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Raasakka A, Kursula P. Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease. Cells 2020; 9:cells9020470. [PMID: 32085570 PMCID: PMC7072810 DOI: 10.3390/cells9020470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023] Open
Abstract
Myelin ensheathes selected axonal segments within the nervous system, resulting primarily in nerve impulse acceleration, as well as mechanical and trophic support for neurons. In the central and peripheral nervous systems, various proteins that contribute to the formation and stability of myelin are present, which also harbor pathophysiological roles in myelin disease. Many myelin proteins have common attributes, including small size, hydrophobic segments, multifunctionality, longevity, and regions of intrinsic disorder. With recent advances in protein biophysical characterization and bioinformatics, it has become evident that intrinsically disordered proteins (IDPs) are abundant in myelin, and their flexible nature enables multifunctionality. Here, we review known myelin IDPs, their conservation, molecular characteristics and functions, and their disease relevance, along with open questions and speculations. We place emphasis on classifying the molecular details of IDPs in myelin, and we correlate these with their various functions, including susceptibility to post-translational modifications, function in protein–protein and protein–membrane interactions, as well as their role as extended entropic chains. We discuss how myelin pathology can relate to IDPs and which molecular factors are potentially involved.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway;
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway;
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Aapistie 7A, FI-90220 Oulu, Finland
- Correspondence:
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Pinkaew D, Chattopadhyay A, King MD, Chunhacha P, Liu Z, Stevenson HL, Chen Y, Sinthujaroen P, McDougal OM, Fujise K. Fortilin binds IRE1α and prevents ER stress from signaling apoptotic cell death. Nat Commun 2017; 8:18. [PMID: 28550308 PMCID: PMC5446404 DOI: 10.1038/s41467-017-00029-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/05/2017] [Indexed: 12/19/2022] Open
Abstract
The endoplasmic reticulum, the cytoplasmic organelle that matures a massive amount of nascent secretory polypeptides, is particularly sensitive to stress. Endoplasmic reticulum stress causes unfolded proteins to populate the organelle, eliciting the unfolded protein response. During the unfolded protein response, GRP78—an endoplasmic reticulum master stress regulator—detaches from three endoplasmic reticulum stress sensors (IRE1α, PERK, and ATF6) and allows them to activate the apoptotic signaling pathway. Fortilin, a pro-survival molecule, is known to inhibit apoptosis by binding and inhibiting p53, but its role in endoplasmic reticulum stress-induced apoptosis remains unknown. Here, we report that fortilin directly interacts with the cytoplasmic domain of IRE1α, inhibits both kinase and endoribonuclease (RNase) activities of the stress sensor, and protects cells against apoptotic cell death at both cellular and whole animal levels. Our data support a role of fortilin in the unfolded protein response and its potential participation in human diseases caused by unfolded protein response. IRE1α is an ER stress sensor, whose activity induces apoptosis. Here, the authors report that fortilin, a pro-survival factor, with yet unknown roles in ER stress, interacts with active IRE1α, inhibits both its kinase end RNase activities, and protects cells from apoptosis both in vitro and in vivo.
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Affiliation(s)
- Decha Pinkaew
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Abhijnan Chattopadhyay
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Matthew D King
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho, 83725, USA
| | - Preedakorn Chunhacha
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Zhihe Liu
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Heather L Stevenson
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA.,The Institute of Translational Sciences, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Yanjie Chen
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Patuma Sinthujaroen
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA
| | - Owen M McDougal
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho, 83725, USA
| | - Ken Fujise
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA. .,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA. .,The Institute of Translational Sciences, University of Texas Medical Branch at Galveston, Galveston, Texas, 77555, USA.
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3
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Cheli VT, Santiago González DA, Spreuer V, Handley V, Campagnoni AT, Paez PM. Golli Myelin Basic Proteins Modulate Voltage-Operated Ca(++) Influx and Development in Cortical and Hippocampal Neurons. Mol Neurobiol 2015; 53:5749-71. [PMID: 26497031 DOI: 10.1007/s12035-015-9499-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 10/19/2015] [Indexed: 12/14/2022]
Abstract
The golli proteins, products of the myelin basic protein gene, are widely expressed in oligodendrocyte progenitor cells and neurons during the postnatal development of the brain. While golli appears to be important for oligodendrocyte migration and differentiation, its function in neuronal development is completely unknown. We have found that golli proteins function as new and novel modulators of voltage-operated Ca(++) channels (VOCCs) in neurons. In vitro, golli knock-out (KO) neurons exhibit decreased Ca(++) influx after plasma membrane depolarization and a substantial maturational delay. Increased expression of golli proteins enhances L-type Ca(++) entry and processes outgrowth in cortical neurons, and pharmacological activation of L-type Ca(++) channels stimulates maturation and prevents cell death in golli-KO neurons. In situ, Ca(++) influx mediated by L-type VOCCs was significantly decreased in cortical and hippocampal neurons of the golli-KO brain. These Ca(++) alterations affect cortical and hippocampal development and the proliferation and survival of neural progenitor cells during the postnatal development of the golli-KO brain. The CA1/3 sections and the dentate gyrus of the hippocampus were reduced in the golli-KO mice as well as the density of dendrites in the somatosensory cortex. Furthermore, the golli-KO mice display abnormal behavior including deficits in episodic memory and reduced anxiety. Because of the expression of the golli proteins within neurons in learning and memory centers of the brain, this work has profound implication in neurodegenerative diseases and neurological disorders.
