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Shadman H, Ziebarth JD, Gallops CE, Luo R, Li Z, Chen HF, Wang Y. Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities. Biophys J 2024; 123:1253-1263. [PMID: 38615193 PMCID: PMC11140466 DOI: 10.1016/j.bpj.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/20/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024] Open
Abstract
Disordered proteins are conformationally flexible proteins that are biologically important and have been implicated in devastating diseases such as Alzheimer's disease and cancer. Unlike stably folded structured proteins, disordered proteins sample a range of different conformations that needs to be accounted for. Here, we treat disordered proteins as polymer chains, and compute a dimensionless quantity called instantaneous shape ratio (Rs), as Rs = Ree2/Rg2, where Ree is end-to-end distance and Rg is radius of gyration. Extended protein conformations tend to have high Ree compared with Rg, and thus have high Rs values, whereas compact conformations have smaller Rs values. We use a scatter plot of Rs (representing shape) against Rg (representing size) as a simple map of conformational landscapes. We first examine the conformational landscape of simple polymer models such as Random Walk, Self-Avoiding Walk, and Gaussian Walk (GW), and we notice that all protein/polymer maps lie within the boundaries of the GW map. We thus use the GW map as a reference and, to assess conformational diversity, we compute the fraction of the GW conformations (fC) covered by each protein/polymer. Disordered proteins all have high fC scores, consistent with their disordered nature. Each disordered protein accesses a different region of the reference map, revealing differences in their conformational ensembles. We additionally examine the conformational maps of the nonviral gene delivery vector polyethyleneimine at various protonation states, and find that they resemble disordered proteins, with coverage of the reference map decreasing with increasing protonation state, indicating decreasing conformational diversity. We propose that our method of combining Rs and Rg in a scatter plot generates a simple, meaningful map of the conformational landscape of a disordered protein, which in turn can be used to assess conformational diversity of disordered proteins.
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Affiliation(s)
- Hossain Shadman
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Jesse D Ziebarth
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Caleb E Gallops
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California
| | - Zhengxin Li
- 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, 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, China
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis, Memphis, Tennessee.
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2
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El Hajjar L, Bridot C, Nguyen M, Cantrelle FX, Landrieu I, Smet-Nocca C. Phosphorylation of Tau Protein by CDK2/cyclin A and GSK3β Recombinant Kinases: Analysis of Phosphorylation Patterns by Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2024; 2754:271-306. [PMID: 38512672 DOI: 10.1007/978-1-0716-3629-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Posttranslational modifications (PTMs) of proteins can be investigated by Nuclear Magnetic Resonance (NMR) spectroscopy as a powerful analytical tool to define modification sites, their relative stoichiometry, and crosstalk between modifications. As a Structural Biology method, NMR provides important additional information on changes in protein conformation and dynamics upon modification as well as a mapping of binding sites upon biomolecular interactions. Indeed, PTMs not only mediate functional modulation in protein-protein interactions, but can also induce diverse structural responses with different biological outcomes. Here we present protocols that have been developed for the production and phosphorylation of the neuronal tau protein. Under its aggregated form, tau is a hallmark of Alzheimer's disease and other neurodegenerative diseases named tauopathies involving tau dysfunction and/or mutations. As a common feature shared by various tauopathies, tau aggregates are found into a form displaying an increased, abnormal phosphorylation, also referred to hyperphosphorylation. We have used NMR to investigate the phosphorylation patterns of tau induced by several kinases or cell extracts, how phosphorylation affects the local and overall conformation of tau, its interactions with partners (proteins, DNA, small-molecules, etc.) including tubulin and microtubules, and its capacity to form insoluble fibrillar aggregates. We present here detailed protocols for in vitro phosphorylation of tau by the recombinant kinases CDK2/cyclin A and GSK3β, the production of the recombinant kinases thereof, as well as the analytical characterization of phosphorylated tau by NMR spectroscopy.
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Affiliation(s)
- Léa El Hajjar
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Clarisse Bridot
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Marine Nguyen
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - François-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Isabelle Landrieu
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS, EMR9002 BSI Integrative Structural Biology, Lille, France
- LabEx (Laboratory of Excellence) DISTALZ (Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease ANR-11-LABX-01), Lille, France
| | - Caroline Smet-Nocca
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.
- CNRS EMR9002 Integrative Structural Biology, Lille, France.
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Pezzotti G, Adachi T, Imamura H, Bristol DR, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Kawai T, Mazda O, Kariu T, Waku T, Nichols FC, Riello P, Rizzolio F, Limongi T, Okuma K. In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis. Int J Mol Sci 2023; 24:13351. [PMID: 37686157 PMCID: PMC10488263 DOI: 10.3390/ijms241713351] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid β (Aβ) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Davide Redolfi Bristol
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
| | - Toru Kariu
- Department of Life Science, Shokei University, Chuo-ku, Kuhonji, Kumamoto 862-8678, Japan;
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan;
| | - Frank C. Nichols
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut, 263 Farmington Avenue, Storrs, CT 06030, USA;
| | - Pietro Riello
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Flavio Rizzolio
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tania Limongi
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
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Górska A, Markiewicz-Gospodarek A, Markiewicz R, Chilimoniuk Z, Borowski B, Trubalski M, Czarnek K. Distribution of Iron, Copper, Zinc and Cadmium in Glia, Their Influence on Glial Cells and Relationship with Neurodegenerative Diseases. Brain Sci 2023; 13:911. [PMID: 37371389 DOI: 10.3390/brainsci13060911] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Recent data on the distribution and influence of copper, zinc and cadmium in glial cells are summarized. This review also examines the relationship between those metals and their role in neurodegenerative diseases like Alzheimer disease, multiple sclerosis, Parkinson disease and Amyotrophic lateral sclerosis, which have become a great challenge for today's physicians. The studies suggest that among glial cells, iron has the highest concentration in oligodendrocytes, copper in astrocytes and zinc in the glia of hippocampus and cortex. Previous studies have shown neurotoxic effects of copper, iron and manganese, while zinc can have a bidirectional effect, i.e., neurotoxic but also neuroprotective effects depending on the dose and disease state. Recent data point to the association of metals with neurodegeneration through their role in the modulation of protein aggregation. Metals can accumulate in the brain with aging and may be associated with age-related diseases.
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Affiliation(s)
- Aleksandra Górska
- Department of Human Anatomy, Medical University of Lublin, 4 Jaczewskiego St., 20-090 Lublin, Poland
| | | | - Renata Markiewicz
- Department of Psychiatric Nursing, Medical University of Lublin, 18 Szkolna St., 20-124 Lublin, Poland
| | - Zuzanna Chilimoniuk
- Student Scientific Group at the Department of Family Medicine, 6a (SPSK1) Langiewicza St., 20-032 Lublin, Poland
| | - Bartosz Borowski
- Students Scientific Association at the Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Mateusz Trubalski
- Students Scientific Association at the Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Katarzyna Czarnek
- Institute of Health Sciences, The John Paul II Catholic University of Lublin, Konstantynów 1 H, 20-708 Lublin, Poland
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5
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Lasorsa A, Bera K, Malki I, Dupré E, Cantrelle FX, Merzougui H, Sinnaeve D, Hanoulle X, Hritz J, Landrieu I. Conformation and Affinity Modulations by Multiple Phosphorylation Occurring in the BIN1 SH3 Domain Binding Site of the Tau Protein Proline-Rich Region. Biochemistry 2023. [PMID: 37167199 DOI: 10.1021/acs.biochem.2c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
An increase in phosphorylation of the Tau protein is associated with Alzheimer's disease (AD) progression through unclear molecular mechanisms. In general, phosphorylation modifies the interaction of intrinsically disordered proteins, such as Tau, with other proteins; however, elucidating the structural basis of this regulation mechanism remains challenging. The bridging integrator-1 gene is an AD genetic determinant whose gene product, BIN1, directly interacts with Tau. The proline-rich motif recognized within a Tau(210-240) peptide by the SH3 domain of BIN1 (BIN1 SH3) is defined as 216PTPP219, and this interaction is modulated by phosphorylation. Phosphorylation of T217 within the Tau(210-240) peptide led to a 6-fold reduction in the affinity, while single phosphorylation at either T212, T231, or S235 had no effect on the interaction. Nonetheless, combined phosphorylation of T231 and S235 led to a 3-fold reduction in the affinity, although these phosphorylations are not within the BIN1 SH3-bound region of the Tau peptide. Using nuclear magnetic resonance (NMR) spectroscopy, these phosphorylations were shown to affect the local secondary structure and dynamics of the Tau(210-240) peptide. Models of the (un)phosphorylated peptides were obtained from molecular dynamics (MD) simulation validated by experimental data and showed compaction of the phosphorylated peptide due to increased salt bridge formation. This dynamic folding might indirectly impact the BIN1 SH3 binding by a decreased accessibility of the binding site. Regulation of the binding might thus not only be due to local electrostatic or steric effects from phosphorylation but also to the modification of the conformational properties of Tau.
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Affiliation(s)
- Alessia Lasorsa
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Idir Malki
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
| | - Elian Dupré
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - François-Xavier Cantrelle
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Hamida Merzougui
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
| | - Davy Sinnaeve
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Xavier Hanoulle
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Isabelle Landrieu
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
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Corsi A, Bombieri C, Valenti MT, Romanelli MG. Tau Isoforms: Gaining Insight into MAPT Alternative Splicing. Int J Mol Sci 2022; 23:ijms232315383. [PMID: 36499709 PMCID: PMC9735940 DOI: 10.3390/ijms232315383] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/27/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Tau microtubule-associated proteins, encoded by the MAPT gene, are mainly expressed in neurons participating in axonal transport and synaptic plasticity. Six major isoforms differentially expressed during cell development and differentiation are translated by alternative splicing of MAPT transcripts. Alterations in the expression of human Tau isoforms and their aggregation have been linked to several neurodegenerative diseases called tauopathies, including Alzheimer's disease, progressive supranuclear palsy, Pick's disease, and frontotemporal dementia with parkinsonism linked to chromosome 17. Great efforts have been dedicated in recent years to shed light on the complex regulatory mechanism of Tau splicing, with a perspective to developing new RNA-based therapies. This review summarizes the most recent contributions to the knowledge of Tau isoform expression and experimental models, highlighting the role of cis-elements and ribonucleoproteins that regulate the alternative splicing of Tau exons.
