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Uusitalo M, Klenow MB, Laulumaa S, Blakeley MP, Simonsen AC, Ruskamo S, Kursula P. Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants. FEBS J 2021; 288:6716-6735. [PMID: 34138518 DOI: 10.1111/febs.16079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022]
Abstract
Peripheral myelin protein 2 (P2) is a fatty acid-binding protein expressed in vertebrate peripheral nervous system myelin, as well as in human astrocytes. Suggested functions of P2 include membrane stacking and lipid transport. Mutations in the PMP2 gene, encoding P2, are associated with Charcot-Marie-Tooth disease (CMT). Recent studies have revealed three novel PMP2 mutations in CMT patients. To shed light on the structure and function of these P2 variants, we used X-ray and neutron crystallography, small-angle X-ray scattering, circular dichroism spectroscopy, computer simulations and lipid binding assays. The crystal and solution structures of the I50del, M114T and V115A variants of P2 showed minor differences to the wild-type protein, whereas their thermal stability was reduced. Vesicle aggregation assays revealed no change in membrane stacking characteristics, while the variants showed altered fatty acid binding. Time-lapse imaging of lipid bilayers indicated formation of double-membrane structures induced by P2, which could be related to its function in stacking of two myelin membrane surfaces in vivo. In order to better understand the links between structure, dynamics and function, the crystal structure of perdeuterated P2 was refined from room temperature data using neutrons and X-rays, and the results were compared to simulations and cryocooled crystal structures. Our data indicate similar properties for all known human P2 CMT variants; while crystal structures are nearly identical, thermal stability and function of CMT variants are impaired. Our data provide new insights into the structure-function relationships and dynamics of P2 in health and disease.
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Affiliation(s)
- Maiju Uusitalo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Martin Berg Klenow
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,European Spallation Source, Lund, Sweden
| | | | - Adam Cohen Simonsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,Department of Biomedicine, University of Bergen, Norway
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2
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Ruskamo S, Krokengen OC, Kowal J, Nieminen T, Lehtimäki M, Raasakka A, Dandey VP, Vattulainen I, Stahlberg H, Kursula P. Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice. J Biol Chem 2020; 295:8692-8705. [PMID: 32265298 DOI: 10.1074/jbc.ra120.013087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Oda C Krokengen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, 33014 Tampere, Finland
| | - Mari Lehtimäki
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Venkata P Dandey
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, 33014 Tampere, Finland; Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; Biocenter Oulu, University of Oulu, 90014 Oulu, Finland; Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
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Laulumaa S, Kursula P. Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites. Molecules 2019; 24:molecules24173044. [PMID: 31443388 PMCID: PMC6749445 DOI: 10.3390/molecules24173044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/28/2023] Open
Abstract
Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C–H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C–H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups, which break planarity rules. For example, in Src homology 3 (SH3) domains, a conserved bent aromatic residue is observed near the ligand binding site. Fatty acid binding protein (FABP) 3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, the deuteration of protein and/or solvent are promising variables in protein crystal optimization.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- European Spallation Source, 22100 Lund, Sweden
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
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Gavira JA, Conejero-Muriel M, Delgado-López JM. Seeding from silica-reinforced lysozyme crystals for neutron crystallography. Acta Crystallogr D Struct Biol 2018; 74:1200-1207. [PMID: 30605134 DOI: 10.1107/s2059798318016054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/13/2018] [Indexed: 11/10/2022] Open
Abstract
The fragility of protein crystals plays an important role in the final quality of the diffraction data and therefore that of the derived three-dimensional structural model. The growth of protein crystals in gels of various natures has been shown to overcome this problem, facilitating the manipulation of the crystals; this is probably owing, amongst other factors, to the incorporation of the gel fibres within the body of the crystal. In this study, lysozyme crystals were grown in silica gel at a wide range of concentrations of up to 22%(v/v) to quantitatively determine the amount of gel incorporated into the crystal structure by means of thermogravimetric analysis. The interaction between the silica fibres and the lysozyme molecules within the crystals was also investigated using Raman spectroscopy and the direct influence on the crystalline protein stability was analysed using differential scanning calorimetry. Finally, the benefits of the use of gel-grown crystals to overgrow protein crystals intended for neutron diffraction are highlighted.
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Affiliation(s)
- Jose A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida las Palmeras 4, 18100 Granada, Spain
| | - Mayte Conejero-Muriel
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida las Palmeras 4, 18100 Granada, Spain
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Sørensen TLM, Hjorth-Jensen SJ, Oksanen E, Andersen JL, Olesen C, Møller JV, Nissen P. Membrane-protein crystals for neutron diffraction. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1208-1218. [PMID: 30605135 DOI: 10.1107/s2059798318012561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/05/2018] [Indexed: 11/10/2022]
Abstract
Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1. The challenges encountered at the various steps in the process from crystal nucleation and growth to crystal mounting are explored, and it is demonstrated that NMX-compatible membrane-protein crystals can indeed be obtained.
