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Shahrajabian MH, Sun W. Characterization of Intrinsically Disordered Proteins in Healthy and Diseased States by Nuclear Magnetic Resonance. Rev Recent Clin Trials 2024; 19:176-188. [PMID: 38409704 DOI: 10.2174/0115748871271420240213064251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 02/28/2024]
Abstract
INTRODUCTION Intrinsically Disordered Proteins (IDPs) are active in different cellular procedures like ordered assembly of chromatin and ribosomes, interaction with membrane, protein, and ligand binding, molecular recognition, binding, and transportation via nuclear pores, microfilaments and microtubules process and disassembly, protein functions, RNA chaperone, and nucleic acid binding, modulation of the central dogma, cell cycle, and other cellular activities, post-translational qualification and substitute splicing, and flexible entropic linker and management of signaling pathways. METHODS The intrinsic disorder is a precise structural characteristic that permits IDPs/IDPRs to be involved in both one-to-many and many-to-one signaling. IDPs/IDPRs also exert some dynamical and structural ordering, being much less constrained in their activities than folded proteins. Nuclear magnetic resonance (NMR) spectroscopy is a major technique for the characterization of IDPs, and it can be used for dynamic and structural studies of IDPs. RESULTS AND CONCLUSION This review was carried out to discuss intrinsically disordered proteins and their different goals, as well as the importance and effectiveness of NMR in characterizing intrinsically disordered proteins in healthy and diseased states.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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2
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Pan Z, Mu J, Chen HF. Balanced Three-Point Water Model OPC3-B for Intrinsically Disordered and Ordered Proteins. J Chem Theory Comput 2023; 19:4837-4850. [PMID: 37452752 DOI: 10.1021/acs.jctc.3c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) play a critical role in many biological processes. Due to the inherent structural flexibility of IDPs, experimental methods present significant challenges for sampling their conformational information at the atomic level. Therefore, molecular dynamics (MD) simulations have emerged as the primary tools for modeling IDPs whose accuracy depend on force field and water model. To enhance the accuracy of physical modeling of IDPs, several force fields have been developed. However, current water models lack precision and underestimate the interaction between water molecules and proteins. Here, we used Monte-Carlo re-weighting method to re-parameterize a three-point water model based on OPC3 for IDPs (named OPC3-B). We benchmarked the performance of OPC3-B compared with nine different water models for 10 IDPs and three ordered proteins. The results indicate that the performance of OPC3-B is better than other water models for both IDPs and ordered proteins. At the same time, OPC3-B possess the power of transferability with other force field to simulate IDPs. This newly developed water model can be used to insight into the research of sequence-disordered-function paradigm for IDPs.
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Affiliation(s)
- Zhengsong Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
| | - Junxi Mu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
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3
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Krokengen OC, Raasakka A, Kursula P. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data. Biochem Biophys Rep 2023; 34:101474. [PMID: 37153862 PMCID: PMC10160357 DOI: 10.1016/j.bbrep.2023.101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Oulu, Finland
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4
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Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
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5
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Ziaei A, Garcia-Miralles M, Radulescu CI, Sidik H, Silvin A, Bae HG, Bonnard C, Yusof NABM, Ferrari Bardile C, Tan LJ, Ng AYJ, Tohari S, Dehghani L, Henry L, Yeo XY, Lee S, Venkatesh B, Langley SR, Shaygannejad V, Reversade B, Jung S, Ginhoux F, Pouladi MA. Ermin deficiency leads to compromised myelin, inflammatory milieu, and susceptibility to demyelinating insult. Brain Pathol 2022; 32:e13064. [PMID: 35285112 PMCID: PMC9425013 DOI: 10.1111/bpa.13064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/09/2022] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Ermin is an actin-binding protein found almost exclusively in the central nervous system (CNS) as a component of myelin sheaths. Although Ermin has been predicted to play a role in the formation and stability of myelin sheaths, this has not been directly examined in vivo. Here, we show that Ermin is essential for myelin sheath integrity and normal saltatory conduction. Loss of Ermin in mice caused de-compacted and fragmented myelin sheaths and led to slower conduction along with progressive neurological deficits. RNA sequencing of the corpus callosum, the largest white matter structure in the CNS, pointed to inflammatory activation in aged Ermin-deficient mice, which was corroborated by increased levels of microgliosis and astrogliosis. The inflammatory milieu and myelin abnormalities were further associated with increased susceptibility to immune-mediated demyelination insult in Ermin knockout mice. Supporting a possible role of Ermin deficiency in inflammatory white matter disorders, a rare inactivating mutation in the ERMN gene was identified in multiple sclerosis patients. Our findings demonstrate a critical role for Ermin in maintaining myelin integrity. Given its near-exclusive expression in myelinating oligodendrocytes, Ermin deficiency represents a compelling "inside-out" model of inflammatory dysmyelination and may offer a new paradigm for the development of myelin stability-targeted therapies.