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Specific phosphorylation of microtubule-associated protein 2c by extracellular signal-regulated kinase reduces interactions at its Pro-rich regions. J Biol Chem 2022; 298:102384. [PMID: 35987383 PMCID: PMC9520037 DOI: 10.1016/j.jbc.2022.102384] [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: 01/17/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022] Open
Abstract
Microtubule-associated protein 2 (MAP2) is an important neuronal target of extracellular signal-regulated kinase 2 (ERK2) involved in Raf signaling pathways, but mechanistic details of MAP2 phosphorylation are unclear. Here, we used NMR spectroscopy to quantitatively describe the kinetics of phosphorylation of individual serines and threonines in the embryonic MAP2 variant MAP2c. We carried out real-time monitoring of phosphorylation to discover major phosphorylation sites that were not identified in previous studies relying on specific antibodies. Our comparison with phosphorylation of MAP2c by a model cyclin-dependent kinase CDK2 and with phosphorylation of the MAP2c homolog Tau revealed differences in phosphorylation profiles that explain specificity of regulation of biological functions of MAP2c and Tau. To probe the molecular basis of the regulatory effect of ERK2, we investigated the interactions of phosphorylated and unphosphorylated MAP2c by NMR with single-residue resolution. As ERK2 phosphorylates mostly outside the regions binding microtubules, we studied the binding of proteins other than tubulin, namely regulatory subunit RIIα of cAMP-dependent protein kinase (PKA), adaptor protein Grb2, Src homology domain 3 of tyrosine kinases Fyn and Abl, and ERK2 itself. We found ERK2 phosphorylation interfered mostly with binding to proline-rich regions of MAP2c. Furthermore, our NMR experiments in SH-SY5Y neuroblastoma cell lysates showed that the kinetics of dephosphorylation are compatible with in-cell NMR studies and that residues targeted by ERK2 and PKA are efficiently phosphorylated in the cell lysates. Taken together, our results provide a deeper characterization of MAP2c phosphorylation and its effects on interactions with other proteins.
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Hernández F, Ferrer I, Pérez M, Zabala JC, Del Rio JA, Avila J. Tau aggregation. Neuroscience 2022; 518:64-69. [PMID: 35525497 DOI: 10.1016/j.neuroscience.2022.04.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
Abstract
Here we revisit tau protein aggregation at primary, secondary, tertiary and quaternary structures. In addition, the presence of non-aggregated tau protein, which has been recently discovered, is also commented on.
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Affiliation(s)
- Félix Hernández
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid, Spain
| | - Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Bellvitge, University Hospital-IDIBELL, Hospitalet de Llobregat, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Mar Pérez
- Departamento de Anatomía Histología y Neurociencia, Facultad de Medicina UAM, Madrid, Spain
| | - Juan Carlos Zabala
- Department of Molecular Biology, Facultad de Medicina, Universidad de Cantabria, Santander 39005 Spain
| | - Jose Antonio Del Rio
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; Department of Cell Biology, Physiology and Immunology, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain; Institute of Neuroscience, University of Barcelona, 08028 Barcelona, Spain
| | - Jesús Avila
- Centro de Biología Molecular 'Severo Ochoa' (CBMSO) CSIC/UAM, Madrid, Spain; Networking Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain.
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Ruiz-Gabarre D, Carnero-Espejo A, Ávila J, García-Escudero V. What's in a Gene? The Outstanding Diversity of MAPT. Cells 2022; 11:840. [PMID: 35269461 PMCID: PMC8909800 DOI: 10.3390/cells11050840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023] Open
Abstract
Tau protein is a microtubule-associated protein encoded by the MAPT gene that carries out a myriad of physiological functions and has been linked to certain pathologies collectively termed tauopathies, including Alzheimer's disease, frontotemporal dementia, Huntington's disease, progressive supranuclear palsy, etc. Alternative splicing is a physiological process by which cells generate several transcripts from one single gene and may in turn give rise to different proteins from the same gene. MAPT transcripts have been proven to be subjected to alternative splicing, generating six main isoforms in the central nervous system. Research throughout the years has demonstrated that the splicing landscape of the MAPT gene is far more complex than that, including at least exon skipping events, the use of 3' and 5' alternative splice sites and, as has been recently discovered, also intron retention. In addition, MAPT alternative splicing has been showed to be regulated spatially and developmentally, further evidencing the complexity of the gene's splicing regulation. It is unclear what would drive the need for the existence of so many isoforms encoded by the same gene, but a wide range of functions have been ascribed to these Tau isoforms, both in physiology and pathology. In this review we offer a comprehensive up-to-date exploration of the mechanisms leading to the outstanding diversity of isoforms expressed from the MAPT gene and the functions in which such isoforms are involved, including their potential role in the onset and development of tauopathies such as Alzheimer's disease.
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Affiliation(s)
- Daniel Ruiz-Gabarre
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Almudena Carnero-Espejo
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Jesús Ávila
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Vega García-Escudero
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
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10
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Kitoka K, Skrabana R, Gasparik N, Hritz J, Jaudzems K. NMR Studies of Tau Protein in Tauopathies. Front Mol Biosci 2021; 8:761227. [PMID: 34859051 PMCID: PMC8632555 DOI: 10.3389/fmolb.2021.761227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Tauopathies, including Alzheimer's disease (AD), are the most troublesome of all age-related chronic conditions, as there are no well-established disease-modifying therapies for their prevention and treatment. Spatio-temporal distribution of tau protein pathology correlates with cognitive decline and severity of the disease, therefore, tau protein has become an appealing target for therapy. Current knowledge of the pathological effects and significance of specific species in the tau aggregation pathway is incomplete although more and more structural and mechanistic insights are being gained using biophysical techniques. Here, we review the application of NMR to structural studies of various tau forms that appear in its aggregation process, focusing on results obtained from solid-state NMR. Furthermore, we discuss implications from these studies and their prospective contribution to the development of new tauopathy therapies.
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Affiliation(s)
- Kristine Kitoka
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Rostislav Skrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- AXON Neuroscience R&D Services SE, Bratislava, Slovakia
| | - Norbert Gasparik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristaps Jaudzems
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
- Faculty of Chemistry, University of Latvia, Riga, Latvia
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11
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Living with the enemy: from protein-misfolding pathologies we know, to those we want to know. Ageing Res Rev 2021; 70:101391. [PMID: 34119687 DOI: 10.1016/j.arr.2021.101391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022]
Abstract
Conformational diseases are caused by the aggregation of misfolded proteins. The risk for such pathologies develops years before clinical symptoms appear, and is higher in people with alpha-1 antitrypsin (AAT) polymorphisms. Thousands of people with alpha-1 antitrypsin deficiency (AATD) are underdiagnosed. Enemy-aggregating proteins may reside in these underdiagnosed AATD patients for many years before a pathology for AATD fully develops. In this perspective review, we hypothesize that the AAT protein could exert a new and previously unconsidered biological effect as an endogenous metal ion chelator that plays a significant role in essential metal ion homeostasis. In this respect, AAT polymorphism may cause an imbalance of metal ions, which could be correlated with the aggregation of amylin, tau, amyloid beta, and alpha synuclein proteins in type 2 diabetes mellitus (T2DM), Alzheimer's and Parkinson's diseases, respectively.
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12
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Grubisha MJ, Sun X, MacDonald ML, Garver M, Sun Z, Paris KA, Patel DS, DeGiosio RA, Lewis DA, Yates NA, Camacho C, Homanics GE, Ding Y, Sweet RA. MAP2 is differentially phosphorylated in schizophrenia, altering its function. Mol Psychiatry 2021; 26:5371-5388. [PMID: 33526823 PMCID: PMC8325721 DOI: 10.1038/s41380-021-01034-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 01/04/2021] [Accepted: 01/15/2021] [Indexed: 01/30/2023]
Abstract
Schizophrenia (Sz) is a highly polygenic disorder, with common, rare, and structural variants each contributing only a small fraction of overall disease risk. Thus, there is a need to identify downstream points of convergence that can be targeted with therapeutics. Reduction of microtubule-associated protein 2 (MAP2) immunoreactivity (MAP2-IR) is present in individuals with Sz, despite no change in MAP2 protein levels. MAP2 is phosphorylated downstream of multiple receptors and kinases identified as Sz risk genes, altering its immunoreactivity and function. Using an unbiased phosphoproteomics approach, we quantified 18 MAP2 phosphopeptides, 9 of which were significantly altered in Sz subjects. Network analysis grouped MAP2 phosphopeptides into three modules, each with a distinct relationship to dendritic spine loss, synaptic protein levels, and clinical function in Sz subjects. We then investigated the most hyperphosphorylated site in Sz, phosphoserine1782 (pS1782). Computational modeling predicted phosphorylation of S1782 reduces binding of MAP2 to microtubules, which was confirmed experimentally. We generated a transgenic mouse containing a phosphomimetic mutation at S1782 (S1782E) and found reductions in basilar dendritic length and complexity along with reduced spine density. Because only a limited number of MAP2 interacting proteins have been previously identified, we combined co-immunoprecipitation with mass spectrometry to characterize the MAP2 interactome in mouse brain. The MAP2 interactome was enriched for proteins involved in protein translation. These associations were shown to be functional as overexpression of wild type and phosphomimetic MAP2 reduced protein synthesis in vitro. Finally, we found that Sz subjects with low MAP2-IR had reductions in the levels of synaptic proteins relative to nonpsychiatric control (NPC) subjects and to Sz subjects with normal and MAP2-IR, and this same pattern was recapitulated in S1782E mice. These findings suggest a new conceptual framework for Sz-that a large proportion of individuals have a "MAP2opathy"-in which MAP function is altered by phosphorylation, leading to impairments of neuronal structure, synaptic protein synthesis, and function.
