöld L, Huang C, Shi X, Xue K. Investigating Different Dynamic pHP1α States in Their KCl-Mediated Liquid-Liquid Phase Separation (LLPS) Using Solid-State NMR (SSNMR) and Molecular Dynamic (MD) Simulations. J Phys Chem B 2024. [PMID: 39387162 DOI: 10.1021/acs.jpcb.4c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
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.
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Affiliation(s)
- Sze Yuet Chin
- Centre of High Field NMR Spectroscopy and Imaging, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
| | - Yinglu Chen
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province 518172, China
| | - Lei Zhao
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province 518172, China
| | - Xinyi Liu
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province 518172, China
| | - Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 637798 Singapore
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 637798 Singapore
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province 518172, China
| | - Kai Xue
- Centre of High Field NMR Spectroscopy and Imaging, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
- School of Physical and Mathematical Science, Nanyang Technological University, 21 Nanyang Link, 637371 Singapore
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Ukmar‐Godec T, Yu T, de Opakua AI, Pantoja CF, Munari F, Zweckstetter M. Conformational diversity of human HP1α. Protein Sci 2024; 33:e5079. [PMID: 38895997 PMCID: PMC11187854 DOI: 10.1002/pro.5079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Heterochromatin protein 1 alpha (HP1α) is an evolutionarily conserved protein that binds chromatin and is important for gene silencing. The protein comprises 191 residues arranged into three disordered regions and two structured domains, the chromo and chromoshadow domain, which associates into a homodimer. While high-resolution structures of the isolated domains of HP1 proteins are known, the structural properties of full-length HP1α remain largely unknown. Using a combination of NMR spectroscopy and structure predictions by AlphaFold2 we provide evidence that the chromo and chromoshadow domain of HP1α engage in direct contacts resulting in a compact chromo/chromoshadow domain arrangement. We further show that HP1β and HP1γ have increased interdomain dynamics when compared to HP1α which may contribute to the distinct roles of different Hp1 isoforms in gene silencing and activation.
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Affiliation(s)
- Tina Ukmar‐Godec
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | - Taekyung Yu
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | - Alain Ibanez de Opakua
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | - Christian F. Pantoja
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
| | | | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE)Translational Structural BiologyGöttingenGermany
- Department of NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
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Ingersoll S, Trouth A, Luo X, Espinoza A, Wen J, Tucker J, Astatike K, Phiel CJ, Kutateladze TG, Wu TP, Ramachandran S, Ren X. Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578969. [PMID: 38370615 PMCID: PMC10871256 DOI: 10.1101/2024.02.05.578969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Facultative heterochromatinization of genomic regulators by Polycomb repressive complex (PRC) 1 and 2 is essential in development and differentiation; however, the underlying molecular mechanisms remain obscure. Using genetic engineering, molecular approaches, and live-cell single-molecule imaging, we quantify the number of proteins within condensates formed through liquid-liquid phase separation (LLPS) and find that in mouse embryonic stem cells (mESCs), approximately 3 CBX2 proteins nucleate many PRC1 and PRC2 subunits to form one non-stoichiometric condensate. We demonstrate that sparse CBX2 prevents Polycomb proteins from migrating to constitutive heterochromatin, demarcates the spatial boundaries of facultative heterochromatin, controls the deposition of H3K27me3, regulates transcription, and impacts cellular differentiation. Furthermore, we show that LLPS of CBX2 is required for the demarcation and deposition of H3K27me3 and is essential for cellular differentiation. Our findings uncover new functional roles of LLPS in the formation of facultative heterochromatin and unravel a new mechanism by which low-abundant proteins nucleate many other proteins to form compartments that enable them to execute their functions.
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Affiliation(s)
- Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Abby Trouth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xinlong Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Espinoza
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
| | - Joey Wen
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Joseph Tucker
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
| | - Kalkidan Astatike
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Christopher J. Phiel
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Tao P. Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
- Department of Integrative Biology, University of Colorado Denver, CO 80217-3364, USA
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