1
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Sutinen A, Jones NC, Hoffmann SV, Ruskamo S, Kursula P. Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane. Biophys Chem 2023; 303:107113. [PMID: 37778197 DOI: 10.1016/j.bpc.2023.107113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.
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Affiliation(s)
- Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland; Department of Biomedicine, University of Bergen, Bergen, Norway.
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2
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Krokengen OC, Raasakka A, Kursula P. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data. Biochem Biophys Rep 2023; 34:101474. [PMID: 37153862 PMCID: PMC10160357 DOI: 10.1016/j.bbrep.2023.101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Oulu, Finland
- Corresponding author. Department of Biomedicine, University of Bergen, Norway.
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3
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Smirnova EV, Rakitina TV, Ziganshin RH, Saratov GA, Arapidi GP, Belogurov AA, Kudriaeva AA. Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics. Cells 2023; 12:cells12060944. [PMID: 36980286 PMCID: PMC10047773 DOI: 10.3390/cells12060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe2+ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.
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Affiliation(s)
- Evgeniya V Smirnova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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4
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Staśkiewicz A, Quagliata M, Real-Fernandez F, Nuti F, Lanzillo R, Brescia-Morra V, Rusche H, Jewginski M, Carotenuto A, Brancaccio D, Aharoni R, Arnon R, Rovero P, Latajka R, Papini AM. Role of Helical Structure in MBP Immunodominant Peptides for Efficient IgM Antibody Recognition in Multiple Sclerosis. Front Chem 2022; 10:885180. [PMID: 35795217 PMCID: PMC9250970 DOI: 10.3389/fchem.2022.885180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022] Open
Abstract
The involvement of Myelin Basic Protein (MBP) in Multiple Sclerosis (MS) has been widely discussed in the literature. This intrinsically disordered protein has an interesting α-helix motif, which can be considered as a conformational epitope. In this work we investigate the importance of the helical structure in antibody recognition by MBP peptides of different lengths. Firstly, we synthesized the peptide MBP (81–106) (1) and observed that its elongation at both N- and C-termini, to obtain the peptide MBP (76–116) (2) improves IgM antibody recognition in SP-ELISA, but destabilizes the helical structure. Conversely, in competitive ELISA, MBP (81–106) (1) is recognized more efficiently by IgM antibodies than MBP (76–116) (2), possibly thanks to its more stable helical structure observed in CD and NMR conformational experiments. These results are discussed in terms of different performances of peptide antigens in the two ELISA formats tested.
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Affiliation(s)
- Agnieszka Staśkiewicz
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Feliciana Real-Fernandez
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Nuti
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Roberta Lanzillo
- Multiple Sclerosis Clinical Care and Research Centre, Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, Naples, Italy
| | - Vincenzo Brescia-Morra
- Multiple Sclerosis Clinical Care and Research Centre, Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, Naples, Italy
| | - Hendrik Rusche
- Fischer Analytics GmbH, Weiler, Germany
- CY PeptLab Platform of Peptide and Protein Chemistry and Biology and UMR 8076 CNRS-BioCIS, CNRS, CY Cergy Paris Université, Neuville sur Oise, France
| | - Michal Jewginski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Rina Aharoni
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Arnon
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
| | - Rafal Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- CY PeptLab Platform of Peptide and Protein Chemistry and Biology and UMR 8076 CNRS-BioCIS, CNRS, CY Cergy Paris Université, Neuville sur Oise, France
- *Correspondence: Anna Maria Papini,
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5
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Chen J, Tieleman DP, Liang Q. Effects of Lid Domain Structural Changes on the Interactions between Peripheral Myelin Protein 2 and a Lipid Bilayer. J Phys Chem Lett 2022; 13:991-996. [PMID: 35060724 DOI: 10.1021/acs.jpclett.1c03961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peripheral myelin protein 2 (P2) plays an important role in the stacking of the myelin membrane and lipid transport. Here we investigate the interactions between P2 and a model myelin membrane using molecular dynamics simulations, focusing on the effect of the L27D mutation and conformational changes in the α2-helix in the lid domain of P2. The L27D mutation weakens the binding of the lid domain of P2 on the membrane. The α2-helix is either folded or unfolded on the membrane. Compared with the α2-helix structure in water, the membrane stabilizes the structure of the α2-helix, whereas the unfolding of the α2-helix reduces the binding affinity of P2 on the membrane. These findings reveal the energetics of the mutant and the structural changes of P2 on the interactions between the protein and the lipid bilayer and help us to understand the microscopic mechanism of the formation of the myelin sheath structure and some neurological disorders.