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Affiliation(s)
- M J Grubisha
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - X Sun
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Tsinghua MD Program, School of Medicine, Tsinghua University, Beijing, China
| | - M L MacDonald
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Garver
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Z Sun
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - K A Paris
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - D S Patel
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A DeGiosio
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D A Lewis
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - N A Yates
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - C Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - G E Homanics
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, Translational Neuroscience Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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13
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Cantrelle FX, Loyens A, Trivelli X, Reimann O, Despres C, Gandhi NS, Hackenberger CPR, Landrieu I, Smet-Nocca C. Phosphorylation and O-GlcNAcylation of the PHF-1 Epitope of Tau Protein Induce Local Conformational Changes of the C-Terminus and Modulate Tau Self-Assembly Into Fibrillar Aggregates. Front Mol Neurosci 2021; 14:661368. [PMID: 34220449 PMCID: PMC8249575 DOI: 10.3389/fnmol.2021.661368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Phosphorylation of the neuronal microtubule-associated Tau protein plays a critical role in the aggregation process leading to the formation of insoluble intraneuronal fibrils within Alzheimer's disease (AD) brains. In recent years, other posttranslational modifications (PTMs) have been highlighted in the regulation of Tau (dys)functions. Among these PTMs, the O-β-linked N-acetylglucosaminylation (O-GlcNAcylation) modulates Tau phosphorylation and aggregation. We here focus on the role of the PHF-1 phospho-epitope of Tau C-terminal domain that is hyperphosphorylated in AD (at pS396/pS404) and encompasses S400 as the major O-GlcNAc site of Tau while two additional O-GlcNAc sites were found in the extreme C-terminus at S412 and S413. Using high resolution NMR spectroscopy, we showed that the O-GlcNAc glycosylation reduces phosphorylation of PHF-1 epitope by GSK3β alone or after priming by CDK2/cyclin A. Furthermore, investigations of the impact of PTMs on local conformation performed in small peptides highlight the role of S404 phosphorylation in inducing helical propensity in the region downstream pS404 that is exacerbated by other phosphorylations of PHF-1 epitope at S396 and S400, or O-GlcNAcylation of S400. Finally, the role of phosphorylation and O-GlcNAcylation of PHF-1 epitope was probed in in-vitro fibrillization assays in which O-GlcNAcylation slows down the rate of fibrillar assembly while GSK3β phosphorylation stimulates aggregation counteracting the effect of glycosylation.
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Affiliation(s)
- François-Xavier Cantrelle
- Risk Factors and Molecular Determinants of Aging-Related Diseases, U1167, Institut Pasteur de Lille, CHU Lille, INSERM, University of Lille, Lille, France.,CNRS, ERL9002 - Integrative Structural Biology, Lille, France
| | - Anne Loyens
- Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, U1172, CHU Lille, INSERM, University of Lille, Lille, France
| | - Xavier Trivelli
- Université de Lille, CNRS, INRAE, Centrale Lille, Université d'Artois, Lille, France
| | - Oliver Reimann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Clément Despres
- Risk Factors and Molecular Determinants of Aging-Related Diseases, U1167, Institut Pasteur de Lille, CHU Lille, INSERM, University of Lille, Lille, France
| | - Neha S Gandhi
- Centre for Genomics and Personalised Health, Cancer and Ageing Research Program, School of Chemistry and Physics, Faculty of Science and Engineering, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Isabelle Landrieu
- Risk Factors and Molecular Determinants of Aging-Related Diseases, U1167, Institut Pasteur de Lille, CHU Lille, INSERM, University of Lille, Lille, France.,CNRS, ERL9002 - Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- Risk Factors and Molecular Determinants of Aging-Related Diseases, U1167, Institut Pasteur de Lille, CHU Lille, INSERM, University of Lille, Lille, France.,CNRS, ERL9002 - Integrative Structural Biology, Lille, France
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14
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Rani L, Mallajosyula SS. Phosphorylation-Induced Structural Reorganization in Tau-Paired Helical Filaments. ACS Chem Neurosci 2021; 12:1621-1631. [PMID: 33877805 DOI: 10.1021/acschemneuro.1c00084] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Taupathies involve the deposition of abnormal tau protein into neurofibrillary tangles (NFTs) in the human brain. The abnormally hyperphosphorylated tau dissociates from microtubules and forms insoluble aggregates known as paired helical filaments (PHFs), highlighting the importance of post-translational modifications in taupathies. The present study examines the factors responsible for the structural stability of PHFs in native as well as in phosphorylated and O-GlcNAcylated tau. We carried out molecular dynamics simulations on the R3-R4 repeat domains of the human tau protein to gain atomic insights into the key noncovalent interactions responsible for their unique dimeric C-shaped structure. The structural effects upon post-translational modification were found to be prominent for phosphorylation when compared with O-GlcNAcylation. O-GlcNAcylated tau was found to retain the "C conformation" observed in the native tau PHF, whereas upon phosphorylation, we observed a conformational transition to a more opened "H conformation". We found that this conformational transition is brought about by the loss of a key salt bridge between Lys353 and Asp358 due to the phosphorylation at Ser356 that results in the reorganization of the dimeric interface.
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Affiliation(s)
- Lata Rani
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, Gujarat, India
| | - Sairam S. Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, Gujarat, India
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15
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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16
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Keramidis I, Vourkou E, Papanikolopoulou K, Skoulakis EMC. Functional Interactions of Tau Phosphorylation Sites That Mediate Toxicity and Deficient Learning in Drosophila melanogaster. Front Mol Neurosci 2020; 13:569520. [PMID: 33192295 PMCID: PMC7609872 DOI: 10.3389/fnmol.2020.569520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023] Open
Abstract
Hyperphosphorylated Tau protein is the main component of the neurofibrillary tangles, characterizing degenerating neurons in Alzheimer’s disease and other Tauopathies. Expression of human Tau protein in Drosophila CNS results in increased toxicity, premature mortality and learning and memory deficits. Herein we use novel transgenic lines to investigate the contribution of specific phosphorylation sites previously implicated in Tau toxicity. These three different sites, Ser238, Thr245, and Ser262 were tested either by blocking their phosphorylation, by Ser/Thr to Ala substitution, or pseudophosphorylation, by changing Ser/Thr to Glu. We validate the hypothesis that phosphorylation at Ser262 is necessary for Tau-dependent learning deficits and a “facilitatory gatekeeper” to Ser238 occupation, which is linked to Tau toxicity. Importantly we reveal that phosphorylation at Thr245 acts as a “suppressive gatekeeper”, preventing phosphorylation of many sites including Ser262 and consequently of Ser238. Therefore, we elucidate novel interactions among phosphosites central to Tau mediated neuronal dysfunction and toxicity, likely driven by phosphorylation-dependent conformational plasticity.
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Affiliation(s)
- Iason Keramidis
- Biomedical Sciences Research Centre "Alexander Fleming", Institute for Fundamental Biomedical Research, Vari, Greece
| | - Ergina Vourkou
- Biomedical Sciences Research Centre "Alexander Fleming", Institute for Fundamental Biomedical Research, Vari, Greece.,1st Department of Neurology, Memory and Movement Disorders Clinic, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Biomedical Sciences Research Centre "Alexander Fleming", Institute for Fundamental Biomedical Research, Vari, Greece
| | - Efthimios M C Skoulakis
- Biomedical Sciences Research Centre "Alexander Fleming", Institute for Fundamental Biomedical Research, Vari, Greece
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17
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Barracchia CG, Tira R, Parolini F, Munari F, Bubacco L, Spyroulias GA, D’Onofrio M, Assfalg M. Unsaturated Fatty Acid-Induced Conformational Transitions and Aggregation of the Repeat Domain of Tau. Molecules 2020; 25:molecules25112716. [PMID: 32545360 PMCID: PMC7321374 DOI: 10.3390/molecules25112716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
Background: The intrinsically disordered, amyloidogenic protein Tau associates with diverse classes of molecules, including proteins, nucleic acids, and lipids. Mounting evidence suggests that fatty acid molecules could play a role in the dysfunction of this protein, however, their interaction with Tau remains poorly characterized. Methods: In a bid to elucidate the association of Tau with unsaturated fatty acids at the sub-molecular level, we carried out a variety of solution NMR experiments in combination with circular dichroism and fluorescence measurements. Our study shows that Tau4RD, the highly basic four-repeat domain of Tau, associates strongly with arachidonic and oleic acid assemblies in a high lipid/protein ratio, perturbing their supramolecular states and itself undergoing time-dependent structural adaptation. The structural signatures of Tau4RD/fatty acid aggregates appear similar for arachidonic acid and oleic acid, however, they are distinct from those of another prototypical intrinsically disordered protein, α-synuclein, when bound to these lipids, revealing protein-specific conformational adaptations. Both fatty acid molecules are found to invariably promote the self-aggregation of Tau4RD and of α-synuclein. Conclusions: This study describes the reciprocal influence that Tau4RD and fatty acids exert on their conformational states, contributing to our understanding of fundamental aspects of Tau/lipid co-assembly.
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Affiliation(s)
- Carlo Giorgio Barracchia
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.G.B.); (R.T.); (F.P.); (F.M.); (M.D.)
| | - Roberto Tira
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.G.B.); (R.T.); (F.P.); (F.M.); (M.D.)
| | - Francesca Parolini
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.G.B.); (R.T.); (F.P.); (F.M.); (M.D.)
| | - Francesca Munari
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.G.B.); (R.T.); (F.P.); (F.M.); (M.D.)
| | - Luigi Bubacco
- Department of Biology, University of Padova, 35131 Padova, Italy;
| | | | - Mariapina D’Onofrio
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.G.B.); (R.T.); (F.P.); (F.M.); (M.D.)
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.G.B.); (R.T.); (F.P.); (F.M.); (M.D.)
