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Abstract
Exposure to organophosphorus pesticides (OP) can have chronic adverse effects that are independent of inhibition of acetylcholinesterase, the classic target for acute OP toxicity. In pure proteins, the organophosphorus pesticide chlorpyrifos oxon induces a cross-link between lysine and glutamate (or aspartate) with loss of water. Tubulin is particularly sensitive to OP-induced cross-linking. Our goal was to explore OP-induced cross-linking in a complex protein sample, MAP-rich tubulin from Sus scrofa and to test 8 OP for their capacity to promote isopeptide cross-linking. We treated 100 μg of MAP-rich tubulin with 100 μM chlorpyrifos, chlorpyrifos oxon, methamidophos, paraoxon, diazinon, diazoxon, monocrotophos, or dichlorvos. Each sample was separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and stained with Coomassie blue. Five gel slices (at about 30, 50, 150, and 300 kDa, and the top of the separating gel) were removed from the lanes for each of the eight OP samples and from untreated control lanes. These gel slices were subjected to in-gel trypsin digestion. MSMS fragmentation spectra of the tryptic peptides were examined for isopeptide cross-links. Sixteen spectra yielded convincing evidence for isopeptide cross-linked peptides. Ten were from the chlorpyrifos oxon reaction, 1 from dichlorvos, 1 from paraoxon, 1 from diazinon, and 3 from diazoxon. It was concluded that catalysis of protein cross-linking is a general property of organophosphorus pesticides and pesticide metabolites. Data are available via ProteomeXchange with identifier PXD034529.
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Affiliation(s)
- Lawrence M Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Seda Onder
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,Department of Biochemistry, School of Pharmacy, Hacettepe University, Ankara 06100, Turkey
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 2022; 11:66975. [PMID: 35485925 PMCID: PMC9122500 DOI: 10.7554/elife.66975] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Doublecortin (DCX) is a microtubule (MT)-associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX that explain these disorders are incompletely determined. Here, we describe the molecular architecture of the DCX–MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-electron microscopy, and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving the C-terminal structured domain and its disordered tail, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-terminal tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in its tail, our study shows that lattice-driven self-assembly is an important property of DCX.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, Canada
| | | | | | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Gary Brouhard
- Department of Biology, McGill University, Montreal, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
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3
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Rafiei A, Schriemer DC. A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins. Methods Mol Biol 2022; 2456:211-222. [PMID: 35612744 DOI: 10.1007/978-1-0716-2124-0_14] [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: 11/25/2022]
Abstract
Microtubule-associated proteins (MAPs) engage microtubules (MTs) to regulate both the MT state and wide variety of cytoskeletal functions. A comprehensive understanding of MAPs function requires the structural characterization of physical contacts MAPs make with other proteins, particularly when engaged with the microtubule (MT) lattice. Most of the interaction between MAPs and MTs evade classical structural determination techniques, as the interactions can be both heterogenous and sub-stoichiometric. Crosslinking mass spectrometry (XL-MS) can aid in MAP-MT structure analysis by providing a wealth of residue-based distance restraints. This protocol provides an XL-MS workflow for accurate and unbiased sampling of an equilibrated MAP-MT interaction, involving modifications to the preparation and validation of a MAP-MT construct suitable for crosslinking with fast-sampling heterobifunctional crosslinkers. The distance restrains obtained by this protocol can be used to generate accurate models assembled with an integrative structural modeling approach.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
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Khan N, Pelletier D, McAlear TS, Croteau N, Veyron S, Bayne AN, Black C, Ichikawa M, Khalifa AAZ, Chaaban S, Kurinov I, Brouhard G, Bechstedt S, Bui KH, Trempe JF. Crystal structure of human PACRG in complex with MEIG1 reveals roles in axoneme formation and tubulin binding. Structure 2021; 29:572-586.e6. [PMID: 33529594 DOI: 10.1016/j.str.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/16/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
The Parkin co-regulated gene protein (PACRG) binds at the inner junction between doublet microtubules of the axoneme, a structure found in flagella and cilia. PACRG binds to the adaptor protein meiosis expressed gene 1 (MEIG1), but how they bind to microtubules is unknown. Here, we report the crystal structure of human PACRG in complex with MEIG1. PACRG adopts a helical repeat fold with a loop that interacts with MEIG1. Using the structure of the axonemal doublet microtubule from the protozoan Chlamydomonas reinhardtii and single-molecule fluorescence microscopy, we propose that PACRG binds to microtubules while simultaneously recruiting free tubulin to catalyze formation of the inner junction. We show that the homologous PACRG-like protein also mediates dual tubulin interactions but does not bind MEIG1. Our findings establish a framework to assess the function of the PACRG family of proteins and MEIG1 in regulating axoneme assembly.
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Affiliation(s)
- Nimra Khan
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Dylan Pelletier
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Thomas S McAlear
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Simon Veyron
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Andrew N Bayne
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Corbin Black
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Muneyoshi Ichikawa
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada
| | - Ahmad Abdelzaher Zaki Khalifa
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Sami Chaaban
- Department of Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Igor Kurinov
- NECAT, Cornell University, Department of Chemistry and Chemical Biology, Argonne, IL, USA
| | - Gary Brouhard
- Department of Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Susanne Bechstedt
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Khanh Huy Bui
- Department of Anatomy & Cell Biology, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada; Centre de Recherche en Biologie Structurale - FRQS, McGill University, Montreal, QC, Canada.
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