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Affiliation(s)
- Amin Ziaei
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.,UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Marta Garcia-Miralles
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Carola I Radulescu
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Harwin Sidik
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Aymeric Silvin
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore
| | - Han-Gyu Bae
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.,Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Carine Bonnard
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Nur Amirah Binte Mohammad Yusof
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Costanza Ferrari Bardile
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.,Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liang Juin Tan
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Alvin Yu Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Leila Dehghani
- Department of Neurology, Isfahan Neurosciences Research Centre, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Lily Henry
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Xin Yi Yeo
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Sejin Lee
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Vahid Shaygannejad
- Department of Neurology, Isfahan Neurosciences Research Centre, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Sangyong Jung
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore.,Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, Singapore, Singapore.,Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China.,Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.,Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Ahmad I, Wergeland S, Oveland E, Bø L. A higher proportion of ermin-immunopositive oligodendrocytes in areas of remyelination. PLoS One 2021; 16:e0256155. [PMID: 34437581 PMCID: PMC8389439 DOI: 10.1371/journal.pone.0256155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/01/2021] [Indexed: 12/03/2022] Open
Abstract
Incomplete remyelination is frequent in multiple sclerosis (MS)-lesions, but there is no established marker for recent remyelination. We investigated the role of the oligodendrocyte/myelin protein ermin in de- and remyelination in the cuprizone (CPZ) mouse model, and in MS. The density of ermin+ oligodendrocytes in the brain was significantly decreased after one week of CPZ exposure (p < 0.02). The relative proportion of ermin+ cells compared to cells positive for the late-stage oligodendrocyte marker Nogo-A increased at the onset of remyelination in the corpus callosum (p < 0.02). The density of ermin-positive cells increased in the corpus callosum during the CPZ-phase of extensive remyelination (p < 0.0001). In MS, the density of ermin+ cells was higher in remyelinated lesion areas compared to non-remyelinated areas both in white- (p < 0.0001) and grey matter (p < 0.0001) and compared to normal-appearing white matter (p < 0.001). Ermin immunopositive cells in MS-lesions were not immunopositive for the early-stage oligodendrocyte markers O4 and O1, but a subpopulation was immunopositive for Nogo-A. The data suggest a relatively higher proportion of ermin immunopositivity in oligodendrocytes compared to Nogo-A indicates recent or ongoing remyelination.
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Affiliation(s)
- Intakhar Ahmad
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Bergen, Norway
| | - Stig Wergeland
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Bergen, Norway
| | - Eystein Oveland
- Department of Biomedicine, Proteomics Unit at the University of Bergen (PROBE), University of Bergen, Bergen, Norway
| | - Lars Bø
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Norwegian Multiple Sclerosis Competence Centre, Haukeland University Hospital, Bergen, Norway
- * E-mail:
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7
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Wang S, Wang T, Liu T, Xie RG, Zhao XH, Wang L, Yang Q, Jia LT, Han J. Ermin is a p116 RIP -interacting protein promoting oligodendroglial differentiation and myelin maintenance. Glia 2020; 68:2264-2276. [PMID: 32530539 DOI: 10.1002/glia.23838] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022]
Abstract
Myelin sheaths, which insulate the axons and ensure saltatory conduction of the nerve impulse, are generated and maintained via largely uncharacterized mechanisms. Ermin is an oligodendrocyte-specific protein associated with the cytoskeleton, but how it regulates cytoskeletal remodeling during oligodendrocyte differentiation and its role in myelin maintenance are not clear. To address this, we generated mice constitutively deficient for Ermn, the Ermin-coding gene. We found that aged Ermn-knockout mice exhibit an aberrant myelin architecture, with splitting of myelin layers, peeling of the myelin sheath from axons, and breakdown of myelinated fibers. As a result, these mice had remarkably impaired motor coordination. Ermn knockout also accelerated cuprizone-induced demyelination and exacerbated the associated movement disorders. Ermin was found to contribute to oligodendrocyte morphogenesis by associating with the myosin phosphatase Rho interacting protein (Mprip/p116RIP ) and inactivating RhoA, a GTPase that controls cytoskeletal rearrangement in differentiating cells. These findings provide novel insights into the mechanisms regulating oligodendroglial differentiation, the maintenance of the myelin sheaths, and remyelination.