- Correspondence:
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18
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Song D, Liu H, Luo R, Chen HF. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. J Chem Inf Model 2020; 60:2257-2267. [PMID: 32227937 PMCID: PMC10449432 DOI: 10.1021/acs.jcim.0c00059] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The need for accurate and efficient force fields for modeling 3D structures of macrobiomolecules and in particular intrinsically disordered proteins (IDPs) has increased with recent findings to associate IDPs and human diseases. However, most conventional protein force fields and recent IDP-specific force fields are limited in reproducing accurate structural features of IDPs. Here, we present an environmental specific precise force field (ESFF1) based on CMAP corrections of 71 different sequence environments to improve the accuracy and efficiency of MD simulation for both IDPs and folded proteins. MD simulations of 84 different short peptides, IDPs, and structured proteins show that ESFF1 can accurately reproduce spectroscopic properties for different peptides and proteins whether they are disordered or ordered. The successful ab initio folding of five fast-folding proteins further supports the reliability of ESFF1. The extensive analysis documented here shows that ESFF1 is able to achieve a reasonable balance between ordered and disordered states in protein simulations.
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Affiliation(s)
- Dong Song
- 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
| | - Hao Liu
- 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
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Molecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697-3900, United States
| | - 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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19
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Zhao J, Zhu Y, Song X, Xiao Y, Su G, Liu X, Wang Z, Xu Y, Liu J, Eliezer D, Ramlall TF, Lippens G, Gibson J, Zhang F, Linhardt RJ, Wang L, Wang C. 3‐
O
‐Sulfation of Heparan Sulfate Enhances Tau Interaction and Cellular Uptake. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
| | - Yanan Zhu
- Department of Molecular Pharmacology and PhysiologyUniversity of South Florida Tampa USA
| | - Xuehong Song
- Department of Molecular Pharmacology and PhysiologyUniversity of South Florida Tampa USA
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
| | - Guowei Su
- Division of Chemical Biology and Medicinal ChemistryEshelman School of PharmacyUniversity of North Carolina Chapel Hill USA
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
| | - Zhangjie Wang
- Division of Chemical Biology and Medicinal ChemistryEshelman School of PharmacyUniversity of North Carolina Chapel Hill USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal ChemistryEshelman School of PharmacyUniversity of North Carolina Chapel Hill USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal ChemistryEshelman School of PharmacyUniversity of North Carolina Chapel Hill USA
| | - David Eliezer
- Department of BiochemistryProgram in Structural BiologyWeill Cornell Medical College New York NY USA
| | - Trudy F. Ramlall
- Department of BiochemistryProgram in Structural BiologyWeill Cornell Medical College New York NY USA
| | - Guy Lippens
- Toulouse Biotechnology InstituteCNRS, INRAINSAUniversity of Toulouse 31077 Toulouse France
| | - James Gibson
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
- Department of Chemistry and Chemical BiologyRensselaer Polytechnic Institute Troy NY USA
| | - Robert J. Linhardt
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
- Department of Chemistry and Chemical BiologyRensselaer Polytechnic Institute Troy NY USA
| | - Lianchun Wang
- Department of Molecular Pharmacology and PhysiologyUniversity of South Florida Tampa USA
- Byrd Alzheimer's Research Institute, Morsani College of MedicineUniversity of South Florida Tampa USA
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy NY USA
- Department of Biological SciencesRensselaer Polytechnic Institute Troy NY USA
- Department of Chemistry and Chemical BiologyRensselaer Polytechnic Institute Troy NY USA
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20
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Zhao J, Zhu Y, Song X, Xiao Y, Su G, Liu X, Wang Z, Xu Y, Liu J, Eliezer D, Ramlall TF, Lippens G, Gibson J, Zhang F, Linhardt RJ, Wang L, Wang C. 3-O-Sulfation of Heparan Sulfate Enhances Tau Interaction and Cellular Uptake. Angew Chem Int Ed Engl 2020; 59:1818-1827. [PMID: 31692167 PMCID: PMC6982596 DOI: 10.1002/anie.201913029] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/29/2019] [Indexed: 12/31/2022]
Abstract
Prion-like transcellular spreading of tau in Alzheimer's Disease (AD) is mediated by tau binding to cell surface heparan sulfate (HS). However, the structural determinants for tau-HS interaction are not well understood. Microarray and SPR assays of structurally defined HS oligosaccharides show that a rare 3-O-sulfation (3-O-S) of HS significantly enhances tau binding. In Hs3st1-/- (HS 3-O-sulfotransferase-1 knockout) cells, reduced 3-O-S levels of HS diminished both cell surface binding and internalization of tau. In a cell culture, the addition of a 3-O-S HS 12-mer reduced both tau cell surface binding and cellular uptake. NMR titrations mapped 3-O-S binding sites to the microtubule binding repeat 2 (R2) and proline-rich region 2 (PRR2) of tau. Tau is only the seventh protein currently known to recognize HS 3-O-sulfation. Our work demonstrates that this rare 3-O-sulfation enhances tau-HS binding and likely the transcellular spread of tau, providing a novel target for disease-modifying treatment of AD and other tauopathies.
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Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
| | - Yanan Zhu
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Xuehong Song
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
| | - Guowei Su
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, United States
| | - Xinyue Liu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
| | - Zhangjie Wang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, United States
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, United States
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, United States
| | - David Eliezer
- Department of Biochemistry, Program in Structural Biology, Weill Cornell Medical College, New York, New York, United States
| | - Trudy F. Ramlall
- Department of Biochemistry, Program in Structural Biology, Weill Cornell Medical College, New York, New York, United States
| | - Guy Lippens
- Toulouse Biotechnology Institute, CNRS, INRA, INSA, University of Toulouse, 31077 Toulouse, France
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, United States
| | - Robert J. Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, United States
| | - Lianchun Wang
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, United States
- Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, United States
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21
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Hendus-Altenburger R, Fernandes CB, Bugge K, Kunze MBA, Boomsma W, Kragelund BB. Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range. JOURNAL OF BIOMOLECULAR NMR 2019; 73:713-725. [PMID: 31598803 PMCID: PMC6875518 DOI: 10.1007/s10858-019-00283-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/30/2019] [Indexed: 05/26/2023]
Abstract
Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Catarina B Fernandes
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Micha B A Kunze
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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22
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Kumar A, Narayanan V, Sekhar A. Characterizing Post-Translational Modifications and Their Effects on Protein Conformation Using NMR Spectroscopy. Biochemistry 2019; 59:57-73. [PMID: 31682116 DOI: 10.1021/acs.biochem.9b00827] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of the cellular proteome substantially exceeds the number of genes coded by the DNA of an organism because one or more residues in a majority of eukaryotic proteins are post-translationally modified (PTM) by the covalent conjugation of specific chemical groups. We now know that PTMs alter protein conformation and function in ways that are not entirely understood at the molecular level. NMR spectroscopy has been particularly successful as an analytical tool in elucidating the themes underlying the structural role of PTMs. In this Perspective, we focus on the NMR-based characterization of three abundant PTMs: phosphorylation, acetylation, and glycosylation. We detail NMR methods that have found success in detecting these modifications at a site-specific level. We also highlight NMR studies that have mapped the conformational changes ensuing from these PTMs as well as evaluated their relation to function. The NMR toolbox is expanding rapidly with experiments available to probe not only the average structure of biomolecules but also how this structure changes with time on time scales ranging from picoseconds to seconds. The atomic resolution insights into the biomolecular structure, dynamics, and mechanism accessible from NMR spectroscopy ensure that NMR will continue to be at the forefront of research in the structural biology of PTMs.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Vaishali Narayanan
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560 012 , India
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23
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Yang S, Liu H, Zhang Y, Lu H, Chen H. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. J Chem Inf Model 2019; 59:4793-4805. [DOI: 10.1021/acs.jcim.9b00647] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheng Yang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, 800 Dongchuan Road, Shanghai, 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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24
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Barbier P, Zejneli O, Martinho M, Lasorsa A, Belle V, Smet-Nocca C, Tsvetkov PO, Devred F, Landrieu I. Role of Tau as a Microtubule-Associated Protein: Structural and Functional Aspects. Front Aging Neurosci 2019; 11:204. [PMID: 31447664 PMCID: PMC6692637 DOI: 10.3389/fnagi.2019.00204] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/18/2019] [Indexed: 12/24/2022] Open
Abstract
Microtubules (MTs) play a fundamental role in many vital processes such as cell division and neuronal activity. They are key structural and functional elements in axons, supporting neurite differentiation and growth, as well as transporting motor proteins along the axons, which use MTs as support tracks. Tau is a stabilizing MT associated protein, whose functions are mainly regulated by phosphorylation. A disruption of the MT network, which might be caused by Tau loss of function, is observed in a group of related diseases called tauopathies, which includes Alzheimer’s disease (AD). Tau is found hyperphosphorylated in AD, which might account for its loss of MT stabilizing capacity. Since destabilization of MTs after dissociation of Tau could contribute to toxicity in neurodegenerative diseases, a molecular understanding of this interaction and its regulation is essential.