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Affiliation(s)
- Jinyu Chen
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
| | - D Peter Tieleman
- Centre for Molecular Simulations and Department of Biological Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, P. R. China
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6
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Martinsen V, Kursula P. Multiple sclerosis and myelin basic protein: insights into protein disorder and disease. Amino Acids 2021; 54:99-109. [PMID: 34889995 PMCID: PMC8810476 DOI: 10.1007/s00726-021-03111-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023]
Abstract
Myelin basic protein (MBP) is an abundant protein in central nervous system (CNS) myelin. MBP has long been studied as a factor in the pathogenesis of the autoimmune neurodegenerative disease multiple sclerosis (MS). MS is characterized by CNS inflammation, demyelination, and axonal loss. One of the main theories on the pathogenesis of MS suggests that exposure to foreign antigens causes the activation of cross-reactive T cells in genetically susceptible individuals, with MBP being a possible autoantigen. While a direct role for MBP as a primary antigen in human MS is unclear, it is clear that MBP and its functions in myelin formation and long-term maintenance are linked to MS. This review looks at some key molecular characteristics of MBP and its relevance to MS, as well as the mechanisms of possible molecular mimicry between MBP and some viral antigens. We also discuss the use of serum anti-myelin antibodies as biomarkers for disease. MBP is a prime example of an apparently simple, but in fact biochemically and structurally complex molecule, which is closely linked to both normal nervous system development and neurodegenerative disease.
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Affiliation(s)
- Vebjørn Martinsen
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020, Bergen, Norway. .,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220, Oulu, Finland.
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7
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Matsuo K, Kumashiro M, Gekko K. Characterization of the mechanism of interaction between α1‐acid glycoprotein and lipid membranes by vacuum‐ultraviolet circular‐dichroism spectroscopy. Chirality 2020; 32:594-604. [DOI: 10.1002/chir.23208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation CenterHiroshima University Higashi‐Hiroshima Japan
| | - Munehiro Kumashiro
- Department of Physical Science, Graduate School of ScienceHiroshima University Higashi‐Hiroshima Japan
| | - Kunihiko Gekko
- Hiroshima Synchrotron Radiation CenterHiroshima University Higashi‐Hiroshima Japan
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8
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Gekko K. Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview. Biophys Physicobiol 2019; 16:41-58. [PMID: 30923662 PMCID: PMC6435020 DOI: 10.2142/biophysico.16.0_41] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/13/2019] [Indexed: 12/01/2022] Open
Abstract
Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.
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Affiliation(s)
- Kunihiko Gekko
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan
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9
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Raasakka A, Ruskamo S, Kowal J, Han H, Baumann A, Myllykoski M, Fasano A, Rossano R, Riccio P, Bürck J, Ulrich AS, Stahlberg H, Kursula P. Molecular structure and function of myelin protein P0 in membrane stacking. Sci Rep 2019; 9:642. [PMID: 30679613 PMCID: PMC6345808 DOI: 10.1038/s41598-018-37009-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Compact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in changes of the bilayer properties, but also potentially involves the arrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland
| | - Huijong Han
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anna Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Rocco Rossano
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Paolo Riccio
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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10
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Miles AJ, Wallace BA. CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data. Protein Sci 2018; 27:1717-1722. [PMID: 30168221 PMCID: PMC6194270 DOI: 10.1002/pro.3474] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/11/2022]
Abstract
Circular dichroism (CD) spectroscopy is a highly used method for the examination and characterization of proteins, including, amongst other features, their secondary and tertiary structures, thermal stability, comparisons of wildtype and mutant proteins, and monitoring the binding of small molecules, folding/unfolding pathways, and formation of macromolecular complexes. This article describes CDtoolX, a new, user-friendly, free-to-download-and-use software program that enables processing, displaying, archiving, calibrating, comparisons, and analyses of CD and synchrotron radiation circular dichroism spectroscopic data.
