1
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Steinmetz MO, Prota AE. Structure-based discovery and rational design of microtubule-targeting agents. Curr Opin Struct Biol 2024; 87:102845. [PMID: 38805950 DOI: 10.1016/j.sbi.2024.102845] [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: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Microtubule-targeting agents (MTAs) have demonstrated remarkable efficacy as antitumor, antifungal, antiparasitic, and herbicidal agents, finding applications in the clinical, veterinary, and agrochemical industry. Recent advances in tubulin and microtubule structural biology have provided powerful tools that pave the way for the rational design of innovative small-molecule MTAs for future basic and applied life science applications. In this mini-review, we present the current status of the tubulin and microtubule structural biology field, the recent impact it had on the discovery and rational design of MTAs, and exciting avenues for future MTA research.
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Affiliation(s)
- Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland; University of Basel, Biozentrum, 4056 Basel, Switzerland.
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.
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2
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Gao Q, Vermeulen BJA, Würtz M, Shin H, Erdogdu D, Zheng A, Hofer FW, Neuner A, Pfeffer S, Schiebel E. The structure of the γ-TuRC at the microtubule minus end - not just one solution. Bioessays 2024:e2400117. [PMID: 39044599 DOI: 10.1002/bies.202400117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/25/2024]
Abstract
In cells, microtubules (MTs) assemble from α/β-tubulin subunits at nucleation sites containing the γ-tubulin ring complex (γ-TuRC). Within the γ-TuRC, exposed γ-tubulin molecules act as templates for MT assembly by interacting with α/β-tubulin. The vertebrate γ-TuRC is scaffolded by γ-tubulin-interacting proteins GCP2-6 arranged in a specific order. Interestingly, the γ-tubulin molecules in the γ-TuRC deviate from the cylindrical geometry of MTs, raising the question of how the γ-TuRC structure changes during MT nucleation. Recent studies on the structure of the vertebrate γ-TuRC attached to the end of MTs came to varying conclusions. In vitro assembly of MTs, facilitated by an α-tubulin mutant, resulted in a closed, cylindrical γ-TuRC showing canonical interactions between all γ-tubulin molecules and α/β-tubulin subunits. Conversely, native MTs formed in a frog extract were capped by a partially closed γ-TuRC, with some γ-tubulin molecules failing to align with α/β-tubulin. This review discusses these outcomes, along with the broader implications.
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Affiliation(s)
- Qi Gao
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Bram J A Vermeulen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Martin Würtz
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Hyesu Shin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Dilara Erdogdu
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Anjun Zheng
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Florian W Hofer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
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3
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Brito C, Serna M, Guerra P, Llorca O, Surrey T. Transition of human γ-tubulin ring complex into a closed conformation during microtubule nucleation. Science 2024; 383:870-876. [PMID: 38305685 DOI: 10.1126/science.adk6160] [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: 09/01/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open conformation that deviates from the microtubule structure, raising the question of the nucleation mechanism. In this study, we determined cryo-electron microscopy structures of human γTuRC bound to a nascent microtubule. Structural changes of the complex into a closed conformation ensure that γTuRC templates the 13-protofilament microtubules that exist in human cells. Closure is mediated by a latch that interacts with incorporating tubulin, making it part of the closing mechanism. Further rearrangements involve all γTuRC subunits and the removal of the actin-containing luminal bridge. Our proposed mechanism of microtubule nucleation by human γTuRC relies on large-scale structural changes that are likely the target of regulation in cells.
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Affiliation(s)
- Cláudia Brito
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marina Serna
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pablo Guerra
- Cryo-Electron Microscopy Platform-IBMB CSIC, Joint Electron Microscopy Center at ALBA (JEMCA), Barcelona, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Thomas Surrey
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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4
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Gonzalez SJ, Heckel JM, Goldblum RR, Reid TA, McClellan M, Gardner MK. Rapid binding to protofilament edge sites facilitates tip tracking of EB1 at growing microtubule plus-ends. eLife 2024; 13:e91719. [PMID: 38385657 PMCID: PMC10883673 DOI: 10.7554/elife.91719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
EB1 is a key cellular protein that delivers regulatory molecules throughout the cell via the tip-tracking of growing microtubule plus-ends. Thus, it is important to understand the mechanism for how EB1 efficiently tracks growing microtubule plus-ends. It is widely accepted that EB1 binds with higher affinity to GTP-tubulin subunits at the growing microtubule tip, relative to GDP-tubulin along the microtubule length. However, it is unclear whether this difference in affinity alone is sufficient to explain the tip-tracking of EB1 at growing microtubule tips. Previously, we found that EB1 binds to exposed microtubule protofilament-edge sites at a ~70 fold faster rate than to closed-lattice sites, due to diffusional steric hindrance to binding. Thus, we asked whether rapid protofilament-edge binding could contribute to efficient EB1 tip tracking. A computational simulation with differential EB1 on-rates based on closed-lattice or protofilament-edge binding, and with EB1 off-rates that were dependent on the tubulin hydrolysis state, robustly recapitulated experimental EB1 tip tracking. To test this model, we used cell-free biophysical assays, as well as live-cell imaging, in combination with a Designed Ankyrin Repeat Protein (DARPin) that binds exclusively to protofilament-edge sites, and whose binding site partially overlaps with the EB1 binding site. We found that DARPin blocked EB1 protofilament-edge binding, which led to a decrease in EB1 tip tracking on dynamic microtubules. We conclude that rapid EB1 binding to microtubule protofilament-edge sites contributes to robust EB1 tip tracking at the growing microtubule plus-end.
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Affiliation(s)
- Samuel J Gonzalez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Julia M Heckel
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Rebecca R Goldblum
- Department of Biophysics, Molecular Biology, and Biochemistry, University of Minnesota, Minneapolis, United States
- Medical Scientist Training Program, University of Minnesota, Minneapolis, United States
| | - Taylor A Reid
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Mark McClellan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
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5
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Taheri A, Wang Z, Singal B, Guo F, Al-Bassam J. Cryo-EM structures of the tubulin cofactors reveal the molecular basis for the biogenesis of alpha/beta-tubulin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577855. [PMID: 38405852 PMCID: PMC10889022 DOI: 10.1101/2024.01.29.577855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Microtubule polarity and dynamic polymerization originate from the self-association properties of the a-tubulin heterodimer. For decades, it has remained poorly understood how the tubulin cofactors, TBCD, TBCE, TBCC, and the Arl2 GTPase mediate a-tubulin biogenesis from α- and β-tubulins. Here, we use cryogenic electron microscopy to determine structures of tubulin cofactors bound to αβ-tubulin. These structures show that TBCD, TBCE, and Arl2 form a heterotrimeric cage-like TBC-DEG assembly around the a-tubulin heterodimer. TBCD wraps around Arl2 and almost entirely encircles -tubulin, while TBCE forms a lever arm that anchors along the other end of TBCD and rotates α-tubulin. Structures of the TBC-DEG-αβ-tubulin assemblies bound to TBCC reveal the clockwise rotation of the TBCE lever that twists a-tubulin by pulling its C-terminal tail while TBCD holds -tubulin in place. Altogether, these structures uncover transition states in αβ-tubulin biogenesis, suggesting a vise-like mechanism for the GTP-hydrolysis dependent a-tubulin biogenesis mediated by TBC-DEG and TBCC. These structures provide the first evidence of the critical functions of the tubulin cofactors as enzymes that regulate the invariant organization of αβ-tubulin, by catalyzing α- and β-tubulin assembly, disassembly, and subunit exchange which are crucial for regulating the polymerization capacities of αβ-tubulins into microtubules.