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Affiliation(s)
- Pascale Barbier
- Fac Pharm, Aix Marseille Univ., Centre National de la Recherche Scientifique (CNRS), Inst Neurophysiopathol (INP), Fac Pharm, Marseille, France
| | - Orgeta Zejneli
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Lille, France.,Univ. Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), CHU-Lille, UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT (JPArc), Lille, France
| | - Marlène Martinho
- Aix Marseille Univ., Centre National de la Recherche Scientifique (CNRS), UMR 7281, Bioénergétique et Ingénierie des Protéines (BIP), Marseille, France
| | - Alessia Lasorsa
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Lille, France
| | - Valérie Belle
- Aix Marseille Univ., Centre National de la Recherche Scientifique (CNRS), UMR 7281, Bioénergétique et Ingénierie des Protéines (BIP), Marseille, France
| | - Caroline Smet-Nocca
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Lille, France
| | - Philipp O Tsvetkov
- Fac Pharm, Aix Marseille Univ., Centre National de la Recherche Scientifique (CNRS), Inst Neurophysiopathol (INP), Fac Pharm, Marseille, France
| | - François Devred
- Fac Pharm, Aix Marseille Univ., Centre National de la Recherche Scientifique (CNRS), Inst Neurophysiopathol (INP), Fac Pharm, Marseille, France
| | - Isabelle Landrieu
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Lille, France
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25
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Despres C, Di J, Cantrelle FX, Li Z, Huvent I, Chambraud B, Zhao J, Chen J, Chen S, Lippens G, Zhang F, Linhardt R, Wang C, Klärner FG, Schrader T, Landrieu I, Bitan G, Smet-Nocca C. Major Differences between the Self-Assembly and Seeding Behavior of Heparin-Induced and in Vitro Phosphorylated Tau and Their Modulation by Potential Inhibitors. ACS Chem Biol 2019; 14:1363-1379. [PMID: 31046227 PMCID: PMC6636790 DOI: 10.1021/acschembio.9b00325] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Self-assembly of
the microtubule-associated protein tau into neurotoxic
oligomers, fibrils, and paired helical filaments, and cell-to-cell
spreading of these pathological tau species are critical processes
underlying the pathogenesis of Alzheimer’s disease and other
tauopathies. Modulating the self-assembly process and inhibiting formation
and spreading of such toxic species are promising strategies for therapy
development. A challenge in investigating tau self-assembly in vitro
is that, unlike most amyloidogenic proteins, tau does not aggregate
in the absence of posttranslational modifications (PTM), aggregation
inducers, or preformed seeds. The most common induction method is
addition of polyanions, such as heparin; yet, this artificial system
may not represent adequately tau self-assembly in vivo, which is driven
by aberrant phosphorylation and other PTMs, potentially leading to
in vitro data that do not reflect the behavior of tau and its interaction
with modulators in vivo. To tackle these challenges, methods for in
vitro phosphorylation of tau to produce aggregation-competent forms
recently have been introduced (Despres
et al. (2017) Proc. Natl. Acad. Sci. U.S.A., 114, 9080−908528784767). However, the oligomerization, seeding, and interaction
with assembly modulators of the different forms of tau have not been
studied to date. To address these knowledge gaps, we compared here
side-by-side the self-assembly and seeding activity of heparin-induced
tau with two forms of in vitro phosphorylated tau and tested how the
molecular tweezer CLR01, a negatively charged compound, affected these
processes. Tau was phosphorylated by incubation either with activated
extracellular signal-regulated kinase 2 or with a whole rat brain
extract. Seeding activity was measured using a fluorescence-resonance
energy transfer-based biosensor-cell method. We also used solution-state
NMR to investigate the binding sites of CLR01 on tau and how they
were impacted by phosphorylation. Our systematic structure–activity
relationship study demonstrates that heparin-induced tau behaves differently
from in vitro phosphorylated tau. The aggregation rates of the different
forms are distinct as is the intracellular localization of the induced
aggregates, which resemble brain-derived tau strains suggesting that
heparin-induced tau and in vitro phosphorylated tau have different
conformations, properties, and activities. CLR01 inhibits aggregation
and seeding of both heparin-induced and in vitro phosphorylated tau
dose-dependently, although heparin induction interferes with the interaction
between CLR01 and tau.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianle Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Shiguo Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Guy Lippens
- Lille University CNRS UMR 8576, UGSF, F-59000 Lille, France
| | | | - Robert Linhardt
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | | | - Frank-Gerrit Klärner
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
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26
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Didonna A, Opal P. The role of neurofilament aggregation in neurodegeneration: lessons from rare inherited neurological disorders. Mol Neurodegener 2019; 14:19. [PMID: 31097008 PMCID: PMC6524292 DOI: 10.1186/s13024-019-0318-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
Many neurodegenerative disorders, including Parkinson's, Alzheimer's, and amyotrophic lateral sclerosis, are well known to involve the accumulation of disease-specific proteins. Less well known are the accumulations of another set of proteins, neuronal intermediate filaments (NFs), which have been observed in these diseases for decades. NFs belong to the family of cytoskeletal intermediate filament proteins (IFs) that give cells their shape; they determine axonal caliber, which controls signal conduction; and they regulate the transport of synaptic vesicles and modulate synaptic plasticity by binding to neurotransmitter receptors. In the last two decades, a number of rare disorders caused by mutations in genes that encode NFs or regulate their metabolism have been discovered. These less prevalent disorders are providing novel insights into the role of NF aggregation in the more common neurological disorders.
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Affiliation(s)
- Alessandro Didonna
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Puneet Opal
- Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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27
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Danis C, Dupré E, Hanoulle X, Landrieu I, Lasorsa A, Neves JF, Schneider R, Smet-Nocca C. Nuclear Magnetic Resonance Spectroscopy Insights into Tau Structure in Solution: Impact of Post-translational Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1184:35-45. [PMID: 32096026 DOI: 10.1007/978-981-32-9358-8_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although Tau is an intrinsically disordered protein, some level of structure can still be defined, corresponding to short stretches of dynamic secondary structures and a preferential global fold described as an ensemble of conformations. These structures can be modified by Tau phosphorylation, and potentially other post-translational modifications. The analytical capacity of Nuclear Magnetic Resonance (NMR) spectroscopy provides the advantage of offering a residue-specific view of these modifications, allowing to link specific sites to a particular structure. The cis or trans conformation of X-Proline peptide bonds is an additional characteristic parameter of Tau structure that is targeted and modified by prolyl cis/trans isomerases. The challenge in molecular characterization of Tau lies in being able to link structural parameters to functional consequences in normal functions and dysfunctions of Tau, including potential misfolding on the path to aggregation and/or perturbation of the interactions of Tau with its many molecular partners. Phosphorylation of Ser and Thr residues has the potential to impact the local and global structure of Tau.
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Affiliation(s)
- Clément Danis
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Elian Dupré
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Xavier Hanoulle
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Isabelle Landrieu
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
| | - Alessia Lasorsa
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - João Filipe Neves
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Robert Schneider
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Caroline Smet-Nocca
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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28
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Lasorsa A, Malki I, Cantrelle FX, Merzougui H, Boll E, Lambert JC, Landrieu I. Structural Basis of Tau Interaction With BIN1 and Regulation by Tau Phosphorylation. Front Mol Neurosci 2018; 11:421. [PMID: 30487734 PMCID: PMC6246682 DOI: 10.3389/fnmol.2018.00421] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
Bridging integrator-1 (BIN1) gene is associated with an increased risk to develop Alzheimer's disease, a tauopathy characterized by intra-neuronal accumulation of phosphorylated Tau protein as paired helical filaments. Direct interaction of BIN1 and Tau proteins was demonstrated to be mediated through BIN1 SH3 C-terminal domain and Tau (210-240) peptide within Tau proline-rich domain. We previously showed that BIN1 SH3 interaction with Tau is decreased by phosphorylation within Tau proline-rich domain, of at least T231. In addition, the BIN1/Tau interaction is characterized by a dynamic equilibrium between a closed and open conformations of BIN1 isoform 1, involving an intramolecular interaction with its C-terminal BIN1 SH3 domain. However, the role of the BIN1/Tau interaction, and its potential dysregulation in Alzheimer's disease, is not yet fully understood. Here we showed that within Tau (210-240) peptide, among the two proline-rich motifs potentially recognized by SH3 domains, only motif P216TPPTR221 is bound by BIN1 SH3. A structural model of the complex between BIN1 SH3 and Tau peptide (213-229), based on nuclear magnetic resonance spectroscopy data, revealed the molecular detail of the interaction. P216 and P219 within the proline-rich motif were in direct contact with the aromatic F588 and W562 of the BIN1 SH3 domain. The contact surface is extended through electrostatic interactions between the positively charged R221 and K224 residues of Tau peptide and those negatively charged of BIN1 SH3, corresponding to E556 and E557. We next investigated the impact of multiple Tau phosphorylations within Tau (210-240) on its interaction with BIN1 isoform 1. Tau (210-240) phosphorylated at four different sites (T212, T217, T231, and S235), contrary to unphosphorylated Tau, was unable to compete with the intramolecular interaction of BIN1 SH3 domain with its CLAP domain. In accordance, the affinity of BIN1 SH3 for phosphorylated Tau (210-240) peptide was reduced, with a five-fold increase in the dissociation constant, from a Kd of 44 to 256 μM. This study highlights the complexity of the regulation of BIN1 isoform 1 with Tau. As abnormal phosphorylation of Tau is linked to the pathology development, this regulation by phosphorylation might have important functional consequences.
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Affiliation(s)
| | - Idir Malki
- CNRS UMR8576, Lille University, Lille, France
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29
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Abstract
NMR spectroscopy has proven to be a key method for studying intrinsically disordered proteins (IDPs). Nonetheless, traditional NMR methods developed for solving structures of ordered protein complexes are insufficient for the full characterization of dynamic IDP complexes, where the energy landscape is broader and more rugged. Furthermore, due to their high sensitivity to environmental changes, NMR studies of IDP complexes must be conducted with extra care and the observed NMR parameters thoroughly evaluated to enable disentanglement of binding events from ensemble distribution changes. In this chapter, written for the non-NMR expert, we start out by outlining sample preparation for IDP complexes, guide through the recording and evaluation of diagnostic 1H,15N-HSQC spectra, and delineate more sophisticated NMR strategies to follow for the particular type of complex. The most relevant experiments are then described in terms of aims, needs, pitfalls, analysis, and expected outcomes, with references to recent examples.