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Affiliation(s)
- V T Cheli
- Hunter James Kelly Research Institute, Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, SUNY, University at Buffalo, NYS Center of Excellence, 701 Ellicott St., Buffalo, NY, 14203, USA
| | - D A Santiago González
- Hunter James Kelly Research Institute, Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, SUNY, University at Buffalo, NYS Center of Excellence, 701 Ellicott St., Buffalo, NY, 14203, USA
| | - V Spreuer
- Hunter James Kelly Research Institute, Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, SUNY, University at Buffalo, NYS Center of Excellence, 701 Ellicott St., Buffalo, NY, 14203, USA
| | - V Handley
- Semel Institute for Neuroscience and Human Behavior, Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Neuroscience Research Building, 635 Charles Young Drive, Los Angeles, CA, 90095, USA
| | - A T Campagnoni
- Semel Institute for Neuroscience and Human Behavior, Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, UCLA, Neuroscience Research Building, 635 Charles Young Drive, Los Angeles, CA, 90095, USA
| | - P M Paez
- Hunter James Kelly Research Institute, Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, SUNY, University at Buffalo, NYS Center of Excellence, 701 Ellicott St., Buffalo, NY, 14203, USA.
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Alonso S, Bär M. Modeling domain formation of MARCKS and protein kinase C at cellular membranes. ACTA ACUST UNITED AC 2014. [DOI: 10.1140/epjnbp14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Structured functional domains of myelin basic protein: cross talk between actin polymerization and Ca(2+)-dependent calmodulin interaction. Biophys J 2011; 101:1248-56. [PMID: 21889463 DOI: 10.1016/j.bpj.2011.07.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 07/15/2011] [Accepted: 07/22/2011] [Indexed: 11/22/2022] Open
Abstract
The 18.5-kDa myelin basic protein (MBP), the most abundant isoform in human adult myelin, is a multifunctional, intrinsically disordered protein that maintains compact assembly of the sheath. Solution NMR spectroscopy and a hydrophobic moment analysis of MBP's amino-acid sequence have previously revealed three regions with high propensity to form strongly amphipathic α-helices. These regions, located in the central, N- and C-terminal parts of the protein, have been shown to play a role in the interactions of MBP with cytoskeletal proteins, Src homology 3-domain-containing proteins, Ca(2+)-activated calmodulin (Ca(2+)-CaM), and myelin-mimetic membrane bilayers. Here, we have further characterized the structure-function relationship of these three domains. We constructed three recombinant peptides derived from the 18.5-kDa murine MBP: (A22-K56), (S72-S107), and (S133-S159) (which are denoted α1, α2, and α3, respectively). We used a variety of biophysical methods (circular dichroism spectroscopy, isothermal titration calorimetry, transmission electron microscopy, fluorimetry, and solution NMR spectroscopy and chemical shift index analysis) to characterize the interactions of these peptides with actin and Ca(2+)-CaM. Our results show that all three peptides can adopt α-helical structure inherently even in aqueous solution. Both α1- and α3-peptides showed strong binding with Ca(2+)-CaM, and both adopted an α-helical conformation upon interaction, but the binding of the α3-peptide appeared to be more dynamic. Only the α1-peptide exhibited actin polymerization and bundling activity, and the addition of Ca(2+)-CaM resulted in depolymerization of actin that had been polymerized by α1. The results of this study proved that there is an N-terminal binding domain in MBP for Ca(2+)-CaM (in addition to the primary site located in the C-terminus), and that it is sufficient for CaM-induced actin depolymerization. These three domains of MBP represent molecular recognition fragments with multiple roles in both membrane- and protein-association.
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The multiple roles of myelin protein genes during the development of the oligodendrocyte. ASN Neuro 2010; 2:e00027. [PMID: 20017732 PMCID: PMC2814326 DOI: 10.1042/an20090051] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 12/14/2009] [Accepted: 12/17/2009] [Indexed: 11/22/2022] Open
Abstract
It has become clear that the products of several of the earliest identified myelin protein genes perform functions that extend beyond the myelin sheath. Interestingly, these myelin proteins, which comprise proteolipid protein, 2′,3′-cyclic nucleotide 3′-phosphodiesterase and the classic and golli MBPs (myelin basic proteins), play important roles during different stages of oligodendroglial development. These non-myelin-related functions are varied and include roles in the regulation of process outgrowth, migration, RNA transport, oligodendrocyte survival and ion channel modulation. However, despite the wide variety of cellular functions performed by the different myelin genes, the route by which they achieve these many functions seems to converge upon a common mechanism involving Ca2+ regulation, cytoskeletal rearrangements and signal transduction. In the present review, the newly emerging functions of these myelin proteins will be described, and these will then be discussed in the context of their contribution to oligodendroglial development.