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6
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McCormick LA, Cleary JM, Hancock WO, Rice LM. Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends. eLife 2024; 12:RP89231. [PMID: 38180336 PMCID: PMC10945504 DOI: 10.7554/elife.89231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
GTP-tubulin is preferentially incorporated at growing microtubule ends, but the biochemical mechanism by which the bound nucleotide regulates the strength of tubulin:tubulin interactions is debated. The 'self-acting' (cis) model posits that the nucleotide (GTP or GDP) bound to a particular tubulin dictates how strongly that tubulin interacts, whereas the 'interface-acting' (trans) model posits that the nucleotide at the interface of two tubulin dimers is the determinant. We identified a testable difference between these mechanisms using mixed nucleotide simulations of microtubule elongation: with a self-acting nucleotide, plus- and minus-end growth rates decreased in the same proportion to the amount of GDP-tubulin, whereas with interface-acting nucleotide, plus-end growth rates decreased disproportionately. We then experimentally measured plus- and minus-end elongation rates in mixed nucleotides and observed a disproportionate effect of GDP-tubulin on plus-end growth rates. Simulations of microtubule growth were consistent with GDP-tubulin binding at and 'poisoning' plus-ends but not at minus-ends. Quantitative agreement between simulations and experiments required nucleotide exchange at terminal plus-end subunits to mitigate the poisoning effect of GDP-tubulin there. Our results indicate that the interfacial nucleotide determines tubulin:tubulin interaction strength, thereby settling a longstanding debate over the effect of nucleotide state on microtubule dynamics.
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Affiliation(s)
- Lauren A McCormick
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical CenterDallasUnited States
| | - Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State UniversityState CollegeUnited States
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State UniversityState CollegeUnited States
| | - Luke M Rice
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical CenterDallasUnited States
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7
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Romer B, Travis SM, Mahon BP, McManus CT, Jeffrey PD, Coudray N, Raghu R, Rale MJ, Zhong ED, Bhabha G, Petry S. Conformational states of the microtubule nucleator, the γ-tubulin ring complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572162. [PMID: 38187763 PMCID: PMC10769196 DOI: 10.1101/2023.12.19.572162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Microtubules (MTs) perform essential functions in the cell, and it is critical that they are made at the correct cellular location and cell cycle stage. This nucleation process is catalyzed by the γ-tubulin ring complex (γ-TuRC), a cone-shaped protein complex composed of over 30 subunits. Despite recent insight into the structure of vertebrate γ-TuRC, which shows that its diameter is wider than that of a MT, and that it exhibits little of the symmetry expected for an ideal MT template, the question of how γ-TuRC achieves MT nucleation remains open. Here, we utilized single particle cryo-EM to identify two conformations of γ-TuRC. The helix composed of 14 γ-tubulins at the top of the γ-TuRC cone undergoes substantial deformation, which is predominantly driven by bending of the hinge between the GRIP1 and GRIP2 domains of the γ-tubulin complex proteins. However, surprisingly, this deformation does not remove the inherent asymmetry of γ-TuRC. To further investigate the role of γ-TuRC conformational change, we used cryo electron-tomography (cryo-ET) to obtain a 3D reconstruction of γ-TuRC bound to a nucleated MT, providing insight into the post-nucleation state. Rigid-body fitting of our cryo-EM structures into this reconstruction suggests that the MT lattice is nucleated by spokes 2 through 14 of the γ-tubulin helix, which entails spokes 13 and 14 becoming more structured than what is observed in apo γ-TuRC. Together, our results allow us to propose a model for conformational changes in γ-TuRC and how these may facilitate MT formation in a cell.
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Affiliation(s)
- Brianna Romer
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sophie M. Travis
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian P. Mahon
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Present address: Molecular Structure and Design, Bristol Myers Squibb, Princeton, NJ, USA
| | - Collin T. McManus
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nicolas Coudray
- Department of Cell Biology, NYU School of Medicine, New York City, NY, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
| | - Rishwanth Raghu
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Michael J. Rale
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Present address: Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ellen D. Zhong
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Gira Bhabha
- Department of Cell Biology, NYU School of Medicine, New York City, NY, USA
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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8
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Wranik M, Kepa MW, Beale EV, James D, Bertrand Q, Weinert T, Furrer A, Glover H, Gashi D, Carrillo M, Kondo Y, Stipp RT, Khusainov G, Nass K, Ozerov D, Cirelli C, Johnson PJM, Dworkowski F, Beale JH, Stubbs S, Zamofing T, Schneider M, Krauskopf K, Gao L, Thorn-Seshold O, Bostedt C, Bacellar C, Steinmetz MO, Milne C, Standfuss J. A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers. Nat Commun 2023; 14:7956. [PMID: 38042952 PMCID: PMC10693631 DOI: 10.1038/s41467-023-43523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/10/2023] [Indexed: 12/04/2023] Open
Abstract
Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.