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30
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Zhang H, Zhu X, Pascual G, Wadia JS, Keogh E, Hoozemans JJ, Siregar B, Inganäs H, Stoop EJM, Goudsmit J, Apetri A, Koudstaal W, Wilson IA. Structural Basis for Recognition of a Unique Epitope by a Human Anti-tau Antibody. Structure 2018; 26:1626-1634.e4. [PMID: 30318466 DOI: 10.1016/j.str.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/23/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023]
Abstract
Aggregation of the hyperphosphorylated protein tau into neurofibrillary tangles and neuropil threads is a hallmark of Alzheimer disease (AD). Identification and characterization of the epitopes recognized by anti-tau antibodies might shed light on the molecular mechanisms of AD pathogenesis. Here we report on the biochemical and structural characterization of a tau-specific monoclonal antibody CBTAU-24.1, which was isolated from the human memory B cell repertoire. Immunohistochemical staining with CBTAU-24.1 specifically detects pathological tau structures in AD brain samples. The crystal structure of CBTAU-24.1 Fab with a phosphorylated tau peptide revealed recognition of a unique epitope (Ser235-Leu243) in the tau proline-rich domain. Interestingly, the antibody can bind tau regardless of phosphorylation state of its epitope region and also recognizes both monomeric and paired helical filament tau irrespective of phosphorylation status. This human anti-tau antibody and its unique epitope may aid in development of diagnostics and/or therapeutic AD strategies.
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Affiliation(s)
- Heng Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Pascual
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Jehangir S Wadia
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Elissa Keogh
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Jeroen J Hoozemans
- Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Berdien Siregar
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Hanna Inganäs
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Esther J M Stoop
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Jaap Goudsmit
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Adrian Apetri
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Wouter Koudstaal
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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31
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Dan A, Chen HF. Secondary structures transition of tau protein with intrinsically disordered proteins specific force field. Chem Biol Drug Des 2018; 93:242-253. [PMID: 30259679 DOI: 10.1111/cbdd.13407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 02/06/2023]
Abstract
Microtubule-associated Tau protein plays a key role in assembling microtubule and modulating the functional organization of the neuron and developing axonal morphology, growth, and polarity. The pathological Tau can aggregate into cross-beta amyloid as one of the hallmarks for Alzheimer's disease (AD). Therefore, one of the top priorities in AD research is to figure out the structural model of Tau aggregation and to screen the inhibitors. The latest generation intrinsically disordered protein specific force field ff14IDPSFF significantly improved the distributions of heterogeneous conformations for intrinsically disordered proteins (IDPs). Here, the molecular dynamics (MD) simulations with three force fields of ff14SB, ff14IDPs, and ff14IDPSFF were employed to investigate the secondary structures transition of Tau (267-312) fragment. The results indicate that ff14IDPSFF can generate more heterogeneous conformers, and the predicted secondary structural distribution is closer to that of the experimental observation. In addition, predicted secondary chemical shifts from ff14IDPSFF are the most approach to those of experiment. Secondary structures transition kinetics for Tau(267-312) with ff14IDPSFF shows that the secondary structures were gradually transformed from α-helix to β-strand and the β-strand located at the regions of the residues 274-280 and residues 305-311. Besides, the driving force for the secondary structures transition of Tau(267-312) is mainly hydrophobic interactions which located at hexa-peptides 275 VQIINK280 and 306 VQIVYK311 . Secondary structure transition of Tau protein can give insight into the aggregation mechanism for AD.
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Affiliation(s)
- Aohuan Dan
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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32
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Liu H, Song D, Lu H, Luo R, Chen HF. Intrinsically disordered protein-specific force field CHARMM36IDPSFF. Chem Biol Drug Des 2018; 92:1722-1735. [DOI: 10.1111/cbdd.13342] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Dong Song
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering; University of California; Irvine California
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
- Shanghai Center for Bioinformation Technology; Shanghai China
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Melková K, Zapletal V, Jansen S, Nomilner E, Zachrdla M, Hritz J, Nováček J, Zweckstetter M, Jensen MR, Blackledge M, Žídek L. Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics. J Biol Chem 2018; 293:13297-13309. [PMID: 29925592 DOI: 10.1074/jbc.ra118.001769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein 2c (MAP2c) is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c. The relaxation rates revealed large differences in flexibility of individual regions of MAP2c, with the lowest flexibility observed in the known and proposed binding sites. Quantitative conformational analyses of chemical shifts, small-angle X-ray scattering (SAXS), and paramagnetic relaxation enhancement measurements disclosed that MAP2c regions interacting with important protein partners, including Fyn tyrosine kinase, plectin, and PKA, adopt specific conformations. High populations of polyproline II and α-helices were found in Fyn- and plectin-binding sites of MAP2c, respectively. The region binding the regulatory subunit of PKA consists of two helical motifs bridged by a more extended conformation. Of note, although MAP2c and Tau did not differ substantially in their conformations in regions of high sequence identity, we found that they differ significantly in long-range interactions, dynamics, and local conformation motifs in their N-terminal domains. These results highlight that the N-terminal regions of MAP2c provide important specificity to its regulatory roles and indicate a close relationship between MAP2c's biological functions and conformational behavior.
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Affiliation(s)
- Kateřina Melková
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Zapletal
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Séverine Jansen
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Erik Nomilner
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milan Zachrdla
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Nováček
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - Markus Zweckstetter
- the Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,the German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Strasse 3a, 37075 Göttingen, Germany, and
| | | | | | - Lukáš Žídek
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic, .,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
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Csizmok V, Forman-Kay JD. Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications. Curr Opin Struct Biol 2018; 48:58-67. [DOI: 10.1016/j.sbi.2017.10.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/07/2017] [Accepted: 10/13/2017] [Indexed: 12/18/2022]
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35
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Brici D, Götz J, Nisbet RM. A Novel Antibody Targeting Tau Phosphorylated at Serine 235 Detects Neurofibrillary Tangles. J Alzheimers Dis 2018; 61:899-905. [DOI: 10.3233/jad-170610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- David Brici
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD, Australia
| | - Rebecca M. Nisbet
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD, Australia
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36
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Ke PC, Sani MA, Ding F, Kakinen A, Javed I, Separovic F, Davis TP, Mezzenga R. Implications of peptide assemblies in amyloid diseases. Chem Soc Rev 2017; 46:6492-6531. [PMID: 28702523 PMCID: PMC5902192 DOI: 10.1039/c7cs00372b] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Neurodegenerative disorders and type 2 diabetes are global epidemics compromising the quality of life of millions worldwide, with profound social and economic implications. Despite the significant differences in pathology - much of which are poorly understood - these diseases are commonly characterized by the presence of cross-β amyloid fibrils as well as the loss of neuronal or pancreatic β-cells. In this review, we document research progress on the molecular and mesoscopic self-assembly of amyloid-beta, alpha synuclein, human islet amyloid polypeptide and prions, the peptides and proteins associated with Alzheimer's, Parkinson's, type 2 diabetes and prion diseases. In addition, we discuss the toxicities of these amyloid proteins based on their self-assembly as well as their interactions with membranes, metal ions, small molecules and engineered nanoparticles. Through this presentation we show the remarkable similarities and differences in the structural transitions of the amyloid proteins through primary and secondary nucleation, the common evolution from disordered monomers to alpha-helices and then to β-sheets when the proteins encounter the cell membrane, and, the consensus (with a few exceptions) that off-pathway oligomers, rather than amyloid fibrils, are the toxic species regardless of the pathogenic protein sequence or physicochemical properties. In addition, we highlight the crucial role of molecular self-assembly in eliciting the biological and pathological consequences of the amyloid proteins within the context of their cellular environments and their spreading between cells and organs. Exploiting such structure-function-toxicity relationship may prove pivotal for the detection and mitigation of amyloid diseases.
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Affiliation(s)
- Pu Chun Ke
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Marc-Antonie Sani
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Aleksandr Kakinen
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ibrahim Javed
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Thomas P. Davis
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Raffaele Mezzenga
- ETH Zurich, Department of Health Science & Technology, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
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37
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Effect of Phosphorylation on a Human-like Osteopontin Peptide. Biophys J 2017; 112:1586-1596. [PMID: 28445750 PMCID: PMC5406370 DOI: 10.1016/j.bpj.2017.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/25/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022] Open
Abstract
The last decade established that the dynamic properties of the phosphoproteome are central to function and its modulation. The temporal dimension of phosphorylation effects remains nonetheless poorly understood, particularly for intrinsically disordered proteins. Osteopontin, selected for this study due to its key role in biomineralization, is expressed in many species and tissues to play a range of distinct roles. A notable property of highly phosphorylated isoforms of osteopontin is their ability to sequester nanoclusters of calcium phosphate to form a core-shell structure, in a fluid that is supersaturated but stable. In Biology, this process enables soft and hard tissues to coexist in the same organism with relative ease. Here, we extend our understanding of the effect of phosphorylation on a disordered protein, the recombinant human-like osteopontin rOPN. The solution structures of the phosphorylated and unphosphorylated rOPN were investigated by small-angle x-ray scattering and no significant changes were detected on the radius of gyration or maximum interatomic distance. The picosecond-to-nanosecond dynamics of the hydrated powders of the two rOPN forms were further compared by elastic and quasi-elastic incoherent neutron scattering. Phosphorylation was found to block some nanosecond side-chain motions while increasing the flexibility of other side chains on the faster timescale. Phosphorylation can thus selectively change the dynamic behavior of even a highly disordered protein such as osteopontin. Through such an effect on rOPN, phosphorylation can direct allosteric mechanisms, interactions with substrates, cofactors and, in this case, amorphous or crystalline biominerals.