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7
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Rao KP, Vani G, Kumar K, Sinha AK. Rhythmic expression of mitogen activated protein kinase activity in rice. Mol Cells 2009; 28:417-22. [PMID: 19855939 DOI: 10.1007/s10059-009-0137-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 08/12/2009] [Accepted: 08/26/2009] [Indexed: 10/20/2022] Open
Abstract
Mitogen activated protein kinase (MAPK) are known to get activated during various stress signals and transduce the message from the cell membrane to the nucleus for appropriate cellular reorganization. Though, a certain basal activity of MAPK is often observed in the control plants. Prolonged exposure of rice plants to lowered or elevated temperature exhibited a rhythm in the activation of MAPKs. We analyzed existence of a possible endogenous rhythm in the activity of MAPKs in rice plants. The plants growing at constant temperature entrained in 16/8 h day-night cycle showed diurnal rhythm in activity. When the activation of MAPK was tested under continuous conditions by shifting plants to continuous darkness for a period of 72 h, the periodic rhythm persisted and followed a circadian pattern. Analysis of the transcripts of group A, B and C members of MAPKs under above conditions by quantitative real time PCR revealed that the members of group C exhibit periodic rhythm. Our data indicates that the MAP kinase activity in rice follows rhythmic expression in a circadian manner.
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Majava V, Wang C, Myllykoski M, Kangas SM, Kang SU, Hayashi N, Baumgärtel P, Heape AM, Lubec G, Kursula P. Structural analysis of the complex between calmodulin and full-length myelin basic protein, an intrinsically disordered molecule. Amino Acids 2009; 39:59-71. [PMID: 19855925 DOI: 10.1007/s00726-009-0364-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 10/07/2009] [Indexed: 11/28/2022]
Abstract
Myelin basic protein (MBP) is present between the cytoplasmic leaflets of the compact myelin membrane in both the peripheral and central nervous systems, and characterized to be intrinsically disordered in solution. One of the best-characterized protein ligands for MBP is calmodulin (CaM), a highly acidic calcium sensor. We pulled down MBP from human brain white matter as the major calcium-dependent CaM-binding protein. We then used full-length brain MBP, and a peptide from rodent MBP, to structurally characterize the MBP-CaM complex in solution by small-angle X-ray scattering, NMR spectroscopy, synchrotron radiation circular dichroism spectroscopy, and size exclusion chromatography. We determined 3D structures for the full-length protein-protein complex at different stoichiometries and detect ligand-induced folding of MBP. We also obtained thermodynamic data for the two CaM-binding sites of MBP, indicating that CaM does not collapse upon binding to MBP, and show that CaM and MBP colocalize in myelin sheaths. In addition, we analyzed the post-translational modifications of rat brain MBP, identifying a novel MBP modification, glucosylation. Our results provide a detailed picture of the MBP-CaM interaction, including a 3D model of the complex between full-length proteins.
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Affiliation(s)
- Viivi Majava
- Department of Biochemistry, University of Oulu, PO Box 3000, 90014, Oulu, Finland
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Musse AA, Gao W, Rangaraj G, Boggs JM, Harauz G. Myelin basic protein co-distributes with other PI(4,5)P2-sequestering proteins in Triton X-100 detergent-resistant membrane microdomains. Neurosci Lett 2009; 450:32-6. [DOI: 10.1016/j.neulet.2008.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 11/06/2008] [Accepted: 11/09/2008] [Indexed: 10/21/2022]
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Musse AA, Gao W, Homchaudhuri L, Boggs JM, Harauz G. Myelin basic protein as a "PI(4,5)P2-modulin": a new biological function for a major central nervous system protein. Biochemistry 2008; 47:10372-82. [PMID: 18767817 DOI: 10.1021/bi801302b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 18.5 kDa isoform of myelin basic protein (MBP) is multifunctional and has previously been shown to have structural and phenomenological similarities with domains of other membrane- and cytoskeleton-associated proteins such as MARCKS (myristoylated alanine-rich C kinase substrate). Here, we have investigated whether 18.5 kDa MBP can sequester phosphatidylinositol-(4,5)-bis-phosphate (PI(4,5)P 2) in membranes, like MARCKS and other "PIPmodulins" do. Using fluorescence-quenching and electron paramagnetic resonance (EPR) spectroscopy, and model membranes containing BODIPY-FL- or proxyl-labeled PI(4,5)P 2, respectively, we have demonstrated that MBP laterally sequesters PI(4,5)P 2. The MBP-PI(4,5)P 2 interactions are electrostatic, partially cholesterol-dependent, and sensitive to phosphorylation, deimination, and Ca (2+)-CaM binding. Confocal microscopy of cultured oligodendrocytes also revealed patched colocalization of MBP and PI(4,5)P 2, indicating the spatial clustering of PI(4,5)P 2 in the plasma membrane. On the basis of these findings as well as the overwhelming convergence of functional properties, modifying enzymes, and interaction partners, we propose that MBP is mechanistically related to GAP-43, MARCKS, and CAP-23. During myelinogenesis, it may mediate calcium and phosphorylation-sensitive plasma membrane availability of PI(4,5)P 2. This regulation of PI(4,5)P 2 availability at the cell cortex may be coupled to the elaboration and outgrowth of the membranous cellular processes by oligodendrocytes.