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Affiliation(s)
- Maximilian Wranik
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland.
| | - Michal W Kepa
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland.
| | - Emma V Beale
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Quentin Bertrand
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Hannah Glover
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Dardan Gashi
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Melissa Carrillo
- Laboratory of Nanoscale Biology, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Yasushi Kondo
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Robin T Stipp
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Georgii Khusainov
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
| | - Karol Nass
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Dmitry Ozerov
- Scientific Computing, Theory and Data Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Claudio Cirelli
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Philip J M Johnson
- Laboratory for Nonlinear Optics, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Florian Dworkowski
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - John H Beale
- Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Scott Stubbs
- Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Thierry Zamofing
- Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Marco Schneider
- Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Kristina Krauskopf
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany
| | - Li Gao
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany
| | - Christoph Bostedt
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
- LUXS Laboratory for Ultrafast X-ray Sciences, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Camila Bacellar
- Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Christopher Milne
- Femtosecond X-ray Experiments Instrument, European XFEL GmbH, Schenefeld, Germany
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland
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9
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Henkin G, Brito C, Thomas C, Surrey T. The minus-end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules. J Cell Biol 2023; 222:e202304020. [PMID: 37615667 PMCID: PMC10450741 DOI: 10.1083/jcb.202304020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
During mitosis, microtubules in the spindle turn over continuously. At spindle poles, where microtubule minus ends are concentrated, microtubule nucleation and depolymerization, the latter required for poleward microtubule flux, happen side by side. How these seemingly antagonistic processes of nucleation and depolymerization are coordinated is not understood. Here, we reconstitute this coordination in vitro combining different pole-localized activities. We find that the spindle pole-localized kinesin-13 KIF2A is a microtubule minus-end depolymerase, in contrast to its paralog MCAK. Due to its asymmetric activity, KIF2A still allows microtubule nucleation from the γ-tubulin ring complex (γTuRC), which serves as a protective cap shielding the minus end against KIF2A binding. Efficient γTuRC uncapping requires the combined action of KIF2A and a microtubule severing enzyme, leading to treadmilling of the uncapped microtubule driven by KIF2A. Together, these results provide insight into the molecular mechanisms by which a minimal protein module coordinates microtubule nucleation and depolymerization at spindle poles consistent with their role in poleward microtubule flux.
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Affiliation(s)
- Gil Henkin
- Centre for Genomic Regulation(CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cláudia Brito
- Centre for Genomic Regulation(CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Thomas Surrey
- Centre for Genomic Regulation(CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
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10
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McCormick LA, Cleary JM, Hancock WO, Rice LM. Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539131. [PMID: 37205370 PMCID: PMC10187237 DOI: 10.1101/2023.05.03.539131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
GTP-tubulin is preferentially incorporated at growing microtubule ends, but the biochemical mechanism by which the bound nucleotide regulates the strength of tubulin:tubulin interactions is debated. The 'self-acting' (cis) model posits that the nucleotide (GTP or GDP) bound to a particular tubulin dictates how strongly that tubulin interacts, whereas the 'interface-acting' (trans) model posits that the nucleotide at the interface of two tubulin dimers is the determinant. We identified a testable difference between these mechanisms using mixed nucleotide simulations of microtubule elongation: with self-acting nucleotide, plus- and minus-end growth rates decreased in the same proportion to the amount of GDP-tubulin, whereas with interface-acting nucleotide, plus-end growth rates decreased disproportionately. We then experimentally measured plus- and minus-end elongation rates in mixed nucleotides and observed a disproportionate effect of GDP-tubulin on plus-end growth rates. Simulations of microtubule growth were consistent with GDP-tubulin binding at and 'poisoning' plus-ends but not at minus-ends. Quantitative agreement between simulations and experiments required nucleotide exchange at terminal plus-end subunits to mitigate the poisoning effect of GDP-tubulin there. Our results indicate that the interfacial nucleotide determines tubulin:tubulin interaction strength, thereby settling a longstanding debate over the effect of nucleotide state on microtubule dynamics.
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Affiliation(s)
- Lauren A McCormick
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical Center, Dallas, TX
| | - Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA
| | - Luke M Rice
- Department of Biophysics and Biochemistry, the University of Texas Southwestern Medical Center, Dallas, TX
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11
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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12
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Chu Y, Tian Z, Yang M, Li W. Conformation and energy investigation of microtubule longitudinal dynamic instability induced by natural products. Chem Biol Drug Des 2023; 102:444-456. [PMID: 36509697 DOI: 10.1111/cbdd.14189] [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] [Received: 05/11/2022] [Revised: 08/29/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
The natural products plinabulin, docetaxel, and vinblastine are microtubule targeting agents (MTAs). They have been used alone or in combination in cancer treatment. However, the exact nature of their effects on microtubule (MT) polymerization dynamics is poorly understood. To elucidate the longitudinal conformational and energetic changes during MT dynamics, a total of 140 ns molecular dynamic simulations combined with binding free energy calculations were performed on seven tubulin models. The results indicated that the drugs disrupted MT polymerization by altering both MT conformation and binding free energy of the neighboring tubulin subunits. The combination of plinabulin and docetaxel destabilized MT polymerization due to bending MT and weakening the polarity of tubulin polymerization. The new combination of docetaxel and vinblastine synergistically enhanced MT depolymerization and bending, while plinabulin and vinblastine had no synergistic inhibitory effects. The results were verified by the tubulin assembly assay. Our study obtained a comprehensive understanding of the action mechanisms of three natural drugs and their combinations on MT dynamic, provided theoretical guidance for new MTA combinations, and would promote the optimal use of MTA and contribute to developing new MTAs as anticancer agents.
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Affiliation(s)
- Yanyan Chu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenhua Tian
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Mengke Yang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Wenbao Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Innovation Center for Marine Drug Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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13
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Gaudreault F, Baardsnes J, Martynova Y, Dachon A, Hogues H, Corbeil CR, Purisima EO, Arbour M, Sulea T. Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold. Front Mol Biosci 2023; 10:1253689. [PMID: 37692063 PMCID: PMC10484509 DOI: 10.3389/fmolb.2023.1253689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Accurate protein-protein docking remains challenging, especially for artificial biologics not coevolved naturally against their protein targets, like antibodies and other engineered scaffolds. We previously developed ProPOSE, an exhaustive docker with full atomistic details, which delivers cutting-edge performance by allowing side-chain rearrangements upon docking. However, extensive protein backbone flexibility limits its practical applicability as indicated by unbound docking tests. To explore the usefulness of ProPOSE on systems with limited backbone flexibility, here we tested the engineered scaffold DARPin, which is characterized by its relatively rigid protein backbone. A prospective screening campaign was undertaken, in which sequence-diversified DARPins were docked and ranked against a directed epitope on the target protein BCL-W. In this proof-of-concept study, only a relatively small set of 2,213 diverse DARPin interfaces were selected for docking from the huge theoretical library from mutating 18 amino-acid positions. A computational selection protocol was then applied for enrichment of binders based on normalized computed binding scores and frequency of binding modes against the predefined epitope. The top-ranked 18 designed DARPin interfaces were selected for experimental validation. Three designs exhibited binding affinities to BCL-W in the nanomolar range comparable to control interfaces adopted from known DARPin binders. This result is encouraging for future screening and engineering campaigns of DARPins and possibly other similarly rigid scaffolds against targeted protein epitopes. Method limitations are discussed and directions for future refinements are proposed.