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Affiliation(s)
- Shan Wang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Tao Wang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Tao Liu
- Key Laboratory of Modern Teaching Technology, Shaanxi Normal University, Xi'an, China
| | - Rou-Gang Xie
- Department of Neurobiology and Collaborative Innovation Center for Brain Science, Fourth Military Medical University, Xi'an, China
| | - Xiang-Hui Zhao
- Department of Neurobiology and Collaborative Innovation Center for Brain Science, Fourth Military Medical University, Xi'an, China
| | - Lei Wang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Qian Yang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Lin-Tao Jia
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Jing Han
- Key Laboratory of Modern Teaching Technology, Shaanxi Normal University, Xi'an, China
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8
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Sustentacular Cell Enwrapment of Olfactory Receptor Neuronal Dendrites: An Update. Genes (Basel) 2020; 11:genes11050493. [PMID: 32365880 PMCID: PMC7291085 DOI: 10.3390/genes11050493] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
The pseudostratified olfactory epithelium (OE) may histologically appear relatively simple, but the cytological relations among its cell types, especially those between olfactory receptor neurons (ORNs) and olfactory sustentacular cells (OSCs), prove more complex and variable than previously believed. Adding to the complexity is the short lifespan, persistent neurogenesis, and continuous rewiring of the ORNs. Contrary to the common belief that ORN dendrites are mostly positioned between OSCs, recent findings indicate a sustentacular cell enwrapped configuration for a majority of mature ORN dendrites at the superficial layer of the OE. After vertically sprouting out from the borderlines between OSCs, most of the immature ORN dendrites undergo a process of sideways migration and terminal maturation to become completely invaginated into and enwrapped by OSCs. Trailing the course of the dendritic sideways migration is the mesodendrite (mesentery of the enwrapped dendrite) made of closely apposed, cell junction connected plasma membrane layers of neighboring folds of the host sustentacular cell. Only a minority of the mature ORN dendrites at the OE apical surface are found at the borderlines between OSCs (unwrapped). Below I give a brief update on the cytoarchitectonic relations between the ORNs and OSCs of the OE. Emphasis is placed on the enwrapment of ORN dendrites by OSCs, on the sideways migration of immature ORN dendrites after emerging from the OE surface, and on the terminal maturation of the ORNs. Functional implications of ORN dendrite enwrapment and a comparison with myelination or Remak’s bundling of axons or axodendrites in the central and peripheral nervous system are also discussed.
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9
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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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10
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci U S A 2019; 116:20446-20452. [PMID: 31548393 DOI: 10.1073/pnas.1907251116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
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11
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Faigle W, Cruciani C, Wolski W, Roschitzki B, Puthenparampil M, Tomas-Ojer P, Sellés-Moreno C, Zeis T, Jelcic I, Schaeren-Wiemers N, Sospedra M, Martin R. Brain Citrullination Patterns and T Cell Reactivity of Cerebrospinal Fluid-Derived CD4 + T Cells in Multiple Sclerosis. Front Immunol 2019; 10:540. [PMID: 31024521 PMCID: PMC6467957 DOI: 10.3389/fimmu.2019.00540] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/27/2019] [Indexed: 01/11/2023] Open
Abstract
Immune responses to citrullinated peptides have been described in autoimmune diseases like rheumatoid arthritis (RA) and multiple sclerosis (MS). We investigated the post-translational modification (PTM), arginine to citrulline, in brain tissue of MS patients and controls (C) by proteomics and subsequently the cellular immune response of cerebrospinal fluid (CSF)-infiltrating T cells to citrullinated and unmodified peptides of myelin basic protein (MBP). Using specifically adapted tissue extraction- and combined data interpretation protocols we could establish a map of citrullinated proteins by identifying more than 80 proteins with two or more citrullinated peptides in human brain tissue. We report many of them for the first time. For the already described citrullinated proteins MBP, GFAP, and vimentin, we could identify additional citrullinated sites. The number of modified proteins in MS white matter was higher than control tissue. Citrullinated peptides are considered neoepitopes that may trigger autoreactivity. We used newly identified epitopes and previously reported immunodominant myelin peptides in their citrullinated and non-citrullinated form to address the recognition of CSF-infiltrating CD4+ T cells from 22 MS patients by measuring proliferation and IFN-γ secretion. We did not detect marked responses to citrullinated peptides, but slightly more strongly to the non-modified version. Based on these data, we conclude that citrullination does not appear to be an important activating factor of a T cell response, but could be the consequence of an immune- or inflammatory response. Our approach allowed us to perform a deep proteome analysis and opens new technical possibilities to analyze complex PTM patterns on minute quantities of rare tissue samples.