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Affiliation(s)
- Abdiwahab A Musse
- Department of Molecular and Cellular Biology and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
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Bamm VV, Ahmed MAM, Ladizhansky V, Harauz G. Purification and spectroscopic characterization of the recombinant BG21 isoform of murine golli myelin basic protein. J Neurosci Res 2007; 85:272-84. [PMID: 17131428 DOI: 10.1002/jnr.21129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A recombinant form of the murine Golli-myelin basic protein (MBP) isoform BG21 (rmBG21) has been expressed in E. coli, and isolated to 96% purity via metal chelation chromatography. Characteristic yields were 6-8 mg protein per liter of culture in either minimal M9 or standard Luria-Bertani media. Circular dichroism spectroscopy showed that rmBG21 had a large proportion of random coil in aqueous solution, but gained alpha-helix in the presence of monosialoganglioside G(M1) and PI(4)P, as well as in the membrane-mimetic solvent trifluoroethanol. Bioinformatics analyses of the amino acid sequence of rmBG21 predicted an N-terminal calmodulin (CaM)-binding site. It was determined by fluorescence spectroscopy and dynamic light scattering that rmBG21 and CaM interacted weakly in a 1:1 ratio in a Ca(2+)-dependent manner. Solution NMR spectra of uniformly [(13)C(15)N]-labeled protein in aqueous buffer were consistent with it being an extended protein; spectral quality was independent of temperature. Thus, like "classic" MBP and the Golli-MBP isoform J37, rmBG21 is intrinsically disordered, implying multi functionality, and that its conformation depends on its environment and bound ligands.
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Affiliation(s)
- Vladimir V Bamm
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
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12
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Fitzner D, Schneider A, Kippert A, Möbius W, Willig KI, Hell SW, Bunt G, Gaus K, Simons M. Myelin basic protein-dependent plasma membrane reorganization in the formation of myelin. EMBO J 2006; 25:5037-48. [PMID: 17036049 PMCID: PMC1630406 DOI: 10.1038/sj.emboj.7601376] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 09/11/2006] [Indexed: 11/09/2022] Open
Abstract
During vertebrate development, oligodendrocytes wrap their plasma membrane around axons to produce myelin, a specialized membrane highly enriched in galactosylceramide (GalC) and cholesterol. Here, we studied the formation of myelin membrane sheets in a neuron-glia co-culture system. We applied different microscopy techniques to visualize lipid packing and dynamics in the oligodendroglial plasma membrane. We used the fluorescent dye Laurdan to examine the lipid order with two-photon microscopy and observed that neurons induce a dramatic lipid condensation of the oligodendroglial membrane. On a nanoscale resolution, using stimulated emission depletion and fluorescence resonance energy transfer microscopy, we demonstrated a neuronal-dependent clustering of GalC in oligodendrocytes. Most importantly these changes in lipid organization of the oligodendroglial plasma membrane were not observed in shiverer mice that do not express the myelin basic protein. Our data demonstrate that neurons induce the condensation of the myelin-forming bilayer in oligodendrocytes and that MBP is involved in this process of plasma membrane rearrangement. We propose that this mechanism is essential for myelin to perform its insulating function during nerve conduction.
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Affiliation(s)
- Dirk Fitzner
- Centre for Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Anja Schneider
- Centre for Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Angelika Kippert
- Centre for Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Wiebke Möbius
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Katrin I Willig
- Department of NanoBiophotonics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Gertrude Bunt
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - Katharina Gaus
- Centre for Vascular Research at the School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mikael Simons
- Centre for Biochemistry and Molecular Cell Biology, University of Göttingen, Göttingen, Germany
- Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
- Centre for Biochemistry and Molecular Cell Biology, Max-Planck Institute for Experimental Medicine, University of Göttingen, Hermann Rein Str. 3, 37073 Göttingen, Germany. Tel.: +49 551 3899533; Fax: +49 551 3899201; E-mail:
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Harauz G, Musse AA. A Tale of Two Citrullines—Structural and Functional Aspects of Myelin Basic Protein Deimination in Health and Disease. Neurochem Res 2006; 32:137-58. [PMID: 16900293 DOI: 10.1007/s11064-006-9108-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2006] [Indexed: 02/03/2023]
Abstract
Myelin basic protein (MBP) binds to negatively charged lipids on the cytosolic surface of oligodendrocyte membranes and is responsible for adhesion of these surfaces in the multilayered myelin sheath. The pattern of extensive post-translational modifications of MBP is dynamic during normal central nervous system (CNS) development and during myelin degeneration in multiple sclerosis (MS), affecting its interactions with the myelin membranes and with other molecules. In particular, the degree of deimination (or citrullination) of MBP is correlated with the severity of MS, and may represent a primary defect that precedes neurodegeneration due to autoimmune attack. That the degree of MBP deimination is also high in early CNS development indicates that this modification plays major physiological roles in myelin assembly. In this review, we describe the structural and functional consequences of MBP deimination in healthy and diseased myelin.
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Affiliation(s)
- George Harauz
- Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
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Mishra NS, Tuteja R, Tuteja N. Signaling through MAP kinase networks in plants. Arch Biochem Biophys 2006; 452:55-68. [PMID: 16806044 DOI: 10.1016/j.abb.2006.05.001] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 05/04/2006] [Accepted: 05/05/2006] [Indexed: 01/01/2023]
Abstract
Protein phosphorylation is the most important mechanism for controlling many fundamental cellular processes in all living organisms including plants. A specific class of serine/threonine protein kinases, the mitogen-activated protein kinases (MAP kinases) play a central role in the transduction of various extra- and intracellular signals and are conserved throughout eukaryotes. These generally function via a cascade of networks, where MAP kinase (MAPK) is phosphorylated and activated by MAPK kinase (MAPKK), which itself is activated by MAPKK kinase (MAPKKK). Signaling through MAP kinase cascade can lead to cellular responses including cell division, differentiation as well as response to various stresses. In plants, MAP kinases are represented by multigene families and are organized into a complex network for efficient transmission of specific stimuli. Putative plant MAP kinase cascades have been postulated based on experimental analysis of in vitro interactions between specific MAP kinase components. These cascades have been tested in planta following expression of epitope-tagged kinases in protoplasts. It is known that signaling for cell division and stress responses in plants are mediated through MAP kinases and even auxin, ABA and possibly ethylene and cytokinin also utilize a MAP kinase pathway. Most of the biotic (pathogens and pathogen-derived elicitors) including wounding and abiotic stresses (salinity, cold, drought, and oxidative) can induce defense responses in plants through MAP kinase pathways. In this article we have covered the historical background, biochemical assay, activation/inactivation, and targets of MAP kinases with emphasis on plant MAP kinases and the responses regulated by them. The cross-talk between plant MAP kinases is also discussed to bring out the complexity within this three-component module.
