6 results on '"Oda C. Krokengen"'
Search Results
2. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data
- Author
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Oda C. Krokengen, Arne Raasakka, and Petri Kursula
- Subjects
Myelin ,Intrinsically disordered protein ,Membrane binding ,AlphaFold2 ,Small-angle X-ray scattering ,Circular dichroism spectroscopy ,Biology (General) ,QH301-705.5 ,Biochemistry ,QD415-436 - 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.
- Published
- 2023
- Full Text
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3. Neuropathy-related mutations alter the membrane binding properties of the human myelin protein P0 cytoplasmic tail.
- Author
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Arne Raasakka, Salla Ruskamo, Robert Barker, Oda C Krokengen, Guro H Vatne, Cecilie K Kristiansen, Erik I Hallin, Maximilian W A Skoda, Ulrich Bergmann, Hanna Wacklin-Knecht, Nykola C Jones, Søren V Hoffmann, and Petri Kursula
- Subjects
Medicine ,Science - Abstract
Schwann cells myelinate selected axons in the peripheral nervous system (PNS) and contribute to fast saltatory conduction via the formation of compact myelin, in which water is excluded from between tightly adhered lipid bilayers. Peripheral neuropathies, such as Charcot-Marie-Tooth disease (CMT) and Dejerine-Sottas syndrome (DSS), are incurable demyelinating conditions that result in pain, decrease in muscle mass, and functional impairment. Many Schwann cell proteins, which are directly involved in the stability of compact myelin or its development, are subject to mutations linked to these neuropathies. The most abundant PNS myelin protein is protein zero (P0); point mutations in this transmembrane protein cause CMT subtype 1B and DSS. P0 tethers apposing lipid bilayers together through its extracellular immunoglobulin-like domain. Additionally, P0 contains a cytoplasmic tail (P0ct), which is membrane-associated and contributes to the physical properties of the lipid membrane. Six CMT- and DSS-associated missense mutations have been reported in P0ct. We generated recombinant disease mutant variants of P0ct and characterized them using biophysical methods. Compared to wild-type P0ct, some mutants have negligible differences in function and folding, while others highlight functionally important amino acids within P0ct. For example, the D224Y variant of P0ct induced tight membrane multilayer stacking. Our results show a putative molecular basis for the hypermyelinating phenotype observed in patients with this particular mutation and provide overall information on the effects of disease-linked mutations in a flexible, membrane-binding protein segment. Using neutron reflectometry, we additionally show that P0ct embeds deep into a lipid bilayer, explaining the observed effects of P0ct on the physical properties of the membrane.
- Published
- 2019
- Full Text
- View/download PDF
4. The intrinsically disordered protein glue of myelin: Linking AlphaFold2 predictions to experimental data
- Author
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Oda C. Krokengen, Arne Raasakka, and Petri Kursula
- Abstract
Numerous human proteins are either partially or fully classified as intrinsically disordered proteins (IDPs). Due to their 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 ligands, which could be 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 known to be 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 previously published data related to solution structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the characterised membrane-binding sites on both proteins. We furthermore analyse the fits of the models to SAXS data from the same IDPs. Artificial intelligence-based models of IDPs appear to be able to provide detailed information on the ligand-bound state of these proteins, instead of the form dominating free in solution. We further discuss the implications of the predictions for normal mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
- Published
- 2022
5. Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice
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Ilpo Vattulainen, Arne Raasakka, Petri Kursula, Julia Kowal, Salla Ruskamo, Tuomo Nieminen, M. Lehtimaki, Venkata P. Dandey, Henning Stahlberg, Oda C. Krokengen, Tampere University, Research group: Biological Physics and Soft Matter, Research area: Computational Physics, Physics, and Department of Physics
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0301 basic medicine ,P2-PROTEIN ,116 Chemical sciences ,ACID-BINDING PROTEIN ,Gene mutation ,ADHESION ,Charcot-Marie-Tooth disease ,Biochemistry ,114 Physical sciences ,03 medical and health sciences ,Myelin ,membrane structure ,medicine ,PO PROTEIN ,SCATTERING ,membrane protein ,ddc:610 ,protein structure ,proteolipid ,Lipid bilayer ,Molecular Biology ,030102 biochemistry & molecular biology ,Chemistry ,Bilayer ,Peripheral membrane protein ,membrane bilayer ,Membrane structure ,LOCALIZATION ,Cell Biology ,molecular dynamics ,PHOSPHOLIPID-MEMBRANES ,3. Good health ,myelin ,030104 developmental biology ,medicine.anatomical_structure ,Membrane protein ,RESOLUTION ,Biophysics ,neuropathy ,FATTY-ACIDS ,CRYSTALLIZATION ,Membrane biophysics ,membrane biophysics - Abstract
