1
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Matsuo T, Peters J. Sub-Nanosecond Dynamics of Pathologically Relevant Bio-Macromolecules Observed by Incoherent Neutron Scattering. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081259. [PMID: 36013438 PMCID: PMC9410404 DOI: 10.3390/life12081259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 01/22/2023]
Abstract
Incoherent neutron scattering (iNS) is one of the most powerful techniques to study the dynamical behavior of bio-macromolecules such as proteins and lipid molecules or whole cells. This technique has widely been used to elucidate the fundamental aspects of molecular motions that manifest in the bio-macromolecules in relation to their intrinsic molecular properties and biological functions. Furthermore, in the last decade, iNS studies focusing on a possible relationship between molecular dynamics and biological malfunctions, i.e., human diseases and disorders, have gained importance. In this review, we summarize recent iNS studies on pathologically relevant proteins and lipids and discuss how the findings are of importance to elucidate the molecular mechanisms of human diseases and disorders that each study targets. Since some diseases such as amyloidosis have become more relevant in the aging society, research in this field will continue to develop further and be more important in the current increasing trend for longevity worldwide.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai 319-1106, Ibaraki, Japan
- Dept. of Physics, Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
- Correspondence: (T.M.); (J.P.)
| | - Judith Peters
- Dept. of Physics, Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
- Correspondence: (T.M.); (J.P.)
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2
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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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3
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Matsuo T, De Francesco A, Peters J. Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering. Front Mol Biosci 2022; 8:812096. [PMID: 35111814 PMCID: PMC8801425 DOI: 10.3389/fmolb.2021.812096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Japan
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
| | - Alessio De Francesco
- Institut Laue-Langevin, Grenoble, France
- CNR-IOM and INSIDE@ILL C/O Operative Group in Grenoble (OGG), Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institut Universitaire de France, Paris, France
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
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4
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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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5
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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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6
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Laulumaa S, Koza MM, Seydel T, Kursula P, Natali F. A Quasielastic Neutron Scattering Investigation on the Molecular Self-Dynamics of Human Myelin Protein P2. J Phys Chem B 2019; 123:8178-8185. [PMID: 31483648 DOI: 10.1021/acs.jpcb.9b05320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human myelin protein P2 is a membrane binding protein believed to maintain correct lipid composition and organization in peripheral nerve myelin. Its function is related to its ability to stack membranes, and this function can be enhanced by the P38G mutation, whereby the overall protein structure does not change but the molecular dynamics increase. Mutations in P2 are linked to human peripheral neuropathy. Here, the dynamics of wild-type P2 and the P38G variant were studied using quasielastic neutron scattering on time scales from 10 ps to 1 ns at 300 K. The results suggest that the mutant protein dynamics are increased on both the fastest and the slowest measured time scales, by increasing the dynamics amplitude and/or the portion of atoms participating in the movement.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,European Spallation Source , Lund , Sweden
| | | | | | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,Department of Biomedicine , University of Bergen , Bergen , Norway
| | - Francesca Natali
- Institut Laue-Langevin , Grenoble , France.,CNR-IOM, OGG , Grenoble , France
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Barletta GP, Franchini G, Corsico B, Fernandez-Alberti S. Fatty Acid and Retinol-Binding Protein: Unusual Protein Conformational and Cavity Changes Dictated by Ligand Fluctuations. J Chem Inf Model 2019; 59:3545-3555. [PMID: 31365253 DOI: 10.1021/acs.jcim.9b00364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipid-binding proteins (LBPs) are soluble proteins responsible for the uptake, transport, and storage of a large variety of hydrophobic lipophilic molecules including fatty acids, steroids, and other lipids in the cellular environment. Among the LBPs, fatty acid binding proteins (FABPs) present preferential binding affinities for long-chain fatty acids. While most of FABPs in vertebrates and invertebrates present similar β-barrel structures with ligands accommodated in their central cavity, parasitic nematode worms exhibit additional unusual α-helix rich fatty acid- and retinol-binding proteins (FAR). Herein, we report the comparison of extended molecular dynamics (MD) simulations performed on the ligand-free and palmitic acid-bond states of the Necator americanus FAR-1 (Na-FAR-1) with respect to other classical β-barrel FABPs. Principal component analysis (PCA) has been used to identify the different conformations adopted by each system during MD simulations. The α-helix fold encompasses a complex internal ligand-binding cavity with a remarkable conformational plasticity that allows reversible switching between distinct states in the holo-Na-FAR-1. The cavity can change up to one-third of its size affected by conformational changes of the protein-ligand complex. Besides, the ligand inside the cavity is not fixed but experiences large conformational changes between bent and stretched conformations. These changes in the ligand conformation follow changes in the cavity size dictated by the transient protein conformation. On the contrary, protein-ligand complex in β-barrel FABPs fluctuates around a unique conformation. The significantly more flexible holo-Na-FAR-1 ligand-cavity explains its larger ligand multiplicity respect to β-barrel FABPs.