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Affiliation(s)
- Andrew J. Miles
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUnited Kingdom
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUnited Kingdom
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11
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Tuusa J, Raasakka A, Ruskamo S, Kursula P. Myelin-derived and putative molecular mimic peptides share structural properties in aqueous and membrane-like environments. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s40893-017-0021-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Ozgen H, Baron W, Hoekstra D, Kahya N. Oligodendroglial membrane dynamics in relation to myelin biogenesis. Cell Mol Life Sci 2016; 73:3291-310. [PMID: 27141942 PMCID: PMC4967101 DOI: 10.1007/s00018-016-2228-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
In the central nervous system, oligodendrocytes synthesize a specialized membrane, the myelin membrane, which enwraps the axons in a multilamellar fashion to provide fast action potential conduction and to ensure axonal integrity. When compared to other membranes, the composition of myelin membranes is unique with its relatively high lipid to protein ratio. Their biogenesis is quite complex and requires a tight regulation of sequential events, which are deregulated in demyelinating diseases such as multiple sclerosis. To devise strategies for remedying such defects, it is crucial to understand molecular mechanisms that underlie myelin assembly and dynamics, including the ability of specific lipids to organize proteins and/or mediate protein-protein interactions in healthy versus diseased myelin membranes. The tight regulation of myelin membrane formation has been widely investigated with classical biochemical and cell biological techniques, both in vitro and in vivo. However, our knowledge about myelin membrane dynamics, such as membrane fluidity in conjunction with the movement/diffusion of proteins and lipids in the membrane and the specificity and role of distinct lipid-protein and protein-protein interactions, is limited. Here, we provide an overview of recent findings about the myelin structure in terms of myelin lipids, proteins and membrane microdomains. To give insight into myelin membrane dynamics, we will particularly highlight the application of model membranes and advanced biophysical techniques, i.e., approaches which clearly provide an added value to insight obtained by classical biochemical techniques.
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Affiliation(s)
- Hande Ozgen
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Wia Baron
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
| | - Dick Hoekstra
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nicoletta Kahya
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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13
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Substitutions mimicking deimination and phosphorylation of 18.5-kDa myelin basic protein exert local structural effects that subtly influence its global folding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1262-77. [DOI: 10.1016/j.bbamem.2016.02.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/30/2016] [Accepted: 02/17/2016] [Indexed: 11/20/2022]
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14
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Matsuo K, Maki Y, Namatame H, Taniguchi M, Gekko K. Conformation of membrane-bound proteins revealed by vacuum-ultraviolet circular-dichroism and linear-dichroism spectroscopy. Proteins 2016; 84:349-59. [PMID: 26756612 DOI: 10.1002/prot.24981] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/09/2015] [Accepted: 12/19/2015] [Indexed: 12/16/2022]
Abstract
Knowledge of the conformations of a water-soluble protein bound to a membrane is important for understanding the membrane-interaction mechanisms and the membrane-mediated functions of the protein. In this study we applied vacuum-ultraviolet circular-dichroism (VUVCD) and linear-dichroism (LD) spectroscopy to analyze the conformations of α-lactalbumin (LA), thioredoxin (Trx), and β-lactoglobulin (LG) bound to phosphatidylglycerol liposomes. The VUVCD analysis coupled with a neural-network analysis showed that these three proteins have characteristic helix-rich conformations involving several helical segments, of which two amphiphilic or hydrophobic segments take part in interactions with the liposome. The LD analysis predicted the average orientations of these helix segments on the liposome: two amphiphilic helices parallel to the liposome surface for LA, two hydrophobic helices perpendicular to the liposome surface for Trx, and a hydrophobic helix perpendicular to and an amphiphilic helix parallel to the liposome surface for LG. This sequence-level information about the secondary structures and orientations was used to formulate interaction models of the three proteins at the membrane surface. This study demonstrates the validity of a combination of VUVCD and LD spectroscopy in conformational analyses of membrane-binding proteins, which are difficult targets for X-ray crystallography and nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Yasuyuki Maki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, 376-8515, Japan