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Affiliation(s)
- Neeti Sanan Mishra
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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15
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Polverini E, Boggs JM, Bates IR, Harauz G, Cavatorta P. Electron paramagnetic resonance spectroscopy and molecular modelling of the interaction of myelin basic protein (MBP) with calmodulin (CaM)—diversity and conformational adaptability of MBP CaM-targets. J Struct Biol 2004; 148:353-69. [PMID: 15522783 DOI: 10.1016/j.jsb.2004.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 07/30/2004] [Indexed: 11/26/2022]
Abstract
The classic 18.5 kDa isoform of murine myelin basic protein (mMBP) has been shown to bind calmodulin (CaM) strongly and specifically in vitro. Here, we have used site-directed spin labelling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy to map more precisely the sites of interaction of recombinant mMBP (rmMBP) with CaM. On the basis of these and previous experimental data, and the predictions of CaM-binding motifs using the Calmodulin Target Database (), three main segments of MBP were suggested for the interaction. The first site is located at the C-terminus; the second one lies in the central portion of the protein and forms an amphipathic alpha-helix in reconstituted myelin-mimetic systems; the third is quite close to the N-terminus. The murine Golli-MBP isoform J37 has also been shown to bind CaM in vitro, and an interaction site was predicted in the N-terminal Golli-specific portion of the protein. From these four segments, we selected peptide fragments of 12-14 residues in length, chosen on the bases of their amphipathicity and CaM-target characteristics. We modelled each of these peptides as alpha-helices, and performed docking simulations to investigate their interactions with the CaM peptide-binding tunnel. Different yet almost equally favourable CaM-binding modes were found for each of them. The experimental SDSL/EPR and theoretical modelling results were in good agreement, and supported the conjecture that there are several plausible CaM-binding sites in MBP, that could be induced into an alpha-helical conformation by their interaction with CaM and account for strong immobilisation of spin-labeled residues in all three segments. Phosphorylation and deimination were also emulated and simulated for known sites of MBP post-translational modification. The results obtained confirmed the appropriate utilisation of simple residue substitutions to mimic the natural modifications, and demonstrated molecular mechanisms by which MBP-CaM interactions could be modulated in vivo.
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Affiliation(s)
- Eugenia Polverini
- Istituto Nazionale per la Fisica della Materia, Dipartimento di Fisica, Università di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy.
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Harauz G, Ishiyama N, Hill CMD, Bates IR, Libich DS, Farès C. Myelin basic protein-diverse conformational states of an intrinsically unstructured protein and its roles in myelin assembly and multiple sclerosis. Micron 2004; 35:503-42. [PMID: 15219899 DOI: 10.1016/j.micron.2004.04.005] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 18.5 kDa isoform of myelin basic protein (MBP) is a major component of the myelin sheath in the central nervous system of higher vertebrates, and a member of a larger family of proteins with a multiplicity of forms and post-translational modifications (PTMs). The 18.5 kDa protein is the exemplar of the family, being most abundant in adult myelin, and thus the most-studied. It is peripherally membrane-associated, but has generally been investigated in isolated form. MBP is an 'intrinsically unstructured' protein with a high proportion (approximately 75%) of random coil, but postulated to have core elements of beta-sheet and alpha-helix. We review here the properties of the MBP family, especially of the 18.5 kDa isoform, and discuss how its three-dimensional (3D) structure may be resolved by direct techniques available to us, viz., X-ray and electron crystallography, and solution and solid-state NMR spectrometry. In particular, we emphasise that creating an appropriate environment in which the protein can adopt a physiologically relevant fold is crucial to such endeavours. By solving the 3D structure of 18.5 kDa MBP and the effects of PTMs, we will attain a better understanding of myelin architecture, and of the molecular mechanisms that transpire in demyelinating diseases such as multiple sclerosis.
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Affiliation(s)
- George Harauz
- Department of Molecular Biology and Genetics, Biophysics Interdepartmental Group, University of Guelph, Room 230, Axelrod Building, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1.
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17
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Libich DS, Hill CMD, Haines JD, Harauz G. Myelin basic protein has multiple calmodulin-binding sites. Biochem Biophys Res Commun 2003; 308:313-9. [PMID: 12901870 DOI: 10.1016/s0006-291x(03)01380-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Myelin basic protein (MBP) has been shown to bind calmodulin (CaM) in a specific Ca(2+)-dependent manner via a primary target sequence at its C-terminus [Protein Sci. 12 (2003) 1507]. Upon deimination of MBP, the nature of the interaction changed significantly, suggesting either a new binding site or different conformers with different affinities for CaM. In order to resolve this issue, we investigated here the CaM-binding properties of N- and C-terminal deletion mutants of MBP using Trp fluorescence spectroscopy and mass spectrometry. We conclude that there is an additional CaM-binding site on MBP in a central segment (we posit murine residues 82-93) that forms an amphipathic alpha-helix.