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Affiliation(s)
- G P Barletta
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352 , B1876BXD Bernal , Argentina
| | - G Franchini
- Instituto de Investigaciones Bioquímicas de La Plata , CONICET-UNLP, Facultad de Ciencias Médicas , calles 60 y 120 s/n , 1900 La Plata , Argentina
| | - B Corsico
- Instituto de Investigaciones Bioquímicas de La Plata , CONICET-UNLP, Facultad de Ciencias Médicas , calles 60 y 120 s/n , 1900 La Plata , Argentina
| | - S Fernandez-Alberti
- Universidad Nacional de Quilmes/CONICET , Roque Saenz Peña 352 , B1876BXD Bernal , Argentina
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8
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Laulumaa S, Nieminen T, Raasakka A, Krokengen OC, Safaryan A, Hallin EI, Brysbaert G, Lensink MF, Ruskamo S, Vattulainen I, Kursula P. Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins. BMC STRUCTURAL BIOLOGY 2018; 18:8. [PMID: 29940944 PMCID: PMC6020228 DOI: 10.1186/s12900-018-0087-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/13/2018] [Indexed: 02/04/2023]
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.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,European Spallation Source (ESS), Lund, Sweden
| | - Tuomo Nieminen
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Oda C Krokengen
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Guillaume Brysbaert
- Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, CNRS UMR8576 UGSF, F-59000, Lille, France
| | - Marc F Lensink
- Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, CNRS UMR8576 UGSF, F-59000, Lille, France
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland.,Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland. .,Department of Biomedicine, University of Bergen, Bergen, Norway.
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9
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Matsuo T, Tominaga T, Kono F, Shibata K, Fujiwara S. Modulation of the picosecond dynamics of troponin by the cardiomyopathy-causing mutation K247R of troponin T observed by quasielastic neutron scattering. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1781-1789. [PMID: 28923663 DOI: 10.1016/j.bbapap.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/18/2017] [Accepted: 09/14/2017] [Indexed: 11/16/2022]
Abstract
Troponin (Tn), consisting of three subunits (TnC, TnI, and TnT), regulates cardiac muscle contraction in a Ca2+-dependent manner. Various point mutations of human cardiac Tn are known to cause familial hypertrophic cardiomyopathy due to aberration of the regulatory function. In this study, we investigated the effects of one of these mutations, K247R of TnT, on the picosecond dynamics of the Tn core domain (Tn-CD), consisting of TnC, TnI and TnT2 (183-288 residues of TnT), by carrying out the quasielastic neutron scattering measurements on the reconstituted Tn-CD containing either the wild-type TnT2 (wtTn-CD) or the mutant TnT2 (K247R-Tn-CD) in the absence and presence of Ca2+. It was found that Ca2+-binding to the wtTn-CD decreases the residence time of atomic motions in the Tn-CD with slight changes in amplitudes, suggesting that the regulatory function mainly requires modulation of frequency of atomic motions. On the other hand, the K247R-Tn-CD shows different dynamic behavior from that of the wtTn-CD both in the absence and presence of Ca2+. In particular, the K247R-Tn-CD exhibits a larger amplitude than the wtTn-CD in the presence of Ca2+, suggesting that the mutant can explore larger conformational space than the wild-type. This increased flexibility should be relevant to the functional aberration of this mutant.
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Affiliation(s)
- Tatsuhito Matsuo
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Tokai, Ibaraki 319-1106, Japan
| | - Fumiaki Kono
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Kaoru Shibata
- Neutron Science Section, J-PARC Center, Tokai, Ibaraki 319-1195, Japan
| | - Satoru Fujiwara
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan.
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10
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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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11
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Raasakka A, Ruskamo S, Kowal J, Barker R, Baumann A, Martel A, Tuusa J, Myllykoski M, Bürck J, Ulrich AS, Stahlberg H, Kursula P. Membrane Association Landscape of Myelin Basic Protein Portrays Formation of the Myelin Major Dense Line. Sci Rep 2017; 7:4974. [PMID: 28694532 PMCID: PMC5504075 DOI: 10.1038/s41598-017-05364-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/26/2017] [Indexed: 01/06/2023] Open
Abstract
Compact myelin comprises most of the dry weight of myelin, and its insulative nature is the basis for saltatory conduction of nerve impulses. The major dense line (MDL) is a 3-nm compartment between two cytoplasmic leaflets of stacked myelin membranes, mostly occupied by a myelin basic protein (MBP) phase. MBP is an abundant myelin protein involved in demyelinating diseases, such as multiple sclerosis. The association of MBP with lipid membranes has been studied for decades, but the MBP-driven formation of the MDL remains elusive at the biomolecular level. We employed complementary biophysical methods, including atomic force microscopy, cryo-electron microscopy, and neutron scattering, to investigate the formation of membrane stacks all the way from MBP binding onto a single membrane leaflet to the organisation of a stable MDL. Our results support the formation of an amorphous protein phase of MBP between two membrane bilayers and provide a molecular model for MDL formation during myelination, which is of importance when understanding myelin assembly and demyelinating conditions.