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Affiliation(s)
- Thomas Lykke Møller Sørensen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Samuel John Hjorth-Jensen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Esko Oksanen
- European Spallation Source ERIC, PO Box 176, 22100 Lund, Sweden
| | | | - Claus Olesen
- Department of Biomedicine, Aarhus University, Ole Worn Alle 3, DK-8000 Aarhus C, Denmark
| | - Jesper Vuust Møller
- Department of Biomedicine, Aarhus University, Ole Worn Alle 3, DK-8000 Aarhus C, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics - DANDRITE, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
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Ruskamo S, Nieminen T, Kristiansen CK, Vatne GH, Baumann A, Hallin EI, Raasakka A, Joensuu P, Bergmann U, Vattulainen I, Kursula P. Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2. Sci Rep 2017; 7:6510. [PMID: 28747762 PMCID: PMC5529448 DOI: 10.1038/s41598-017-06781-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/16/2017] [Indexed: 02/06/2023] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is one of the most common inherited neuropathies. Recently, three CMT1-associated point mutations (I43N, T51P, and I52T) were discovered in the abundant peripheral myelin protein P2. These mutations trigger abnormal myelin structure, leading to reduced nerve conduction velocity, muscle weakness, and distal limb atrophy. P2 is a myelin-specific protein expressed by Schwann cells that binds to fatty acids and membranes, contributing to peripheral myelin lipid homeostasis. We studied the molecular basis of the P2 patient mutations. None of the CMT1-associated mutations alter the overall folding of P2 in the crystal state. P2 disease variants show increased aggregation tendency and remarkably reduced stability, T51P being most severe. In addition, P2 disease mutations affect protein dynamics. Both fatty acid binding by P2 and the kinetics of its membrane interactions are affected by the mutations. Experiments and simulations suggest opening of the β barrel in T51P, possibly representing a general mechanism in fatty acid-binding proteins. Our findings demonstrate that altered biophysical properties and functional dynamics of P2 may cause myelin defects in CMT1 patients. At the molecular level, a few malformed hydrogen bonds lead to structural instability and misregulation of conformational changes related to ligand exchange and membrane binding.
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Affiliation(s)
- Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Tuomo Nieminen
- Department of Physics, Tampere University of Technology, 33720, Tampere, Finland
| | | | - Guro H Vatne
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, 5021, Bergen, Norway
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Päivi Joensuu
- Department of Sustainable Chemistry, Technical Faculty, University of Oulu, 90570, Oulu, Finland
| | - Ulrich Bergmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90220, Oulu, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, 33720, Tampere, Finland
- Department of Physics, University of Helsinki, 00560, Helsinki, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland.
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway.
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7
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Yee AW, Blakeley MP, Moulin M, Haertlein M, Mitchell E, Forsyth VT. Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy. J Appl Crystallogr 2017; 50:660-664. [PMID: 28381984 PMCID: PMC5377354 DOI: 10.1107/s1600576717003624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/07/2017] [Indexed: 01/02/2023] Open
Abstract
The application of IR spectroscopy to the characterization and quality control of samples used in neutron crystallography is described. While neutron crystallography is a growing field, the limited availability of neutron beamtime means that there may be a delay between crystallogenesis and data collection. Since essentially all neutron crystallographic work is carried out using D2O-based solvent buffers, a particular concern for these experiments is the possibility of H2O back-exchange across reservoir or capillary sealants. This may limit the quality of neutron scattering length density maps and of the associated analysis. Given the expense of central facility beamtime and the effort that goes into the production of suitably sized (usually perdeuterated) crystals, a systematic method of exploiting IR spectroscopy for the analysis of back-exchange phenomena in the reservoirs used for crystal growth is valuable. Examples are given in which the characterization of D2O/H2O back-exchange in transthyretin crystals is described.
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Affiliation(s)
- Ai Woon Yee
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
| | - Michael Haertlein
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
| | - Edward Mitchell
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
- European Synchrotron Research Facility, 71 avenue des Martyrs, Grenoble 38043, France
| | - V. Trevor Forsyth
- Life Sciences Group, Institut Laue–Langevin, 71 avenue des Martyrs, Grenoble 38042, France
- Faculty of Natural Sciences, Keele University, Keele ST5 5BG, UK
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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