| | - Hirofumi Namatame
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan
| | - Masaki Taniguchi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, 739-0046, Japan.,Department of Physical Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kunihiko Gekko
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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15
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MyelStones: the executive roles of myelin basic protein in myelin assembly and destabilization in multiple sclerosis. Biochem J 2015; 472:17-32. [DOI: 10.1042/bj20150710] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The classic isoforms of myelin basic protein (MBP, 14–21.5 kDa) are essential to formation of the multilamellar myelin sheath of the mammalian central nervous system (CNS). The predominant 18.5-kDa isoform links together the cytosolic surfaces of oligodendrocytes, but additionally participates in cytoskeletal turnover and membrane extension, Fyn-mediated signalling pathways, sequestration of phosphoinositides and maintenance of calcium homoeostasis. All MBP isoforms are intrinsically disordered proteins (IDPs) that interact via molecular recognition fragments (MoRFs), which thereby undergo local disorder-to-order transitions. Their conformations and associations are modulated by environment and by a dynamic barcode of post-translational modifications, particularly phosphorylation by mitogen-activated and other protein kinases and deimination [a hallmark of demyelination in multiple sclerosis (MS)]. The MBPs are thus to myelin what basic histones are to chromatin. Originally thought to be merely structural proteins forming an inert spool, histones are now known to be dynamic entities involved in epigenetic regulation and diseases such as cancer. Analogously, the MBPs are not mere adhesives of compact myelin, but active participants in oligodendrocyte proliferation and in membrane process extension and stabilization during myelinogenesis. A central segment of these proteins is pivotal in membrane-anchoring and SH3 domain (Src homology 3) interaction. We discuss in the present review advances in our understanding of conformational conversions of this classic basic protein upon membrane association, including new thermodynamic analyses of transitions into different structural ensembles and how a shift in the pattern of its post-translational modifications is associated with the pathogenesis and potentially onset of demyelination in MS.
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16
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Chukhlieb M, Raasakka A, Ruskamo S, Kursula P. The N-terminal cytoplasmic domain of neuregulin 1 type III is intrinsically disordered. Amino Acids 2015; 47:1567-77. [PMID: 25944317 DOI: 10.1007/s00726-015-1998-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Axonally expressed neuregulin 1 (NRG1) type III is a transmembrane protein involved in various neurodevelopmental processes, including myelination and Schwann cell migration. NRG1 type III has one transmembrane domain and a C-terminal extracellular segment, which contains an epidermal growth factor homology domain. Little is known, however, about the intracellular N terminus of NRG1 type III, and the structure-function relationships of this cytoplasmic domain have remained uncharacterized. In the current study, we carried out the first structural and functional studies on the NRG1 type III cytoplasmic domain. Based on sequence analyses, the domain is predicted to be largely disordered, while a strictly conserved region close to the transmembrane segment may contain helical structure and bind metal ions. As shown by synchrotron radiation circular dichroism spectroscopy, the recombinant NRG1 type III cytoplasmic domain was disordered in solution, but it was able to fold partially into a helical structure, especially when both metals and membrane-mimicking compounds were present. NRG1 cytoplasmic tail binding to metals was further confirmed by calorimetry. These results suggest that the juxtamembrane segment of the NRG1 type III cytoplasmic domain may fold onto the membrane surface upon metal binding. Using synchrotron small-angle X-ray scattering, we further proved that the NRG1 cytoplasmic domain is intrinsically disordered, highly elongated, and behaves like a random polymer. Our work provides the first biochemical and biophysical data on the previously unexplored cytoplasmic domain of NRG1 type III, which will help elucidate the detailed structure-function relationships of this domain.
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Affiliation(s)
- Maryna Chukhlieb
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
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