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Affiliation(s)
- Francis Gaudreault
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Yuliya Martynova
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Aurore Dachon
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Hervé Hogues
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Christopher R. Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Enrico O. Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Mélanie Arbour
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
- Institute of Parasitology, McGill University, Montreal, QC, Canada
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14
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Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography. Nat Commun 2023; 14:903. [PMID: 36807348 PMCID: PMC9936131 DOI: 10.1038/s41467-023-36481-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we capture the release of the anti-cancer compound azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of microtubule-destabilizing drugs.
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15
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Computational Approaches to the Rational Design of Tubulin-Targeting Agents. Biomolecules 2023; 13:biom13020285. [PMID: 36830654 PMCID: PMC9952983 DOI: 10.3390/biom13020285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.
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16
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Hoff KJ, Neumann AJ, Moore JK. The molecular biology of tubulinopathies: Understanding the impact of variants on tubulin structure and microtubule regulation. Front Cell Neurosci 2022; 16:1023267. [PMID: 36406756 PMCID: PMC9666403 DOI: 10.3389/fncel.2022.1023267] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Heterozygous, missense mutations in both α- and β-tubulin genes have been linked to an array of neurodevelopment disorders, commonly referred to as "tubulinopathies." To date, tubulinopathy mutations have been identified in three β-tubulin isotypes and one α-tubulin isotype. These mutations occur throughout the different genetic domains and protein structures of these tubulin isotypes, and the field is working to address how this molecular-level diversity results in different cellular and tissue-level pathologies. Studies from many groups have focused on elucidating the consequences of individual mutations; however, the field lacks comprehensive models for the molecular etiology of different types of tubulinopathies, presenting a major gap in diagnosis and treatment. This review highlights recent advances in understanding tubulin structural dynamics, the roles microtubule-associated proteins (MAPs) play in microtubule regulation, and how these are inextricably linked. We emphasize the value of investigating interactions between tubulin structures, microtubules, and MAPs to understand and predict the impact of tubulinopathy mutations at the cell and tissue levels. Microtubule regulation is multifaceted and provides a complex set of controls for generating a functional cytoskeleton at the right place and right time during neurodevelopment. Understanding how tubulinopathy mutations disrupt distinct subsets of those controls, and how that ultimately disrupts neurodevelopment, will be important for establishing mechanistic themes among tubulinopathies that may lead to insights in other neurodevelopment disorders and normal neurodevelopment.
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Affiliation(s)
| | | | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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17
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Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2120098119. [PMID: 35507869 PMCID: PMC9171608 DOI: 10.1073/pnas.2120098119] [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] [Indexed: 11/23/2022] Open
Abstract
Microtubules are dynamic assemblies of αβ-tubulin that are involved in key cellular functions, including cell division and intracellular transport. Microtubule dynamics is inhibited by several families of small molecules, some of which are used in oncology. The extent to which these compounds target the binding sites of cellular partners of tubulin remains poorly characterized. We show here that a region of the CPAP protein binds to the so-called vinca domain of β-tubulin in a way very similar to that of peptide-like inhibitors produced by bacteria and fungi. Therefore, our work identifies a structural convergence for tubulin binding between inhibitors and a regulator of microtubule dynamics. Microtubule dynamics is regulated by various cellular proteins and perturbed by small-molecule compounds. To what extent the mechanism of the former resembles that of the latter is an open question. We report here structures of tubulin bound to the PN2-3 domain of CPAP, a protein controlling the length of the centrioles. We show that an α-helix of the PN2-3 N-terminal region binds and caps the longitudinal surface of the tubulin β subunit. Moreover, a PN2-3 N-terminal stretch lies in a β-tubulin site also targeted by fungal and bacterial peptide-like inhibitors of the vinca domain, sharing a very similar binding mode with these compounds. Therefore, our results identify several characteristic features of cellular partners that bind to this site and highlight a structural convergence of CPAP with small-molecule inhibitors of microtubule assembly.
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18
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Oliva MÁ, Tosat-Bitrián C, Barrado-Gil L, Bonato F, Galindo I, Garaigorta U, Álvarez-Bernad B, París-Ogáyar R, Lucena-Agell D, Giménez-Abián JF, García-Dorival I, Urquiza J, Gastaminza P, Díaz JF, Palomo V, Alonso C. Effect of Clinically Used Microtubule Targeting Drugs on Viral Infection and Transport Function. Int J Mol Sci 2022; 23:ijms23073448. [PMID: 35408808 PMCID: PMC8998746 DOI: 10.3390/ijms23073448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/19/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023] Open
Abstract
Microtubule targeting agents (MTAs) have been exploited mainly as anti-cancer drugs because of their impact on cellular division and angiogenesis. Additionally, microtubules (MTs) are key structures for intracellular transport, which is frequently hijacked during viral infection. We have analyzed the antiviral activity of clinically used MTAs in the infection of DNA and RNA viruses, including SARS-CoV-2, to find that MT destabilizer agents show a higher impact than stabilizers in the viral infections tested, and FDA-approved anti-helminthic benzimidazoles were among the most active compounds. In order to understand the reasons for the observed antiviral activity, we studied the impact of these compounds in motor proteins-mediated intracellular transport. To do so, we used labeled peptide tools, finding that clinically available MTAs impaired the movement linked to MT motors in living cells. However, their effect on viral infection lacked a clear correlation to their effect in motor-mediated transport, denoting the complex use of the cytoskeleton by viruses. Finally, we further delved into the molecular mechanism of action of Mebendazole by combining biochemical and structural studies to obtain crystallographic high-resolution information of the Mebendazole-tubulin complex, which provided insights into the mechanisms of differential toxicity between helminths and mammalians.
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Affiliation(s)
- María Ángela Oliva
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Carlota Tosat-Bitrián
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Lucía Barrado-Gil
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Francesca Bonato
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Inmaculada Galindo
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Consejo Superior de Investigaciones Científicas, Carretera de la Coruña km 7.5, 28040 Madrid, Spain; (I.G.); (I.G.-D.); (J.U.)
| | - Urtzi Garaigorta
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Calle Darwin 3, 28049 Madrid, Spain; (U.G.); (P.G.)
| | - Beatriz Álvarez-Bernad
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Rebeca París-Ogáyar
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Daniel Lucena-Agell
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Juan Francisco Giménez-Abián
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Isabel García-Dorival
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Consejo Superior de Investigaciones Científicas, Carretera de la Coruña km 7.5, 28040 Madrid, Spain; (I.G.); (I.G.-D.); (J.U.)
| | - Jesús Urquiza
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Consejo Superior de Investigaciones Científicas, Carretera de la Coruña km 7.5, 28040 Madrid, Spain; (I.G.); (I.G.-D.); (J.U.)