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Affiliation(s)
- Wolfgang Faigle
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Carolina Cruciani
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Witold Wolski
- Functional Genomics Center Zurich, ETH Zurich & University of Zurich, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, ETH Zurich & University of Zurich, Zurich, Switzerland
| | - Marco Puthenparampil
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Paula Tomas-Ojer
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Carla Sellés-Moreno
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Zeis
- Neurobiology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ivan Jelcic
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Nicole Schaeren-Wiemers
- Neurobiology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mireia Sospedra
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research Section, Neurology Clinic, University Zurich, University Hospital Zurich, Zurich, Switzerland
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12
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Raasakka A, Ruskamo S, Kowal J, Han H, Baumann A, Myllykoski M, Fasano A, Rossano R, Riccio P, Bürck J, Ulrich AS, Stahlberg H, Kursula P. Molecular structure and function of myelin protein P0 in membrane stacking. Sci Rep 2019; 9:642. [PMID: 30679613 PMCID: PMC6345808 DOI: 10.1038/s41598-018-37009-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Compact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in changes of the bilayer properties, but also potentially involves the arrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland
| | - Huijong Han
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anna Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Rocco Rossano
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Paolo Riccio
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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13
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Intrinsic disorder in the regulatory N-terminal domain of diacylglycerol acyltransferase 1 from Brassica napus. Sci Rep 2018; 8:16665. [PMID: 30420764 PMCID: PMC6232145 DOI: 10.1038/s41598-018-34339-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Proteins with multifunctional regulatory domains often demonstrate structural plasticity or protein disorder, allowing the binding of multiple regulatory factors and post-translational modifications. While the importance of protein disorder is clear, it also poses a challenge for in vitro characterization. Here, we report protein intrinsic disorder in a plant molecular system, which despite its prevalence is less studied. We present a detailed biophysical characterization of the entire cytoplasmic N-terminal domain of Brassica napus diacylglycerol acyltransferase, (DGAT1), which includes an inhibitory module and allosteric binding sites. Our results demonstrate that the monomeric N-terminal domain can be stabilized for biophysical characterization and is largely intrinsically disordered in solution. This domain interacts with allosteric modulators of DGAT1, CoA and oleoyl-CoA, at micromolar concentrations. While solution scattering studies indicate conformational heterogeneity in the N-terminal domain of DGAT1, there is a small gain of secondary structure induced by ligand binding.
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14
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Kumagai PS, Araujo APU, Lopes JLS. Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy. Biophys Rev 2017; 9:517-527. [PMID: 28825203 DOI: 10.1007/s12551-017-0314-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/03/2017] [Indexed: 10/25/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is a fast, powerful, well-established, and widely used analytical technique in the biophysical and structural biology community to study protein secondary structure and to track changes in protein conformation in different environments. The use of the intense light of a synchrotron beam as the light source for collecting CD measurements has emerged as an enhanced method, known as synchrotron radiation circular dichroism (SRCD) spectroscopy, that has several advantages over the conventional CD method, including a significant spectral range extension for data collection, deeper access to the lower limit (cut-off) of conventional CD spectroscopy, an improved signal-to-noise ratio to increase accuracy in the measurements, and the possibility to collect measurements in highly absorbing solutions. In this review, we discuss different applications of the SRCD technique by researchers from Latin America. In this context, we specifically look at the use of this method for examining the secondary structure and conformational behavior of proteins belonging to the four main classes of the hierarchical protein domain classification CATH (Class, Architecture, Topology, Homology) database, focusing on the advantages and improvements associated with SRCD spectroscopy in terms of characterizing proteins composed of different structural elements.
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Affiliation(s)
- Patricia S Kumagai
- Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana P U Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jose L S Lopes
- Departamento Física Aplicada, Instituto de Física,, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
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15
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Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Urbanowicz A, Lewandowski D, Szpotkowski K, Figlerowicz M. Tick receptor for outer surface protein A from Ixodes ricinus - the first intrinsically disordered protein involved in vector-microbe recognition. Sci Rep 2016; 6:25205. [PMID: 27112540 PMCID: PMC4844993 DOI: 10.1038/srep25205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/12/2016] [Indexed: 01/02/2023] Open
Abstract
The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.