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Affiliation(s)
- David S Libich
- Department of Molecular Biology and Genetics, Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1
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18
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Libich DS, Hill CM, Bates IR, Hallett FR, Armstrong S, Siemiarczuk A, Harauz G. Interaction of the 18.5-kD isoform of myelin basic protein with Ca2+ -calmodulin: effects of deimination assessed by intrinsic Trp fluorescence spectroscopy, dynamic light scattering, and circular dichroism. Protein Sci 2003; 12:1507-21. [PMID: 12824496 PMCID: PMC2323942 DOI: 10.1110/ps.0303603] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The effects of deimination (conversion of arginyl to citrullinyl residues) of myelin basic protein (MBP) on its binding to calmodulin (CaM) have been examined. Four species of MBP were investigated: unmodified recombinant murine MBP (rmMBP-Cit(0)), an engineered protein with six quasi-citrullinyl (i.e., glutaminyl) residues per molecule (rmMBP-qCit(6)), human component C1 (hMBP-Cit(0)), and human component C8 (hMBP-Cit(6)), both obtained from a patient with multiple sclerosis (MS). Both rmMBP-Cit(0) and hMBP-Cit(0) bound CaM in a Ca(2+)-dependent manner and primarily in a 1:1 stoichiometry, which was verified by dynamic light scattering. Circular dichroic spectroscopy was unable to detect any changes in secondary structure in MBP upon CaM-binding. Inherent Trp fluorescence spectroscopy and a single-site binding model were used to determine the dissociation constants: K(d) = 144 +/- 76 nM for rmMBP-Cit(0), and K(d) = 42 +/- 15 nM for hMBP-Cit(0). For rmMBP-qCit(6) and hMBP-Cit(6), the changes in fluorescence were suggestive of a two-site interaction, although the dissociation constants could not be accurately determined. These results can be explained by a local conformational change induced in MBP by deimination, exposing a second binding site with a weaker association with CaM, or by the existence of several conformers of deiminated MBP. Titration with the collisional quencher acrylamide, and steady-state and lifetime measurements of the fluorescence at 340 nm, showed both dynamic and static components to the quenching, and differences between the unmodified and deiminated proteins that were also consistent with a local conformational change due to deimination.
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Affiliation(s)
- David S. Libich
- Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, and
| | - Christopher M.D. Hill
- Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, and
| | - Ian R. Bates
- Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, and
| | - F. Ross Hallett
- Department of Physics, and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Souzan Armstrong
- Photon Technology International, London, Ontario N6E 2S8, Canada
| | | | - George Harauz
- Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, and
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Hill CMD, Haines JD, Antler CE, Bates IR, Libich DS, Harauz G. Terminal deletion mutants of myelin basic protein: new insights into self-association and phospholipid interactions. Micron 2003; 34:25-37. [PMID: 12694855 DOI: 10.1016/s0968-4328(02)00058-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 18.5kDa isoform of myelin basic protein (MBP) has strong and probably specific interactions with phosphoinositides that are of interest regarding this protein's function, and in effecting its two-dimensional crystallization for structural determination. We have designed and constructed truncation mutants of recombinant 18.5kDa murine myelin basic protein (rmMBP) lacking either the N- or C-terminal third, i.e. rmMBPDeltaN and rmMBPDeltaC, respectively. Both variants rmMBPDeltaC and rmMBPDeltaN generally had a reduced ability to aggregate lipid vesicles, compared to the whole protein, especially at lower protein/lipid ratios. Lipid vesicle cosedimentation showed that both truncated variants exhibited altered binding with phosphatidylinositol (PI). Incubation of these proteins under monolayers comprising PI and a nickel-chelating lipid yielded crystalline arrays of rmMBPDeltaC (but not rmMBPDeltaN) in the absence of high salt or osmolytes, which are required for crystallization of whole protein. This result suggests that the C-terminal segment of MBP is a significant source of conformational heterogeneity, and its removal will facilitate future planar or three-dimensional crystallization attempts. Incubation of rmMBPDeltaN and rmMBPDeltaC under monolayers comprising phosphatidylinositol-4-phosphate and a nickel-chelating lipid yielded tubular structures of opposite chirality, suggesting a synergistic effect of both termini of MBP in organizing myelin lipids.
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Affiliation(s)
- Christopher M D Hill
- Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, University of Guelph, Ont., Canada
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20
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Libich DS, Harauz G. Interactions of the 18.5-kDa isoform of myelin basic protein with Ca(2+)-calmodulin: in vitro studies using fluorescence microscopy and spectroscopy. Biochem Cell Biol 2003; 80:395-406. [PMID: 12234092 DOI: 10.1139/o02-020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interactions of the 18.5-kDa isoform of myelin basic protein (MBP) with calmodulin (CaM) in vitro have been investigated using fluorescence microscopy and spectroscopy. Two forms of MBP were used: the natural bovine C1 charge isomer (bMBP/C1) and a hexahistidine-tagged recombinant murine product (rmMBP), with only minor differences in behaviour being observed. Fragments of each protein generated by digestion with cathepsin D (EC 3.4.23.5) were also evaluated. Using fluorescence microscopy, it was shown that MBP and CaM interacted in the presence of Ca2+ under a variety of conditions, including high urea and salt concentrations, indicating that the interaction was specific and not merely electrostatic in nature. Using cathepsin D digestion fragments of MBP, it was further shown that the carboxyl-terminal domain of MBP interacted with Ca(2+)-CaM, consistent with our theoretical prediction. Spectroscopy of the intrinsic fluorescence of the sole Trp residue of MBP showed that binding was cooperative in nature. The dissociation constants for formation of a 1:1 MBP-Ca(2+)-CaM complex were determined to be 2.1 +/- 0.1 and 2.0 +/- 0.2 microM for bMBP/C1 and rmMBP, respectively. Fluorescence spectroscopy using cathepsin D digestion fragments indicated also that the carboxyl-terminal region of each protein interacted with Ca(2+)-CaM, with dissociation constants of 1.8 +/- 0.2 and 2.8 +/- 0.9 microM for the bMBP/C1 and rmMBP fragments, respectively. These values show a roughly 1000-fold lower affinity of MBP for CaM than other CaM-binding peptides, such as myristoylated alanine-rich C-kinase substrate, that are involved in signal transduction.