Myelin protein P2 is a peripheral membrane protein of the fatty acid-binding protein family that functions in the formation and maintenance of the peripheral nerve myelin sheath. Several P2 gene mutations cause human Charcot-Marie-Tooth neuropathy, but the mature myelin sheath assembly mechanism is unclear. Here, cryo-EM of myelin-like proteolipid multilayers revealed an ordered three-dimensional (3D) lattice of P2 molecules between stacked lipid bilayers, visualizing supramolecular assembly at the myelin major dense line. The data disclosed that a single P2 layer is inserted between two bilayers in a tight intermembrane space of ∼3 nm, implying direct interactions between P2 and two membrane surfaces. X-ray diffraction from P2-stacked bicelle multilayers revealed lateral protein organization, and surface mutagenesis of P2 coupled with structure-function experiments revealed a role for both the portal region of P2 and its opposite face in membrane interactions. Atomistic molecular dynamics simulations of P2 on model membrane surfaces suggested that Arg-88 is critical for P2-membrane interactions, in addition to the helical lid domain. Negatively charged lipid headgroups stably anchored P2 on the myelin-like bilayer surface. Membrane binding may be accompanied by opening of the P2 β-barrel structure and ligand exchange with the apposing bilayer. Our results provide an unprecedented view into an ordered, multilayered biomolecular membrane system induced by the presence of a peripheral membrane protein from human myelin. This is an important step toward deciphering the 3D assembly of a mature myelin sheath at the molecular level. publishedVersion
- Published
- 2020
6. Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the beta barrel in fatty acid binding proteins
- Author
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Arne Raasakka, Erik I. Hallin, Petri Kursula, Marc F. Lensink, Anushik Safaryan, Salla Ruskamo, Oda C. Krokengen, Guillaume Brysbaert, Saara Laulumaa, Ilpo Vattulainen, Tuomo Nieminen, Department of Physics, Tampere University, Physics, University of Eastern Finland, Univ Oulu, Bioctr Oulu, Oulu, Finland, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Helsinki], Falculty of Science [Helsinki], University of Helsinki-University of Helsinki, Institut des Hautes Etudes Scientifiques (IHES), IHES, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki
- Subjects
0301 basic medicine ,Models, Molecular ,Membrane binding ,PREDICTION ,[SDV]Life Sciences [q-bio] ,Mutant ,Lipid Bilayers ,POINT MUTATIONS ,medicine.disease_cause ,Crystallography, X-Ray ,Myelin P2 Protein ,Protein Structure, Secondary ,0302 clinical medicine ,Structural Biology ,Mutant protein ,Charcot-Marie-Tooth Disease ,Fatty acid binding ,Protein stability ,Lipid bilayer ,lcsh:QH301-705.5 ,ComputingMilieux_MISCELLANEOUS ,Mutation ,Calorimetry, Differential Scanning ,Chemistry ,LIPID-MEMBRANES ,Fatty Acids ,FABPS ,DIFFERENT MECHANISMS ,Ligand (biochemistry) ,Myelin ,Research Article ,Phenylalanine ,Molecular Dynamics Simulation ,Molecular dynamics ,114 Physical sciences ,Fatty acid-binding protein ,PERIPHERAL NERVOUS-SYSTEM ,03 medical and health sciences ,medicine ,Humans ,Protein Unfolding ,UCSF-CHIMERA ,Crystal structure ,PHOSPHOLIPID-MEMBRANES ,SIMULATIONS ,030104 developmental biology ,lcsh:Biology (General) ,Structural biology ,RESOLUTION ,Biophysics ,1182 Biochemistry, cell and molecular biology ,030217 neurology & neurosurgery - Abstract
Background Myelin is a multilayered proteolipid sheath wrapped around selected axons in the nervous system. Its constituent proteins play major roles in forming of the highly regular membrane structure. P2 is a myelin-specific protein of the fatty acid binding protein (FABP) superfamily, which is able to stack lipid bilayers together, and it is a target for mutations in the human inherited neuropathy Charcot-Marie-Tooth disease. A conserved residue that has been proposed to participate in membrane and fatty acid binding and conformational changes in FABPs is Phe57. This residue is thought to be a gatekeeper for the opening of the portal region upon ligand entry and egress. Results We performed a structural characterization of the F57A mutant of human P2. The mutant protein was crystallized in three crystal forms, all of which showed changes in the portal region and helix α2. In addition, the behaviour of the mutant protein upon lipid bilayer binding suggested more unfolding than previously observed for wild-type P2. On the other hand, membrane binding rendered F57A heat-stable, similarly to wild-type P2. Atomistic molecular dynamics simulations showed opening of the side of the discontinuous β barrel, giving important indications on the mechanism of portal region opening and ligand entry into FABPs. The results suggest a central role for Phe57 in regulating the opening of the portal region in human P2 and other FABPs, and the F57A mutation disturbs dynamic cross-correlation networks in the portal region of P2. Conclusions Overall, the F57A variant presents similar properties to the P2 patient mutations recently linked to Charcot-Marie-Tooth disease. Our results identify Phe57 as a residue regulating conformational changes that may accompany membrane surface binding and ligand exchange in P2 and other FABPs. Electronic supplementary material The online version of this article (10.1186/s12900-018-0087-2) contains supplementary material, which is available to authorized users.
- Published
- 2018
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