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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
| | - Robert Barker
- School of Physical Sciences, University of Kent, Canterbury, Kent, United Kingdom
- Institut Laue-Langevin (ILL), Grenoble, France
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Anne Martel
- Institut Laue-Langevin (ILL), Grenoble, France
| | - Jussi Tuusa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - 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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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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Stadler AM, Knieps-Grünhagen E, Bocola M, Lohstroh W, Zamponi M, Krauss U. Photoactivation Reduces Side-Chain Dynamics of a LOV Photoreceptor. Biophys J 2016; 110:1064-74. [PMID: 26958884 DOI: 10.1016/j.bpj.2016.01.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/08/2016] [Accepted: 01/20/2016] [Indexed: 11/17/2022] Open
Abstract
We used neutron-scattering experiments to probe the conformational dynamics of the light, oxygen, voltage (LOV) photoreceptor PpSB1-LOV from Pseudomonas putida in both the dark and light states. Global protein diffusion and internal macromolecular dynamics were measured using incoherent neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond timescales. Global protein diffusion of PpSB1-LOV is not influenced by photoactivation. Observation-time-dependent global diffusion coefficients were found, which converge on the nanosecond timescale toward diffusion coefficients determined by dynamic light scattering. Mean-square displacements of localized internal motions and effective force constants, <k'>, describing the resilience of the proteins were determined on the respective timescales. Photoactivation significantly modifies the flexibility and the resilience of PpSB1-LOV. On the fast, picosecond timescale, small changes in the mean-square displacement and <k'> are observed, which are enhanced on the slower, nanosecond timescale. Photoactivation results in a slightly larger resilience of the photoreceptor on the fast, picosecond timescale, whereas in the nanosecond range, a significantly less resilient structure of the light-state protein is observed. For a residue-resolved interpretation of the experimental neutron-scattering data, we analyzed molecular dynamics simulations of the PpSB1-LOV X-ray structure. Based on these data, it is tempting to speculate that light-induced changes in the protein result in altered side-chain mobility mostly for residues on the protruding Jα helix and on the LOV-LOV dimer interface. Our results provide strong experimental evidence that side-chain dynamics play a crucial role in photoactivation and signaling of PpSB1-LOV via modulation of conformational entropy.
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Affiliation(s)
- Andreas M Stadler
- Jülich Centre for Neutron Science (JCNS) and Institute for Complex Systems (ICS), Forschungszentrum Jülich, Jülich, Germany.
| | - Esther Knieps-Grünhagen
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Marco Bocola
- Chair of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Wiebke Lohstroh
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Garching, Germany
| | - Michaela Zamponi
- Jülich Centre for Neutron Science (JCNS), Outstation at MLZ, Forschungszentrum Jülich, Garching, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
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14
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Laulumaa S, Blakeley MP, Raasakka A, Moulin M, Härtlein M, Kursula P. Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2. Acta Crystallogr F Struct Biol Commun 2015; 71:1391-5. [PMID: 26527266 PMCID: PMC4631588 DOI: 10.1107/s2053230x15017902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/24/2015] [Indexed: 11/11/2022] Open
Abstract
The molecular details of the formation of the myelin sheath, a multilayered membrane in the nervous system, are to a large extent unknown. P2 is a peripheral membrane protein from peripheral nervous system myelin, which is believed to play a role in this process. X-ray crystallographic studies and complementary experiments have provided information on the structure-function relationships in P2. In this study, a fully deuterated sample of human P2 was produced. Crystals that were large enough for neutron diffraction were grown by a ten-month procedure of feeding, and neutron diffraction data were collected to a resolution of 2.4 Å from a crystal of 0.09 mm(3) in volume. The neutron crystal structure will allow the positions of H atoms in P2 and its fatty-acid ligand to be visualized, as well as shedding light on the fine details of the hydrogen-bonding networks within the P2 ligand-binding cavity.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- European Spallation Source, Lund, Sweden
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Härtlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
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