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Affiliation(s)
- David S Libich
- Department of Molecular Biology and Genetics, University of Guelph, ON, Canada
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21
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Libich DS, Harauz G. Interactions of the 18.5 kDa isoform of myelin basic protein with Ca2+-calmodulin: in vitro studies using gel shift assays. Mol Cell Biochem 2002; 241:45-52. [PMID: 12482024 DOI: 10.1023/a:1020883409176] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The interactions of the 18.5 kDa isoform of myelin basic protein (MBP) with calmodulin (CaM) in vitro have been investigated using glutaraldehyde or dithiobis[succinimidylpropionate] (DSP) cross-linking, and SDS-polyacrylamide gel electrophoresis. The following forms of MBP were used: the natural bovine C1 charge isomer (bMBP/C1) and a recombinant murine product (rmMBP), and their fragments generated by digestion with cathepsin D (EC 3.4.23.5). In physiological buffers (10 mM HEPES-NaOH, pH 7.4, 5 mM CaCl2, 0.0035% glutaraldehyde; or 50 mM HEPES-NaOH, pH 7.4, 100 mM NaCl, 1 mM CaCl2, 0.0035% DSP), MBP and CaM interacted primarily in a 1:1 molar ratio, consistent with previous studies that used 6 M urea, i.e. denaturing conditions. Moreover, the appearance of higher-order bands (not previously observed) suggested that the mechanism of interaction of the two proteins involved a series of relatively complex equilibria, resulting in 2:1 ratios of MBP to CaM. This observation would explain the cooperativity of association inferred from fluorescence studies [13]. Our results demonstrated further that the interaction involved the C-terminal domain of MBP, again in a primarily 1:1 molar ratio with CaM, consistent with our identification of a CaM-binding motif at the C-terminus.
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Affiliation(s)
- David S Libich
- Department of Molecular Biology and Genetics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
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Hill CM, Bates IR, White GF, Hallett FR, Harauz G. Effects of the osmolyte trimethylamine-N-oxide on conformation, self-association, and two-dimensional crystallization of myelin basic protein. J Struct Biol 2002; 139:13-26. [PMID: 12372316 DOI: 10.1016/s1047-8477(02)00513-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The osmolyte trimethylamine-N-oxide (TMAO) is a naturally in vivo occurring "chemical chaperone" that has been shown to stabilise the folding of numerous proteins. Myelin basic protein (MBP) is a molecule that has not yet been suitably crystallized either in three dimensions for X-ray crystallography or in two dimensions for electron crystallography. Here, we describe lipid monolayer crystallization experiments of two species of recombinant murine MBP in the presence of TMAO. One protein was unmodified, whereas the other contained six Arg/Lys-->Gln substitutions to mimic the effects of deimination (i.e., the enzymatic modification of Arg to citrulline), which reduces the net positive charge. Planar arrays of both proteins were formed on binary lipid monolayers containing a nickel-chelating lipid and a phosphoinositide. In the presence of TMAO, the diffraction spots of these arrays became sharper and more distinct than in its absence, indicating some improvement of crystallinity. The osmolyte also induced the formation of epitaxial growth of protein arrays, especially with the mutant protein. However, none of these assemblies was sufficiently ordered to extract high-resolution structural information. Circular dichroic spectroscopy showed that MBP gained no increase in ordered secondary structure in the presence of TMAO in bulk solution, whereas it did in the presence of lipids. Dynamic light-scattering experiments confirmed that the MBP preparations were monomodal under the optimal crystallization conditions determined by electron microscopy trials. The salt and osmolyte concentrations used were shown to result in a largely unassociated population of MBP. The amino acid composition of MBP overwhelmingly favours a disordered state, and a neural-network-based scheme predicted large segments that would be unlikely to adopt a regular conformation. Thus, this protein has an inherently disordered nature, which mitigates strongly against its crystallization for high-resolution structure determination.