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Affiliation(s)
- Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Dominik Lewandowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Kamil Szpotkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland.,Institute of Computing Science, University of Technology, Poznan, 60-965, Poland
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17
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McCusker CD, Athippozhy A, Diaz-Castillo C, Fowlkes C, Gardiner DM, Voss SR. Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation. BMC DEVELOPMENTAL BIOLOGY 2015; 15:45. [PMID: 26597593 PMCID: PMC4657325 DOI: 10.1186/s12861-015-0095-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023]
Abstract
Background The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern of the missing structure. Observations from recent and historic studies suggest that blastema cells vary in their potential to pattern distal structures during the regeneration process; some cells are plastic and can be reprogrammed to obtain new positional information while others are stable. Our previous studies showed that positional information has temporal and spatial components of variation; early bud (EB) and apical late bud (LB) blastema cells are plastic while basal-LB cells are stable. To identify the potential cellular and molecular basis of this variation, we compared these three cell populations using histological and transcriptional approaches. Results Histologically, the basal-LB sample showed greater tissue organization than the EB and apical-LB samples. We also observed that cell proliferation was more abundant in EB and apical-LB tissue when compared to basal-LB and mature stump tissue. Lastly, we found that genes associated with cellular differentiation were expressed more highly in the basal-LB samples. Conclusions Our results characterize histological and transcriptional differences between EB and apical-LB tissue compared to basal-LB tissue. Combined with our results from a previous study, we hypothesize that the stability of positional information is associated with tissue organization, cell proliferation, and pathways of cellular differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0095-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Antony Athippozhy
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
| | - Carlos Diaz-Castillo
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - Charless Fowlkes
- Donald Bren School of Information and Computer Science, University of California, Irvine, CA, 92602, USA.
| | - David M Gardiner
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - S Randal Voss
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
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18
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Human adenosine A2A receptor binds calmodulin with high affinity in a calcium-dependent manner. Biophys J 2015; 108:903-917. [PMID: 25692595 DOI: 10.1016/j.bpj.2014.12.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/02/2014] [Accepted: 12/16/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding how ligands bind to G-protein-coupled receptors and how binding changes receptor structure to affect signaling is critical for developing a complete picture of the signal transduction process. The adenosine A2A receptor (A2AR) is a particularly interesting example, as it has an exceptionally long intracellular carboxyl terminus, which is predicted to be mainly disordered. Experimental data on the structure of the A2AR C-terminus is lacking, because published structures of A2AR do not include the C-terminus. Calmodulin has been reported to bind to the A2AR C-terminus, with a possible binding site on helix 8, next to the membrane. The biological meaning of the interaction as well as its calcium dependence, thermodynamic parameters, and organization of the proteins in the complex are unclear. Here, we characterized the structure of the A2AR C-terminus and the A2AR C-terminus-calmodulin complex using different biophysical methods, including native gel and analytical gel filtration, isothermal titration calorimetry, NMR spectroscopy, and small-angle X-ray scattering. We found that the C-terminus is disordered and flexible, and it binds with high affinity (Kd = 98 nM) to calmodulin without major conformational changes in the domain. Calmodulin binds to helix 8 of the A2AR in a calcium-dependent manner that can displace binding of A2AR to lipid vesicles. We also predicted and classified putative calmodulin-binding sites in a larger group of G-protein-coupled receptors.
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19
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Abstract
Myelination of axons in the nervous system of vertebrates enables fast, saltatory impulse propagation, one of the best-understood concepts in neurophysiology. However, it took a long while to recognize the mechanistic complexity both of myelination by oligodendrocytes and Schwann cells and of their cellular interactions. In this review, we highlight recent advances in our understanding of myelin biogenesis, its lifelong plasticity, and the reciprocal interactions of myelinating glia with the axons they ensheath. In the central nervous system, myelination is also stimulated by axonal activity and astrocytes, whereas myelin clearance involves microglia/macrophages. Once myelinated, the long-term integrity of axons depends on glial supply of metabolites and neurotrophic factors. The relevance of this axoglial symbiosis is illustrated in normal brain aging and human myelin diseases, which can be studied in corresponding mouse models. Thus, myelinating cells serve a key role in preserving the connectivity and functions of a healthy nervous system.
