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Maier J, Sieme D, Wong LE, Dar F, Wienands J, Becker S, Griesinger C. Quantitative description of the phase-separation behavior of the multivalent SLP65-CIN85 complex. PNAS Nexus 2024; 3:pgae079. [PMID: 38463037 PMCID: PMC10923291 DOI: 10.1093/pnasnexus/pgae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024]
Abstract
Biomolecular condensates play a major role in cell compartmentalization, besides membrane-enclosed organelles. The multivalent SLP65 and CIN85 proteins are proximal B-cell antigen receptor (BCR) signal effectors and critical for proper immune responses. In association with intracellular vesicles, the two effector proteins form phase separated condensates prior to antigen stimulation, thereby preparing B lymphocytes for rapid and effective activation upon BCR ligation. Within this tripartite system, 6 proline-rich motifs (PRMs) of SLP65 interact promiscuously with 3 SH3 domains of the CIN85 monomer, establishing 18 individual SH3-PRM interactions whose individual dissociation constants we determined. Based on these 18 dissociation constants, we measured the phase-separation properties of the natural SLP65/CIN85 system as well as designer constructs that emphasize the strongest SH3/PRM interactions. By modeling these various SLP65/CIN85 constructs with the program LASSI (LAttice simulation engine for Sticker and Spacer Interactions), we reproduced the observed phase-separation properties. In addition, LASSI revealed a deviation in the experimental measurement, which was independently identified as a previously unknown intramolecular interaction. Thus, thermodynamic properties of the individual PRM/SH3 interactions allow us to model the phase-separation behavior of the SLP65/CIN85 system faithfully.
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Affiliation(s)
- Joachim Maier
- Department of NMR Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Daniel Sieme
- Department of NMR Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Leo E Wong
- Department of NMR Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Furqan Dar
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63130, USA
| | - Jürgen Wienands
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Stefan Becker
- Department of NMR Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute (MPI) for Multidisciplinary Sciences, 37077 Göttingen, Germany
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Sicoli G, Sieme D, Overkamp K, Khalil M, Backer R, Griesinger C, Willbold D, Rezaei-Ghaleh N. Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins. Nat Commun 2024; 15:1610. [PMID: 38383529 PMCID: PMC10881997 DOI: 10.1038/s41467-024-45788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid-liquid phase separation is the key process underlying formation of membrane-less compartments in cells. A highly dynamic cellular body with rapid component exchange is Cajal body (CB), which supports the extensive compositional dynamics of the RNA splicing machinery, spliceosome. Here, we select an arginine-glycine (RG)-rich segment of coilin, the major component of CB, establish its RNA-induced phase separation, and through combined use of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) probes, interrogate its dynamics within the crowded interior of formed droplets. Taking advantage of glycine-based singlet-states, we show that glycines retain a large level of sub-nanoseconds dynamics inside the coilin droplets. Furthermore, the continuous-wave (CW) and electron-electron dipolar (PELDOR) and electron-nucleus hyperfine coupling EPR data (HYSCORE) support the RNA-induced formation of dynamic coilin droplets with high coilin peptide concentrations. The combined NMR and EPR data reveal the high dynamics of the RG-rich coilin within droplets and suggest its potential role in the large dynamics of CBs.
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Affiliation(s)
- Giuseppe Sicoli
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Kerstin Overkamp
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Mahdi Khalil
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Robin Backer
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Dieter Willbold
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany
| | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany.
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Sieme D, Engelke M, Rezaei-Ghaleh N, Becker S, Wienands J, Griesinger C. Autoinhibition in the Signal Transducer CIN85 Modulates B Cell Activation. J Am Chem Soc 2024; 146:399-409. [PMID: 38111344 PMCID: PMC10786037 DOI: 10.1021/jacs.3c09586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Signal transduction by the ligated B cell antigen receptor (BCR) depends on the preorganization of its intracellular components, such as the effector proteins SLP65 and CIN85 within phase-separated condensates. These liquid-like condensates are based on the interaction between three Src homology 3 (SH3) domains and the corresponding proline-rich recognition motifs (PRM) in CIN85 and SLP65, respectively. However, detailed information on the protein conformation and how it impacts the capability of SLP65/CIN85 condensates to orchestrate BCR signal transduction is still lacking. This study identifies a hitherto unknown intramolecular SH3:PRM interaction between the C-terminal SH3 domain (SH3C) of CIN85 and an adjacent PRM. We used high-resolution nuclear magnetic resonance (NMR) experiments to study the flexible linker region containing the PRM and determined the extent of the interaction in multidomain constructs of the protein. Moreover, we observed that the phosphorylation of a serine residue located in the immediate vicinity of the PRM regulates this intramolecular interaction. This allows for a dynamic modulation of CIN85's valency toward SLP65. B cell culture experiments further revealed that the PRM/SH3C interaction is crucial for maintaining the physiological level of SLP65/CIN85 condensate formation, activation-induced membrane recruitment of CIN85, and subsequent mobilization of Ca2+. Our findings therefore suggest that the intramolecular interaction with the adjacent disordered linker is effective in modulating CIN85's valency both in vitro and in vivo. This therefore constitutes a powerful way for the modulation of SLP65/CIN85 condensate formation and subsequent B cell signaling processes within the cell.