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Affiliation(s)
- Christopher M Hill
- Department of Molecular Biology and Genetics, University of Guelph, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1
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Bates IR, Libich DS, Wood DD, Moscarello MA, Harauz G. An Arg/Lys-->Gln mutant of recombinant murine myelin basic protein as a mimic of the deiminated form implicated in multiple sclerosis. Protein Expr Purif 2002; 25:330-41. [PMID: 12135568 DOI: 10.1016/s1046-5928(02)00017-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The degree of post-translational enzymatic deimination (conversion of arginyl to citrullinyl residues) of myelin basic protein (MBP) is correlated with the severity of the human autoimmune disease multiple sclerosis (MS). It is difficult to obtain large quantities of deiminated MBP from natural sources (autopsy material), and in vitro deimination using peptidylarginine deiminase (EC 3.5.3.15) is both non-specific and irreproducible. Since there is no known codon for citrulline, we have constructed a mutant form of recombinant murine MBP (rmMBP) in which 5 Arg and 1 Lys residues have been replaced by Gln as the most reasonable analogue of Cit. The residues were chosen to correspond to the 6 Arg residues in human MBP which are most commonly deiminated in chronic MS. The mutant species, rmMBP-qCit(6) where the "q" represents "quasi-," was probed by numerous biochemical and biophysical techniques. Highly homogeneous protein preparations were obtained using a modified expression system which minimised spurious misincorporation of Lys for Arg, as ascertained by electrospray ionisation mass spectrometry. The mutant form rmMBP-qCit(6) had a reduced ability to aggregate lipid vesicles, a slightly greater susceptibility to digestion by cathepsin D, a greater proportion of random secondary structure, and different conformational responses to lipids, compared with the unmodified rmMBP. Overall, the mutant protein's properties were consistent with the effects of deimination and support its use as a model for evaluating the effects of this modification.
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Affiliation(s)
- Ian R Bates
- Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1
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Maurer-Stroh S, Eisenhaber B, Eisenhaber F. N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J Mol Biol 2002; 317:541-57. [PMID: 11955008 DOI: 10.1006/jmbi.2002.5426] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects but it requires a low rate of false positive hits in addition to a sufficient sensitivity. Our previous analysis of substrate protein sequence variability, NMT sequences and 3D structures has revealed motif properties in addition to the known PROSITE motif that are utilized in a new predictor described here. The composite prediction function (with separate ad hoc parameterization (a) for queries from non-fungal eukaryotes and their viruses and (b) for sequences from fungal species) consists of terms evaluating amino acid type preferences at sequences positions close to the N terminus as well as terms penalizing deviations from the physical property pattern of amino acid side-chains encoded in multi-residue correlation within the motif sequence. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set as well as with kinetic data for model substrates. The sensitivity in recognizing documented NMT substrates is above 95 % for both taxon-specific versions. The corresponding rate of false positive prediction (for sequences with an N-terminal glycine residue) is close to 0.5 %; thus, the technique is applicable for large-scale automated sequence database annotation. The predictor is available as public WWW-server with the URL http://mendel.imp.univie.ac.at/myristate/. Additionally, we propose a version of the predictor that identifies a number of proteolytic protein processing sites at internal glycine residues and that evaluates possible N-terminal myristoylation of the protein fragments.A scan of public protein databases revealed new potential NMT targets for which the myristoyl modification may be of critical importance for biological function. Among others, the list includes kinases, phosphatases, proteasomal regulatory subunit 4, kinase interacting proteins KIP1/KIP2, protozoan flagellar proteins, homologues of mitochondrial translocase TOM40, of the neuronal calcium sensor NCS-1 and of the cytochrome c-type heme lyase CCHL. Analyses of complete eukaryote genomes indicate that about 0.5 % of all encoded proteins are apparent NMT substrates except for a higher fraction in Arabidopsis thaliana ( approximately 0.8 %).
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Ishiyama N, Bates IR, Hill CM, Wood DD, Matharu P, Viner NJ, Moscarello MA, Harauz G. The effects of deimination of myelin basic protein on structures formed by its interaction with phosphoinositide-containing lipid monolayers. J Struct Biol 2001; 136:30-45. [PMID: 11858705 DOI: 10.1006/jsbi.2001.4421] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The recombinant 18.5-kDa charge isoform of murine myelin basic protein (rmMBP) is unmodified posttranslationally and was used to study the effects of deimination, i.e., the conversion of arginyl to citrullinyl residues, on the protein's interactions with itself and with lipids. The unmodified species rmMBP-Cit(0) (i.e., containing no citrullinyl residues) interacted with binary monolayers containing acidic (phosphatidylinositol) and nickel-chelating lipids to form paracrystalline arrays with 4.8-nm spacing. A sample of protein was deiminated to an average of 9 citrullinyl residues per molecule of protein, yielding rmMBP-Cit(9). Under both low- and high-salt conditions, this species formed better-ordered domains than rmMBP-Cit(0), viz., planar crystalline assemblies. Thus, deimination of MBP resulted in a significant alteration of its lipid-organizing and self-interaction properties that might be operative in myelin in vivo, especially in progression of the autoimmune disease multiple sclerosis. Comparisons of amino acid sequences indicated significant similarities of MBP with filaggrin, a protein that is deiminated in another autoimmune disease, rheumatoid arthritis, suggesting that comparable epitopes could be targeted in both pathologies. In contrast, binary lipid monolayers consisting of phosphatidylinositol-4-phosphate (or phosphatidylinositol-4,5-bisphosphate) and a nickel-chelating lipid formed helical tubular vesicular structures, which appeared to be induced and/or stabilized by rmMBP, especially in its deiminated form. Sequence comparisons with other actin- and phosphoinositide-binding proteins (vinculin, ActA, MARCKS) suggested that the carboxyl-terminal segment of MBP could form an amphipathic alpha helix and was the phosphoinositide binding site.
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Affiliation(s)
- N Ishiyama
- Department of Molecular Biology and Genetics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
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