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Affiliation(s)
- Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany; ,
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20
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Balu R, Knott R, Cowieson NP, Elvin CM, Hill AJ, Choudhury NR, Dutta NK. Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin. Sci Rep 2015; 5:10896. [PMID: 26042819 PMCID: PMC4455251 DOI: 10.1038/srep10896] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/21/2015] [Indexed: 01/08/2023] Open
Abstract
Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.
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Affiliation(s)
- Rajkamal Balu
- Ian Wark Research Institute, University of South Australia, Mawson Lakes campus, Mawson lakes, South Australia 5095, Australia
| | - Robert Knott
- ANSTO, Private Mail Bag, Kirrawee, New South Wales 2232, Australia
| | - Nathan P. Cowieson
- Centre for Synchrotron Science, Monash University, Victoria 3800, Australia
| | - Christopher M. Elvin
- CSIRO Agriculture, Level 6, Queensland Bioscience Precinct, St Lucia, Queensland 4067, Australia
| | - Anita J. Hill
- CSIRO Manufacturing, Clayton, Victoria 3168, Australia
| | - Namita R. Choudhury
- Ian Wark Research Institute, University of South Australia, Mawson Lakes campus, Mawson lakes, South Australia 5095, Australia
| | - Naba K. Dutta
- Ian Wark Research Institute, University of South Australia, Mawson Lakes campus, Mawson lakes, South Australia 5095, Australia
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21
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Chukhlieb M, Raasakka A, Ruskamo S, Kursula P. The N-terminal cytoplasmic domain of neuregulin 1 type III is intrinsically disordered. Amino Acids 2015; 47:1567-77. [PMID: 25944317 DOI: 10.1007/s00726-015-1998-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Axonally expressed neuregulin 1 (NRG1) type III is a transmembrane protein involved in various neurodevelopmental processes, including myelination and Schwann cell migration. NRG1 type III has one transmembrane domain and a C-terminal extracellular segment, which contains an epidermal growth factor homology domain. Little is known, however, about the intracellular N terminus of NRG1 type III, and the structure-function relationships of this cytoplasmic domain have remained uncharacterized. In the current study, we carried out the first structural and functional studies on the NRG1 type III cytoplasmic domain. Based on sequence analyses, the domain is predicted to be largely disordered, while a strictly conserved region close to the transmembrane segment may contain helical structure and bind metal ions. As shown by synchrotron radiation circular dichroism spectroscopy, the recombinant NRG1 type III cytoplasmic domain was disordered in solution, but it was able to fold partially into a helical structure, especially when both metals and membrane-mimicking compounds were present. NRG1 cytoplasmic tail binding to metals was further confirmed by calorimetry. These results suggest that the juxtamembrane segment of the NRG1 type III cytoplasmic domain may fold onto the membrane surface upon metal binding. Using synchrotron small-angle X-ray scattering, we further proved that the NRG1 cytoplasmic domain is intrinsically disordered, highly elongated, and behaves like a random polymer. Our work provides the first biochemical and biophysical data on the previously unexplored cytoplasmic domain of NRG1 type III, which will help elucidate the detailed structure-function relationships of this domain.
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Affiliation(s)
- Maryna Chukhlieb
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
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Han H, Myllykoski M, Ruskamo S, Wang C, Kursula P. Myelin-specific proteins: a structurally diverse group of membrane-interacting molecules. Biofactors 2013; 39:233-41. [PMID: 23780694 DOI: 10.1002/biof.1076] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 11/15/2012] [Indexed: 12/15/2022]
Abstract
The myelin sheath is a multilayered membrane in the nervous system, which has unique biochemical properties. Myelin carries a set of specific high-abundance proteins, the structure and function of which are still poorly understood. The proteins of the myelin sheath are involved in a number of neurological diseases, including autoimmune diseases and inherited neuropathies. In this review, we briefly discuss the structural properties and functions of selected myelin-specific proteins (P0, myelin oligodendrocyte glycoprotein, myelin-associated glycoprotein, myelin basic protein, myelin-associated oligodendrocytic basic protein, P2, proteolipid protein, peripheral myelin protein of 22 kDa, 2',3'-cyclic nucleotide 3'-phosphodiesterase, and periaxin); such properties include, for example, interactions with lipid bilayers and the presence of large intrinsically disordered regions in some myelin proteins. A detailed understanding of myelin protein structure and function at the molecular level will be required to fully grasp their physiological roles in the myelin sheath.
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Affiliation(s)
- Huijong Han
- Department of Biochemistry and Biocenter Oulu, University of Oulu, Oulu, Finland
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