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Calle Darwin 3, 28049 Madrid, Spain; (U.G.); (P.G.)
| | - José Fernando Díaz
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
| | - Valle Palomo
- Unidad BICS, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (M.Á.O.); (C.T.-B.); (L.B.-G.); (F.B.); (B.Á.-B.); (R.P.-O.); (D.L.-A.); (J.F.G.-A.); (J.F.D.)
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
- IMDEA Nanociencia, Faraday 9, 28049 Madrid, Spain
- Correspondence: (V.P.); (C.A.); Tel.: +34-913476896 (C.A.)
| | - Covadonga Alonso
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Consejo Superior de Investigaciones Científicas, Carretera de la Coruña km 7.5, 28040 Madrid, Spain; (I.G.); (I.G.-D.); (J.U.)
- Correspondence: (V.P.); (C.A.); Tel.: +34-913476896 (C.A.)
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19
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Wang J, Miller DD, Li W. Molecular interactions at the colchicine binding site in tubulin: An X-ray crystallography perspective. Drug Discov Today 2022; 27:759-776. [PMID: 34890803 PMCID: PMC8901563 DOI: 10.1016/j.drudis.2021.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/27/2021] [Accepted: 12/02/2021] [Indexed: 01/02/2023]
Abstract
Tubulin is an important cancer drug target. Compounds that bind at the colchicine site in tubulin have attracted significant interest as they are generally less affected by multidrug resistance than other potential drugs. Modeling is useful in understanding the interactions between tubulin and colchicine binding site inhibitors (CBSIs), but because the colchicine binding site contains two flexible loops whose conformations are highly ligand-dependent, modeling has its limitations. X-ray crystallography provides experimental pictures of tubulin-ligand interactions at this challenging colchicine site. Since 2004, when the first X-ray structure of tubulin in complex with N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) was published, many X-ray crystal structures have been reported for tubulin complexes involving the colchicine binding site. In this review, we summarize the crystal structures of tubulin in complexes with various CBSIs, aiming to facilitate the discovery of new generations of tubulin inhibitors.
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Affiliation(s)
| | | | - Wei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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20
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Mühlethaler T, Olieric N, Ehrhard VA, Wranik M, Standfuss J, Sharma A, Prota AE, Steinmetz MO. Crystallization Systems for the High-Resolution Structural Analysis of Tubulin-Ligand Complexes. Methods Mol Biol 2022; 2430:349-374. [PMID: 35476344 DOI: 10.1007/978-1-0716-1983-4_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Since the first moderate resolution, structural description of Taxol bound to tubulin by electron crystallography in 1998, several tubulin crystal systems have been developed and optimized for the high-resolution analysis of tubulin-ligand complexes by X-ray crystallography. Here we describe three tubulin crystal systems that have allowed investigating the molecular mechanisms of action of a large number of diverse anti-tubulin agents.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Valentin A Ehrhard
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Maximilian Wranik
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Ashwani Sharma
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland.
- University of Basel, Biozentrum, Basel, Switzerland.
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21
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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22
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Gaillard N, Sharma A, Abbaali I, Liu T, Shilliday F, Cook AD, Ehrhard V, Bangera M, Roberts AJ, Moores CA, Morrissette N, Steinmetz MO. Inhibiting parasite proliferation using a rationally designed anti-tubulin agent. EMBO Mol Med 2021; 13:e13818. [PMID: 34661376 PMCID: PMC8573600 DOI: 10.15252/emmm.202013818] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
Infectious diseases caused by apicomplexan parasites remain a global public health threat. The presence of multiple ligand-binding sites in tubulin makes this protein an attractive target for anti-parasite drug discovery. However, despite remarkable successes as anti-cancer agents, the rational development of protozoan parasite-specific tubulin drugs has been hindered by a lack of structural and biochemical information on protozoan tubulins. Here, we present atomic structures for a protozoan tubulin and microtubule and delineate the architectures of apicomplexan tubulin drug-binding sites. Based on this information, we rationally designed the parasite-specific tubulin inhibitor parabulin and show that it inhibits growth of parasites while displaying no effects on human cells. Our work presents for the first time the rational design of a species-specific tubulin drug providing a framework to exploit structural differences between human and protozoa tubulin variants enabling the development of much-needed, novel parasite inhibitors.
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Affiliation(s)
- Natacha Gaillard
- Laboratory of Biomolecular ResearchDivision of Biology and ChemistryPaul Scherrer InstitutVilligenSwitzerland
| | - Ashwani Sharma
- Laboratory of Biomolecular ResearchDivision of Biology and ChemistryPaul Scherrer InstitutVilligenSwitzerland
| | - Izra Abbaali
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA
| | - Tianyang Liu
- Institute of Structural and Molecular BiologyBirkbeck, University of LondonLondonUK
| | - Fiona Shilliday
- Institute of Structural and Molecular BiologyBirkbeck, University of LondonLondonUK
| | - Alexander D Cook
- Institute of Structural and Molecular BiologyBirkbeck, University of LondonLondonUK
| | - Valentin Ehrhard
- Laboratory of Biomolecular ResearchDivision of Biology and ChemistryPaul Scherrer InstitutVilligenSwitzerland
| | - Mamata Bangera
- Institute of Structural and Molecular BiologyBirkbeck, University of LondonLondonUK
| | - Anthony J Roberts
- Institute of Structural and Molecular BiologyBirkbeck, University of LondonLondonUK
| | - Carolyn A Moores
- Institute of Structural and Molecular BiologyBirkbeck, University of LondonLondonUK
| | - Naomi Morrissette
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA
| | - Michel O Steinmetz
- Laboratory of Biomolecular ResearchDivision of Biology and ChemistryPaul Scherrer InstitutVilligenSwitzerland
- Biozentrum University of BaselBaselSwitzerland
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23
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Nasedkin A, Ermilova I, Swenson J. Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:927-940. [PMID: 34215900 PMCID: PMC8448678 DOI: 10.1007/s00249-021-01553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Microtubules are essential parts of the cytoskeleton that are built by polymerization of tubulin heterodimers into a hollow tube. Regardless that their structures and functions have been comprehensively investigated in a modern soft matter, it is unclear how properties of tubulin heterodimer influence and promote the self-assembly. A detailed knowledge of such structural mechanisms would be helpful in drug design against neurodegenerative diseases, cancer, diabetes etc. In this work atomistic molecular dynamics simulations were used to investigate the fundamental dynamics of tubulin heterodimers in a sheet and a short microtubule utilizing well-equilibrated structures. The breathing motions of the tubulin heterodimers during assembly show that the movement at the lateral interface between heterodimers (wobbling) dominates in the lattice. The simulations of the protofilament curvature agrees well with recently published experimental data, showing curved protofilaments at polymerization of the microtubule plus end. The tubulin heterodimers exposed at the microtubule minus end were less curved and displayed altered interactions at the site of sheet closure around the outmost heterodimers, which may slow heterodimer binding and polymerization, providing a potential explanation for the limited dynamics observed at the minus end.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
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24
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Rice LM, Moritz M, Agard DA. Microtubules form by progressively faster tubulin accretion, not by nucleation-elongation. J Cell Biol 2021; 220:211894. [PMID: 33734292 PMCID: PMC7980253 DOI: 10.1083/jcb.202012079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 01/14/2023] Open
Abstract
Microtubules are dynamic polymers that play fundamental roles in all eukaryotes. Despite their importance, how new microtubules form is poorly understood. Textbooks have focused on variations of a nucleation–elongation mechanism in which monomers rapidly equilibrate with an unstable oligomer (nucleus) that limits the rate of polymer formation; once formed, the polymer then elongates efficiently from this nucleus by monomer addition. Such models faithfully describe actin assembly, but they fail to account for how more complex polymers like hollow microtubules assemble. Here, we articulate a new model for microtubule formation that has three key features: (1) microtubules initiate via rectangular, sheet-like structures that grow faster the larger they become; (2) the dominant pathway proceeds via accretion, the stepwise addition of longitudinal or lateral layers; and (3) a “straightening penalty” to account for the energetic cost of tubulin’s curved-to-straight conformational transition. This model can quantitatively fit experimental assembly data, providing new insights into biochemical determinants and assembly pathways for microtubule nucleation.