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38
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Hendus-Altenburger R, Lambrughi M, Terkelsen T, Pedersen SF, Papaleo E, Lindorff-Larsen K, Kragelund BB. A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1). Cell Signal 2017; 37:40-51. [PMID: 28554535 DOI: 10.1016/j.cellsig.2017.05.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) are involved in many pivotal cellular processes including phosphorylation and signalling. The structural and functional effects of phosphorylation of IDPs remain poorly understood and difficult to predict. Thus, a need exists to identify motifs that confer phosphorylation-dependent perturbation of the local preferences for forming e.g. helical structures as well as motifs that do not. The disordered distal tail of the Na+/H+ exchanger 1 (NHE1) is six-times phosphorylated (S693, S723, S726, S771, T779, S785) by the mitogen activated protein kinase 2 (MAPK1, ERK2). Using NMR spectroscopy, we found that two out of those six phosphorylation sites had a stabilizing effect on transient helices. One of these was further investigated by circular dichroism and NMR spectroscopy as well as by molecular dynamic simulations, which confirmed the stabilizing effect and resulted in the identification of a short linear motif for helix stabilisation: [S/T]-P-{3}-[R/K] where [S/T] is the phosphorylation-site. By analysing IDP and phosphorylation site databases we found that the motif is significantly enriched around known phosphorylation sites, supporting a potential wider-spread role in phosphorylation-mediated regulation of intrinsically disordered proteins. The identification of such motifs is important for understanding the molecular mechanism of cellular signalling, and is crucial for the development of predictors for the structural effect of phosphorylation; a tool of relevance for understanding disease-promoting mutations that for example interfere with signalling for instance through constitutive active and often cancer-promoting signalling.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Strandboulevarden 49, 2100 Copenhagen, Denmark.
| | - Thilde Terkelsen
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Strandboulevarden 49, 2100 Copenhagen, Denmark.
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark.
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Strandboulevarden 49, 2100 Copenhagen, Denmark.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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39
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Lucato CM, Lupton CJ, Halls ML, Ellisdon AM. Amyloidogenicity at a Distance: How Distal Protein Regions Modulate Aggregation in Disease. J Mol Biol 2017; 429:1289-1304. [PMID: 28342736 DOI: 10.1016/j.jmb.2017.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022]
Abstract
The misfolding of proteins to form amyloid is a key pathological feature of several progressive, and currently incurable, diseases. A mechanistic understanding of the pathway from soluble, native protein to insoluble amyloid is crucial for therapeutic design, and recent efforts have helped to elucidate the key molecular events that trigger protein misfolding. Generally, either global or local structural perturbations occur early in amyloidogenesis to expose aggregation-prone regions of the protein that can then self-associate to form toxic oligomers. Surprisingly, these initiating structural changes are often caused or influenced by protein regions distal to the classically amyloidogenic sequences. Understanding the importance of these distal regions in the pathogenic process has highlighted many remaining knowledge gaps regarding the precise molecular events that occur in classic aggregation pathways. In this review, we discuss how these distal regions can influence aggregation in disease and the recent technical and conceptual advances that have allowed this insight.
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Affiliation(s)
- Christina M Lucato
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher J Lupton
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew M Ellisdon
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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40
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Zabik NL, Imhof MM, Martic-Milne S. Structural evaluations of tau protein conformation: methodologies and approaches. Biochem Cell Biol 2017; 95:338-349. [PMID: 28278386 DOI: 10.1139/bcb-2016-0227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Protein-misfolding diseases are based on a common principle of aggregation initiated by intra- and inter-molecular contacts. The structural and conformational changes induced by biochemical transformations such as post-translational modifications (PTMs), often lead to protein unfolding and misfolding. Thus, these order-to-disorder or disorder-to-order transitions may regulate cellular function. Tau, a neuronal protein, regulates microtubule (MT) structure and overall cellular integrity. However, misfolded tau modified by PTMs results in MT destabilization, toxic tau aggregate formation, and ultimately cell death, leading to neurodegeneration. Currently, the lack of structural information surrounding tau severely limits understanding of neurodegeneration. This minireview focuses on the current methodologies and approaches aimed at probing tau conformation and the role of conformation in various aspects of tau biochemistry. The recent applications of nuclear magnetic resonance, mass spectrometry, Förster resonance electron transfer, and molecular dynamics simulations toward structural analysis of conformational landscapes of tau will be described. The strategies developed for structural evaluation of tau may significantly improve our understanding of misfolding diseases.
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Affiliation(s)
- Nicole L Zabik
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.,Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Matthew M Imhof
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.,Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Sanela Martic-Milne
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.,Department of Chemistry, Oakland University, Rochester, MI 48309, USA
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Xiang S, Kulminskaya N, Habenstein B, Biernat J, Tepper K, Paulat M, Griesinger C, Becker S, Lange A, Mandelkow E, Linser R. A Two-Component Adhesive: Tau Fibrils Arise from a Combination of a Well-Defined Motif and Conformationally Flexible Interactions. J Am Chem Soc 2017; 139:2639-2646. [PMID: 28124562 DOI: 10.1021/jacs.6b09619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fibrillar aggregates of Aβ and Tau in the brain are the major hallmarks of Alzheimer's disease. Most Tau fibers have a twisted appearance, but the twist can be variable and even absent. This ambiguity, which has also been associated with different phenotypes of tauopathies, has led to controversial assumptions about fibril constitution, and it is unclear to-date what the molecular causes of this polymorphism are. To tackle this question, we used solid-state NMR strategies providing assignments of non-seeded three-repeat-domain Tau3RD with an inherent heterogeneity. This is in contrast to the general approach to characterize the most homogeneous preparations by construct truncation or intricate seeding protocols. Here, carbon and nitrogen chemical-shift conservation between fibrils revealed invariable secondary-structure properties, however, with inter-monomer interactions variable among samples. Residues with variable amide shifts are localized mostly to N- and C-terminal regions within the rigid beta structure in the repeat region of Tau3RD. By contrast, the hexapeptide motif in repeat R3, a crucial motif for fibril formation, shows strikingly low variability of all NMR parameters: Starting as a nucleation site for monomer-monomer contacts, this six-residue sequence element also turns into a well-defined structural element upon fibril formation. Given the absence of external causes in vitro, the interplay of structurally differently conserved elements in this protein likely reflects an intrinsic property of Tau fibrils.
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Affiliation(s)
- Shengqi Xiang
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Natalia Kulminskaya
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Birgit Habenstein
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux/CBMN UMR5248 , 2 rue Robert Escarpit, 33600 Pessac, France
| | - Jacek Biernat
- DZNE, German Center for Neurodegenerative Diseases , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,CAESAR Research Center , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Katharina Tepper
- DZNE, German Center for Neurodegenerative Diseases , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,CAESAR Research Center , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Maria Paulat
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Institut für Biologie, Humboldt-Universität zu Berlin , Invalidenstrasse 110, 10115 Berlin, Germany.,Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Eckhard Mandelkow
- DZNE, German Center for Neurodegenerative Diseases , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,CAESAR Research Center , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,Hamburg Outstation, c/o DESY, Max-Planck-Institute for Metabolism Research , Notkestrasse 85, 22607 Hamburg, Germany
| | - Rasmus Linser
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Department Chemistry and Pharmacy, Ludwig-Maximilians-University Munich , Butenandtstrasse 5-13, 81377 Munich, Germany
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42
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Danis C, Despres C, Bessa LM, Malki I, Merzougui H, Huvent I, Qi H, Lippens G, Cantrelle FX, Schneider R, Hanoulle X, Smet-Nocca C, Landrieu I. Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins. J Vis Exp 2016. [PMID: 28060278 DOI: 10.3791/55001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aggregates of the neuronal Tau protein are found inside neurons of Alzheimer's disease patients. Development of the disease is accompanied by increased, abnormal phosphorylation of Tau. In the course of the molecular investigation of Tau functions and dysfunctions in the disease, nuclear magnetic resonance (NMR) spectroscopy is used to identify the multiple phosphorylations of Tau. We present here detailed protocols of recombinant production of Tau in bacteria, with isotopic enrichment for NMR studies. Purification steps that take advantage of Tau's heat stability and high isoelectric point are described. The protocol for in vitro phosphorylation of Tau by recombinant activated ERK2 allows for generating multiple phosphorylations. The protein sample is ready for data acquisition at the issue of these steps. The parameter setup to start recording on the spectrometer is considered next. Finally, the strategy to identify phosphorylation sites of modified Tau, based on NMR data, is explained. The benefit of this methodology compared to other techniques used to identify phosphorylation sites, such as immuno-detection or mass spectrometry (MS), is discussed.
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Affiliation(s)
- Clément Danis
- UMR8576, CNRS, Lille University; UMR-S1172, INSERM CNRS, Lille University
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43
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Avila J, Jiménez JS, Sayas CL, Bolós M, Zabala JC, Rivas G, Hernández F. Tau Structures. Front Aging Neurosci 2016; 8:262. [PMID: 27877124 PMCID: PMC5099159 DOI: 10.3389/fnagi.2016.00262] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/21/2016] [Indexed: 12/25/2022] Open
Abstract
Tau is a microtubule-associated protein that plays an important role in axonal stabilization, neuronal development, and neuronal polarity. In this review, we focus on the primary, secondary, tertiary, and quaternary tau structures. We describe the structure of tau from its specific residues until its conformation in dimers, oligomers, and larger polymers in physiological and pathological situations.
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Affiliation(s)
- Jesus Avila
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-UAM)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades NeurodegenerativasMadrid, Spain
| | - Juan S Jiménez
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid Madrid, Spain
| | - Carmen L Sayas
- Centre for Biomedical Research of the Canary Islands, Institute for Biomedical Technologies, University of La Laguna Tenerife, Spain
| | - Marta Bolós
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-UAM)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades NeurodegenerativasMadrid, Spain
| | - Juan C Zabala
- Departamento de Biología Molecular, Facultad de Medicina, IDIVAL-Universidad de Cantabria Santander, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Felix Hernández
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-UAM)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades NeurodegenerativasMadrid, Spain
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NMR Meets Tau: Insights into Its Function and Pathology. Biomolecules 2016; 6:biom6020028. [PMID: 27338491 PMCID: PMC4919923 DOI: 10.3390/biom6020028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/02/2016] [Accepted: 05/26/2016] [Indexed: 12/21/2022] Open
Abstract
In this review, we focus on what we have learned from Nuclear Magnetic Resonance (NMR) studies on the neuronal microtubule-associated protein Tau. We consider both the mechanistic details of Tau: the tubulin relationship and its aggregation process. Phosphorylation of Tau is intimately linked to both aspects. NMR spectroscopy has depicted accurate phosphorylation patterns by different kinases, and its non-destructive character has allowed functional assays with the same samples. Finally, we will discuss other post-translational modifications of Tau and its interaction with other cellular factors in relationship to its (dys)function.