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Affiliation(s)
- Daniel Sieme
- Department
for NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Engelke
- Institute
for Cellular and Molecular Immunology, Georg-August
University Göttingen, Humboldtallee 34, 37073 Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Institute
of Physical Biology, Heinrich Heine University
Düsseldorf, Universitätsstraße
1, 40225 Düsseldorf, Germany
- Institute
of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Stefan Becker
- Department
for NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jürgen Wienands
- Institute
for Cellular and Molecular Immunology, Georg-August
University Göttingen, Humboldtallee 34, 37073 Göttingen, Germany
| | - Christian Griesinger
- Department
for NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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Sieme D, Rezaei-Ghaleh N. Water dynamics in eutectic solutions of sodium chloride and magnesium sulfate: implications for life in Europa's subsurface ocean and ice shell. Phys Chem Chem Phys 2023; 26:105-115. [PMID: 38054803 DOI: 10.1039/d3cp03455k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Liquid water is essential for life as we know it and the coupling between water and biomolecular dynamics is crucial for life processes. Jupiter's moon Europa is a good candidate for searching for extraterrestrial life in our outer solar system, mainly because a liquid water salty ocean in contact with a rocky seafloor underlies its ice shell. Little, however, is known about the chemical composition of the subglacial ocean of Europa or the brine pockets within its ice shell and their impacts on water dynamics. Here, we employ 1H, 17O, 23Na and 35Cl NMR spectroscopy, especially NMR spin relaxation and diffusion methods, and investigate the mobility of water molecules and ions in eutectic solutions of magnesium sulfate and sodium chloride, two salts ubiquitously present on the surface of Europa, over a range of temperatures and pressures pertinent to Europa's subglacial ocean. The NMR data demonstrate the more pronounced effect of magnesium sulfate compared with sodium chloride on the mobility of water molecules. Even at its much lower eutectic temperature, the sodium chloride solution retains a relatively large level of water mobility. Our results highlight the higher potential of a sodium chloride-rich than magnesium sulfate-rich Europa's ocean to accommodate life and support life origination within the eutectic melts of Europa's ice shell.
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Affiliation(s)
- Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077 Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225 Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428 Jülich, Germany
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Becker S, Giller K, Sieme D, Rezaei-Ghaleh N. Maturation of amyloid β fibrils alters their molecular stability. Phys Chem Chem Phys 2023. [PMID: 37249476 DOI: 10.1039/d3cp01276j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Little is known about how maturation of Alzheimer's disease-related amyloid β (Aβ) fibrils alters their stability and potentially influences their spreading in the brain. Using high-pressure NMR, we show that progression from early to late Aβ40 aggregates enhances the kinetic stability, while ageing during weeks to months enhances their thermodynamic stability.
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Affiliation(s)
- Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Institute of Physical Biology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, D-52428 Jülich, Germany
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Sieme D, Griesinger C, Rezaei-Ghaleh N. Metal Binding to Sodium Heparin Monitored by Quadrupolar NMR. Int J Mol Sci 2022; 23:ijms232113185. [PMID: 36361973 PMCID: PMC9655979 DOI: 10.3390/ijms232113185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Heparins and heparan sulfate polysaccharides are negatively charged glycosaminoglycans and play important roles in cell-to-matrix and cell-to-cell signaling processes. Metal ion binding to heparins alters the conformation of heparins and influences their function. Various experimental techniques have been used to investigate metal ion-heparin interactions, frequently with inconsistent results. Exploiting the quadrupolar 23Na nucleus, we herein develop a 23Na NMR-based competition assay and monitor the binding of divalent Ca2+ and Mg2+ and trivalent Al3+ metal ions to sodium heparin and the consequent release of sodium ions from heparin. The 23Na spin relaxation rates and translational diffusion coefficients are utilized to quantify the metal ion-induced release of sodium ions from heparin. In the case of the Al3+ ion, the complementary approach of 27Al quadrupolar NMR is employed as a direct probe of ion binding to heparin. Our NMR results demonstrate at least two metal ion-binding sites with different affinities on heparin, potentially undergoing dynamic exchange. For the site with lower metal ion binding affinity, the order of Ca2+ > Mg2+ > Al3+ is obtained, in which even the weakly binding Al3+ ion is capable of displacing sodium ions from heparin. Overall, the multinuclear quadrupolar NMR approach employed here can monitor and quantify metal ion binding to heparin and capture different modes of metal ion-heparin binding.
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Affiliation(s)
- Daniel Sieme
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077 Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077 Göttingen, Germany
- Institute of Physical Biology, Heinrich Heine University (HHU) Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428 Jülich, Germany
- Correspondence: or
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