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Affiliation(s)
- Luke M Rice
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Michelle Moritz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco CA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco CA
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25
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Martiel I, Beale JH, Karpik A, Huang CY, Vera L, Olieric N, Wranik M, Tsai CJ, Mühle J, Aurelius O, John J, Högbom M, Wang M, Marsh M, Padeste C. Versatile microporous polymer-based supports for serial macromolecular crystallography. Acta Crystallogr D Struct Biol 2021; 77:1153-1167. [PMID: 34473086 PMCID: PMC8411977 DOI: 10.1107/s2059798321007324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
Serial data collection has emerged as a major tool for data collection at state-of-the-art light sources, such as microfocus beamlines at synchrotrons and X-ray free-electron lasers. Challenging targets, characterized by small crystal sizes, weak diffraction and stringent dose limits, benefit most from these methods. Here, the use of a thin support made of a polymer-based membrane for performing serial data collection or screening experiments is demonstrated. It is shown that these supports are suitable for a wide range of protein crystals suspended in liquids. The supports have also proved to be applicable to challenging cases such as membrane proteins growing in the sponge phase. The sample-deposition method is simple and robust, as well as flexible and adaptable to a variety of cases. It results in an optimally thin specimen providing low background while maintaining minute amounts of mother liquor around the crystals. The 2 × 2 mm area enables the deposition of up to several microlitres of liquid. Imaging and visualization of the crystals are straightforward on the highly transparent membrane. Thanks to their affordable fabrication, these supports have the potential to become an attractive option for serial experiments at synchrotrons and free-electron lasers.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - John H. Beale
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Agnieszka Karpik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
- Institute of Polymer Nanotechnology (INKA), FHNW University of Applied Sciences and Arts Northwestern Switzerland, 5210 Windisch, Switzerland
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Laura Vera
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ching-Ju Tsai
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Jonas Mühle
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
- MAX IV Laboratory, Lund University, Fotongatan 2, 224 84 Lund, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - May Marsh
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Celestino Padeste
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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26
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Regulation of microtubule dynamics, mechanics and function through the growing tip. Nat Rev Mol Cell Biol 2021; 22:777-795. [PMID: 34408299 DOI: 10.1038/s41580-021-00399-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Microtubule dynamics and their control are essential for the normal function and division of all eukaryotic cells. This plethora of functions is, in large part, supported by dynamic microtubule tips, which can bind to various intracellular targets, generate mechanical forces and couple with actin microfilaments. Here, we review progress in the understanding of microtubule assembly and dynamics, focusing on new information about the structure of microtubule tips. First, we discuss evidence for the widely accepted GTP cap model of microtubule dynamics. Next, we address microtubule dynamic instability in the context of structural information about assembly intermediates at microtubule tips. Three currently discussed models of microtubule assembly and dynamics are reviewed. These are considered in the context of established facts and recent data, which suggest that some long-held views must be re-evaluated. Finally, we review structural observations about the tips of microtubules in cells and describe their implications for understanding the mechanisms of microtubule regulation by associated proteins, by mechanical forces and by microtubule-targeting drugs, prominently including cancer chemotherapeutics.
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27
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021; 60:13331-13342. [PMID: 33951246 PMCID: PMC8251789 DOI: 10.1002/anie.202100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Tubulin plays essential roles in vital cellular activities and is the target of a wide range of proteins and ligands. Here, using a combined computational and crystallographic fragment screening approach, we addressed the question of how many binding sites exist in tubulin. We identified 27 distinct sites, of which 11 have not been described previously, and analyzed their relationship to known tubulin-protein and tubulin-ligand interactions. We further observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. Our results offer a unique structural basis for the development of novel small molecules for use as tubulin modulators in basic research applications or as drugs. Furthermore, our method lays down a framework that may help to discover new pockets in other pharmaceutically important targets and characterize them in terms of chemical tractability and allosteric modulation.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Dario Gioia
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
| | - Andrea E. Prota
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - May E. Sharpe
- Swiss Light SourcePaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea Cavalli
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
- Department of Pharmacy and BiotechnologyAlma Mater StudiorumUniversity of Bolognavia Belmeloro 640126BolognaItaly
| | - Michel O. Steinmetz
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
- University of BaselBiozentrum4056BaselSwitzerland
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28
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Dario Gioia
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
| | - Andrea E. Prota
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - May E. Sharpe
- Swiss Light Source Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
- Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna via Belmeloro 6 40126 Bologna Italy
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
- University of Basel Biozentrum 4056 Basel Switzerland
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29
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Abstract
The DARPin® drug platform was established with a vision to expand the medical use of biologics beyond what was possible with monoclonal antibodies. It is based on naturally occurring ankyrin repeat domains that are typically building blocks of multifunctional human proteins. The platform allows for the generation of diverse, well-behaved, multifunctional drug candidates. Recent clinical data illustrate the favorable safety profile of the first DARPin® molecules tested in patients. With the positive phase III results of the most advanced DARPin® drug candidate, abicipar, the DARPin® drug platform is potentially about to achieve its first marketing approval. This review highlights some of the key milestones and decisions encountered when transforming the DARPin® platform from an academic concept to a biotech drug pipeline engine.