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45
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Molecular Mechanism of Pin1–Tau Recognition and Catalysis. J Mol Biol 2016; 428:1760-75. [DOI: 10.1016/j.jmb.2016.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 02/06/2023]
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46
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Regulation of Microtubule Assembly by Tau and not by Pin1. J Mol Biol 2016; 428:1742-59. [PMID: 26996940 DOI: 10.1016/j.jmb.2016.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
Abstract
The molecular mechanism by which the microtubule-associated protein (MAP) tau regulates the formation of microtubules (MTs) is poorly understood. The activity of tau is controlled via phosphorylation at specific Ser/Thr sites. Of those phosphorylation sites, 17 precede a proline, making them potential recognition sites for the peptidyl-prolyl isomerase Pin1. Pin1 binding and catalysis of phosphorylated tau at the AT180 epitope, which was implicated in Alzheimer's disease, has been reported to be crucial for restoring tau's ability to promote MT polymerization in vitro and in vivo [1]. Surprisingly, we discover that Pin1 does not promote phosphorylated tau-induced MT formation in vitro, refuting the commonly accepted model in which Pin1 binding and catalysis on the A180 epitope restores the function of the Alzheimer's associated phosphorylated tau in tubulin assembly [1, 2]. Using turbidity assays, time-resolved small angle X-ray scattering (SAXS), and time-resolved negative stain electron microscopy (EM), we investigate the mechanism of tau-mediated MT assembly and the role of the Thr231 and Ser235 phosphorylation on this process. We discover novel GTP-tubulin ring-shaped species, which are detectable in the earliest stage of tau-induced polymerization and may play a crucial role in the early nucleation phase of MT assembly. Finally, by NMR and SAXS experiments, we show that the tau molecules must be located on the surface of MTs and tubulin rings during the polymerization reaction. The interaction between tau and tubulin is multipartite, with a high affinity interaction of the four tubulin-binding repeats, and a weaker interaction with the proline-rich sequence and the termini of tau.
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Kamah A, Cantrelle FX, Huvent I, Giustiniani J, Guillemeau K, Byrne C, Jacquot Y, Landrieu I, Baulieu EE, Smet C, Chambraud B, Lippens G. Isomerization and Oligomerization of Truncated and Mutated Tau Forms by FKBP52 are Independent Processes. J Mol Biol 2016; 428:1080-1090. [PMID: 26903089 DOI: 10.1016/j.jmb.2016.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/23/2015] [Accepted: 02/13/2016] [Indexed: 10/22/2022]
Abstract
The aggregation of the neuronal Tau protein is one molecular hallmark of Alzheimer's disease and other related tauopathies, but the precise molecular mechanisms of the aggregation process remain unclear. The FK506 binding protein FKBP52 is able to induce oligomers in the pathogenic Tau P301L mutant and in a truncated form of the wild-type human Tau protein. Here, we investigate whether FKBP52's capacity to induce Tau oligomers depends on its prolyl cis/trans isomerase activity. We find that FKBP52 indeed can isomerize selected prolyl bonds in the different Tau proteins, and that this activity is carried solely by its first FK506 binding domain. Its capacity to oligomerize Tau is, however, not linked to this peptidyl-prolyl isomerase activity. In addition, we identified a novel molecular interaction implying the PHF6 peptide of Tau and the FK1/FK2 domains of FKBP52 independent of FK506 binding; these data point toward a non-catalytic molecular interaction that might govern the effect of FKBP52 on Tau.
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Affiliation(s)
- A Kamah
- University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - F X Cantrelle
- University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - I Huvent
- University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - J Giustiniani
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1195, Université Paris XI, Le Kremlin Bicêtre, France
| | - K Guillemeau
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1195, Université Paris XI, Le Kremlin Bicêtre, France
| | - C Byrne
- Sorbonne Universités, UPMC Univ Paris06, Ecole Normale Supérieure-PSL Research University, CNRS UMR 7203, Laboratoire des Biomolécules, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - Y Jacquot
- Sorbonne Universités, UPMC Univ Paris06, Ecole Normale Supérieure-PSL Research University, CNRS UMR 7203, Laboratoire des Biomolécules, 4, Place Jussieu, 75252 Paris Cedex 05, France
| | - I Landrieu
- University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - E E Baulieu
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1195, Université Paris XI, Le Kremlin Bicêtre, France
| | - C Smet
- University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - B Chambraud
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 1195, Université Paris XI, Le Kremlin Bicêtre, France
| | - G Lippens
- University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France; CNRS, INSA-Université Paul Sabatier, LISBP UMR5504, Toulouse, France.
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48
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Sabbagh JJ, Dickey CA. The Metamorphic Nature of the Tau Protein: Dynamic Flexibility Comes at a Cost. Front Neurosci 2016; 10:3. [PMID: 26834532 PMCID: PMC4720746 DOI: 10.3389/fnins.2016.00003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 01/07/2016] [Indexed: 12/28/2022] Open
Abstract
Accumulation of the microtubule associated protein tau occurs in several neurodegenerative diseases including Alzheimer's disease (AD). The tau protein is intrinsically disordered, giving it unique structural properties that can be dynamically altered by post-translational modifications such as phosphorylation and cleavage. Over the last decade, technological advances in nuclear magnetic resonance (NMR) spectroscopy and structural modeling have permitted more in-depth insights into the nature of tau. These studies have helped elucidate how metamorphism of tau makes it ideally suited for dynamic microtubule regulation, but how it also facilitates tau self-assembly, oligomerization, and neurotoxicity. This review will focus on how the distinct structure of tau governs its function, accumulation, and toxicity as well as how other cellular factors such as molecular chaperones control these processes.
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Affiliation(s)
- Jonathan J Sabbagh
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, University of South Florida Tampa, FL, USA
| | - Chad A Dickey
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, University of South Florida Tampa, FL, USA
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49
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Stangner T, Angioletti-Uberti S, Knappe D, Singer D, Wagner C, Hoffmann R, Kremer F. Epitope mapping of monoclonal antibody HPT-101: a study combining dynamic force spectroscopy, ELISA and molecular dynamics simulations. Phys Biol 2015; 12:066018. [PMID: 26689558 DOI: 10.1088/1478-3975/12/6/066018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
By combining enzyme-linked immunosorbent assay (ELISA) and optical tweezers-assisted dynamic force spectroscopy (DFS), we identify for the first time the binding epitope of the phosphorylation-specific monoclonal antibody (mAb) HPT-101 to the Alzheimer's disease relevant peptide tau[pThr231/pSer235] on the level of single amino acids. In particular, seven tau isoforms are synthesized by replacing binding relevant amino acids by a neutral alanine (alanine scanning). From the binding between mAb HPT-101 and the alanine-scan derivatives, we extract specific binding parameters such as bond lifetime τ0, binding length x(ts), free energy of activation ΔG (DFS) and affinity constant K(a) (ELISA, DFS). Based on these quantities, we propose criteria to identify essential, secondary and non-essential amino acids, being representative of the antibody binding epitope. The obtained results are found to be in full accord for both experimental techniques. In order to elucidate the microscopic origin of the change in binding parameters, we perform molecular dynamics (MD) simulations of the free epitope in solution for both its parent and modified form. By taking the end-to-end distance d(E-E) and the distance between the α-carbons d(C-C) of the phosphorylated residues as gauging parameters, we measure how the structure of the epitope depends on the type of substitution. In particular, whereas d(C-C) is sometimes conserved between the parent and modified form, d(E-E) strongly changes depending on the type of substitution, correlating well with the experimental data. These results are highly significant, offering a detailed microscopic picture of molecular recognition.
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Affiliation(s)
- Tim Stangner
- Leipzig University, Department of Experimental Physics I, Linnéstraβe 5, D-04103 Leipzig, Germany
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50
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Ahuja P, Cantrelle FX, Huvent I, Hanoulle X, Lopez J, Smet C, Wieruszeski JM, Landrieu I, Lippens G. Proline Conformation in a Functional Tau Fragment. J Mol Biol 2015; 428:79-91. [PMID: 26655856 DOI: 10.1016/j.jmb.2015.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/05/2015] [Accepted: 11/24/2015] [Indexed: 12/18/2022]
Abstract
The conformational state of distinct prolines can determine the folding of a protein but equally other biological processes when coupled to a conformation-sensitive secondary reaction. For the neuronal tau protein, the importance of proline conformation is underscored by its interaction with different prolyl cis/trans isomerases. The proline conformation would gain even further importance after phosphorylation of the preceding residue by various proline-directed kinases. A number of molecular diseases including Alzheimer's disease and traumatic brain injury were thereby recently qualified as "cistauosis", as they would imply a cis conformation for the pThr231-Pro232 prolyl bond. We here investigate by NMR spectroscopy the conformation of all prolines in a functional Tau fragment, Tau[208-324]. Although we can detect and identify some minor conformers in the cis form, we show that all prolines are for over 90% in the trans conformation. Phosphorylation by CDK2/CycA3, which notably leads to complete modification of the Thr231 residue, does not change this conclusion. Our data hence disagree with the notion that specific prolyl bonds in tau would adopt preferentially the cis conformation.
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Affiliation(s)
- Puneet Ahuja
- UMR8576 CNRS Lille University, 59658 Villeneuve d'Ascq, France
| | | | - Isabelle Huvent
- UMR8576 CNRS Lille University, 59658 Villeneuve d'Ascq, France
| | - Xavier Hanoulle
- UMR8576 CNRS Lille University, 59658 Villeneuve d'Ascq, France
| | - Juan Lopez
- UMR8576 CNRS Lille University, 59658 Villeneuve d'Ascq, France
| | - Caroline Smet
- UMR8576 CNRS Lille University, 59658 Villeneuve d'Ascq, France
| | | | | | - G Lippens
- UMR8576 CNRS Lille University, 59658 Villeneuve d'Ascq, France.
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