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Affiliation(s)
- Michael T Stumpp
- Molecular Partners AG, Wagistrasse 14, 8952, Schlieren, Switzerland
| | - Keith M Dawson
- Molecular Partners AG, Wagistrasse 14, 8952, Schlieren, Switzerland
| | - H Kaspar Binz
- Molecular Partners AG, Wagistrasse 14, 8952, Schlieren, Switzerland. .,Binz Biotech Consulting GmbH, Lüssirainstrasse 52, 6300, Zug, Switzerland.
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30
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Gao L, Meiring JCM, Kraus Y, Wranik M, Weinert T, Pritzl SD, Bingham R, Ntouliou E, Jansen KI, Olieric N, Standfuss J, Kapitein LC, Lohmüller T, Ahlfeld J, Akhmanova A, Steinmetz MO, Thorn-Seshold O. A Robust, GFP-Orthogonal Photoswitchable Inhibitor Scaffold Extends Optical Control over the Microtubule Cytoskeleton. Cell Chem Biol 2021; 28:228-241.e6. [PMID: 33275880 DOI: 10.1016/j.chembiol.2020.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
Optically controlled chemical reagents, termed "photopharmaceuticals," are powerful tools for precise spatiotemporal control of proteins particularly when genetic methods, such as knockouts or optogenetics are not viable options. However, current photopharmaceutical scaffolds, such as azobenzenes are intolerant of GFP/YFP imaging and are metabolically labile, posing severe limitations for biological use. We rationally designed a photoswitchable "SBT" scaffold to overcome these problems, then derivatized it to create exceptionally metabolically robust and fully GFP/YFP-orthogonal "SBTub" photopharmaceutical tubulin inhibitors. Lead compound SBTub3 allows temporally reversible, cell-precise, and even subcellularly precise photomodulation of microtubule dynamics, organization, and microtubule-dependent processes. By overcoming the previous limitations of microtubule photopharmaceuticals, SBTubs offer powerful applications in cell biology, and their robustness and druglikeness are favorable for intracellular biological control in in vivo applications. We furthermore expect that the robustness and imaging orthogonality of the SBT scaffold will inspire other derivatizations directed at extending the photocontrol of a range of other biological targets.
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Affiliation(s)
- Li Gao
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich 81377, Germany
| | - Joyce C M Meiring
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, Netherlands
| | - Yvonne Kraus
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich 81377, Germany
| | - Maximilian Wranik
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Stefanie D Pritzl
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians University of Munich, Munich 80539, Germany
| | - Rebekkah Bingham
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich 81377, Germany
| | - Evangelia Ntouliou
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich 81377, Germany
| | - Klara I Jansen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, Netherlands
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, Netherlands
| | - Theobald Lohmüller
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians University of Munich, Munich 80539, Germany
| | - Julia Ahlfeld
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich 81377, Germany
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584, Netherlands
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland; Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Munich 81377, Germany.
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31
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Ayukawa R, Iwata S, Imai H, Kamimura S, Hayashi M, Ngo KX, Minoura I, Uchimura S, Makino T, Shirouzu M, Shigematsu H, Sekimoto K, Gigant B, Muto E. GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation. J Cell Biol 2021; 220:211760. [PMID: 33544140 PMCID: PMC7871348 DOI: 10.1083/jcb.202007033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleation of microtubules (MTs) is essential for cellular activities, but its mechanism is unknown because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. Here, combining rapid flush negative stain electron microscopy (EM) and kinetic analysis, we demonstrate that the formation of straight oligomers of critical size is essential for nucleation. Both GDP and GTP tubulin form single-stranded oligomers with a broad range of curvatures, but upon nucleation, the curvature distribution of GTP oligomers is shifted to produce a minor population of straight oligomers. With tubulin having the Y222F mutation in the β subunit, the proportion of straight oligomers increases and nucleation accelerates. Our results support a model in which GTP binding generates a minor population of straight oligomers compatible with lateral association and further growth to MTs. This study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.
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Affiliation(s)
- Rie Ayukawa
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Seigo Iwata
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Hiroshi Imai
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Shinji Kamimura
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Masahito Hayashi
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kien Xuan Ngo
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Itsushi Minoura
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Seiichi Uchimura
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Tsukasa Makino
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Hideki Shigematsu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Ken Sekimoto
- Matière et Systèmes Complexes (MSC), CNRS UMR 7057, Université de Paris, Paris, France.,Gulliver, CNRS UMR 7083, ESPCI Paris and Université Paris Sciences et Lettres, Paris, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Etsuko Muto
- Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan
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32
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Knossow M, Campanacci V, Khodja LA, Gigant B. The Mechanism of Tubulin Assembly into Microtubules: Insights from Structural Studies. iScience 2020; 23:101511. [PMID: 32920486 PMCID: PMC7491153 DOI: 10.1016/j.isci.2020.101511] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/03/2020] [Accepted: 08/25/2020] [Indexed: 11/26/2022] Open
Abstract
Microtubules are cytoskeletal components involved in pivotal eukaryotic functions such as cell division, ciliogenesis, and intracellular trafficking. They assemble from αβ-tubulin heterodimers and disassemble in a process called dynamic instability, which is driven by GTP hydrolysis. Structures of the microtubule and of soluble tubulin have been determined by cryo-EM and by X-ray crystallography, respectively. Altogether, these data define the mechanism of tubulin assembly-disassembly at atomic or near-atomic level. We review here the structural changes that occur during assembly, tubulin switching from a curved conformation in solution to a straight one in the microtubule core. We also present more subtle changes associated with GTP binding, leading to tubulin activation for assembly. Finally, we show how cryo-EM and X-ray crystallography are complementary methods to characterize the interaction of tubulin with proteins involved either in intracellular transport or in microtubule dynamics regulation.
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Affiliation(s)
- Marcel Knossow
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Valérie Campanacci
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Liza Ammar Khodja
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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33
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Nosala C, Hagen KD, Hilton N, Chase TM, Jones K, Loudermilk R, Nguyen K, Dawson SC. Disc-associated proteins mediate the unusual hyperstability of the ventral disc in Giardia lamblia. J Cell Sci 2020; 133:jcs.227355. [PMID: 32661087 DOI: 10.1242/jcs.227355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/29/2020] [Indexed: 12/26/2022] Open
Abstract
Giardia lamblia, a widespread parasitic protozoan, attaches to the host gastrointestinal epithelium by using the ventral disc, a complex microtubule (MT) organelle. The 'cup-like' disc is formed by a spiral MT array that scaffolds numerous disc-associated proteins (DAPs) and higher-order protein complexes. In interphase, the disc is hyperstable and has limited MT dynamics; however, it remains unclear how DAPs confer these properties. To investigate mechanisms of hyperstability, we confirmed the disc-specific localization of over 50 new DAPs identified by using both a disc proteome and an ongoing GFP localization screen. DAPs localize to specific disc regions and many lack similarity to known proteins. By screening 14 CRISPRi-mediated DAP knockdown (KD) strains for defects in hyperstability and MT dynamics, we identified two strains - DAP5188KD and DAP6751KD -with discs that dissociate following high-salt fractionation. Discs in the DAP5188KD strain were also sensitive to treatment with the MT-polymerization inhibitor nocodazole. Thus, we confirm here that at least two of the 87 known DAPs confer hyperstable properties to the disc MTs, and we anticipate that other DAPs contribute to disc MT stability, nucleation and assembly.
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Affiliation(s)
- Christopher Nosala
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kari D Hagen
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nicholas Hilton
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tiffany M Chase
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kelci Jones
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Rita Loudermilk
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Kristofer Nguyen
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Scott C Dawson
- Department of Microbiology and Molecular Genetics, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Abstract
The protein kinase MEKK1 activates stress-signaling pathways in response to various cellular stressors, including chemotherapies that disrupt dynamics of the tubulin cytoskeleton. We show that MEKK1 contains a previously uncharacterized domain that can preferentially bind to the curved tubulin heterodimer—which is found in soluble tubulin and at sites of microtubule assembly and disassembly. Mutations that interfere with MEKK1−tubulin binding disrupt microtubule networks in migrating cells and are enriched in patient-derived tumor sequences. These results suggest that MEKK1−tubulin binding may be relevant to cancer progression, and the efficacy of microtubule-disrupting chemotherapies that require the activity of MEKK1. The MEKK1 protein is a pivotal kinase activator of responses to cellular stress. Activation of MEKK1 can trigger various responses, including mitogen-activated protein (MAP) kinases, NF-κB signaling, or cell migration. Notably, MEKK1 activity is triggered by microtubule-targeting chemotherapies, among other stressors. Here we show that MEKK1 contains a previously unidentified tumor overexpressed gene (TOG) domain. The MEKK1 TOG domain binds to tubulin heterodimers—a canonical function of TOG domains—but is unusual in that it appears alone rather than as part of a multi-TOG array, and has structural features distinct from previously characterized TOG domains. MEKK1 TOG demonstrates a clear preference for binding curved tubulin heterodimers, which exist in soluble tubulin and at sites of microtubule polymerization and depolymerization. Mutations disrupting tubulin binding decrease microtubule density at the leading edge of polarized cells, suggesting that tubulin binding may play a role in MEKK1 activity at the cellular periphery. We also show that MEKK1 mutations at the tubulin-binding interface of the TOG domain recur in patient-derived tumor sequences, suggesting selective enrichment of tumor cells with disrupted MEKK1–microtubule association. Together, these findings provide a direct link between the MEKK1 protein and tubulin, which is likely to be relevant to cancer cell migration and response to microtubule-modulating therapies.
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Gudimchuk NB, Ulyanov EV, O'Toole E, Page CL, Vinogradov DS, Morgan G, Li G, Moore JK, Szczesna E, Roll-Mecak A, Ataullakhanov FI, Richard McIntosh J. Mechanisms of microtubule dynamics and force generation examined with computational modeling and electron cryotomography. Nat Commun 2020; 11:3765. [PMID: 32724196 PMCID: PMC7387542 DOI: 10.1038/s41467-020-17553-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
Microtubules are dynamic tubulin polymers responsible for many cellular processes, including the capture and segregation of chromosomes during mitosis. In contrast to textbook models of tubulin self-assembly, we have recently demonstrated that microtubules elongate by addition of bent guanosine triphosphate tubulin to the tips of curving protofilaments. Here we explore this mechanism of microtubule growth using Brownian dynamics modeling and electron cryotomography. The previously described flaring shapes of growing microtubule tips are remarkably consistent under various assembly conditions, including different tubulin concentrations, the presence or absence of a polymerization catalyst or tubulin-binding drugs. Simulations indicate that development of substantial forces during microtubule growth and shortening requires a high activation energy barrier in lateral tubulin-tubulin interactions. Modeling offers a mechanism to explain kinetochore coupling to growing microtubule tips under assisting force, and it predicts a load-dependent acceleration of microtubule assembly, providing a role for the flared morphology of growing microtubule ends.
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Affiliation(s)
- Nikita B Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia.
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia.
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
| | - Evgeni V Ulyanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Eileen O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Cynthia L Page
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Dmitrii S Vinogradov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Garry Morgan
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Gabriella Li
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ewa Szczesna
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Fazoil I Ataullakhanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
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36
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Tong D, Voth GA. Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability. Biophys J 2020; 118:2938-2951. [PMID: 32413312 DOI: 10.1016/j.bpj.2020.04.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
The dynamic instability of microtubules (MTs), which refers to their ability to switch between polymerization and depolymerization states, is crucial for their function. It has been proposed that the growing MT ends are protected by a "GTP cap" that consists of GTP-bound tubulin dimers. When the speed of GTP hydrolysis is faster than dimer recruitment, the loss of this GTP cap will lead the MT to undergo rapid disassembly. However, the underlying atomistic mechanistic details of the dynamic instability remains unclear. In this study, we have performed long-time atomistic molecular dynamics simulations (1 μs for each system) for MT patches as well as a short segment of a closed MT in both GTP- and GDP-bound states. Our results confirmed that MTs in the GDP state generally have weaker lateral interactions between neighboring protofilaments (PFs) and less cooperative outward bending conformational change, where the difference between bending angles of neighboring PFs tends to be larger compared with GTP ones. As a result, when the GDP state tubulin dimer is exposed at the growing MT end, these factors will be more likely to cause the MT to undergo rapid disassembly. We also compared simulation results between the special MT seam region and the remaining material and found that the lateral interactions between MT PFs at the seam region were comparatively much weaker. This finding is consistent with the experimental suggestion that the seam region tends to separate during the disassembly process of an MT.
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Affiliation(s)
- Dudu Tong
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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37
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Ye X, Kim T, Geyer EA, Rice LM. Insights into allosteric control of microtubule dynamics from a buried β-tubulin mutation that causes faster growth and slower shrinkage. Protein Sci 2020; 29:1429-1439. [PMID: 32077153 DOI: 10.1002/pro.3842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/27/2023]
Abstract
αβ-tubulin subunits cycle through a series of different conformations in the polymer lattice during microtubule growing and shrinking. How these allosteric responses to different tubulin:tubulin contacts contribute to microtubule dynamics, and whether the contributions are evolutionarily conserved, remains poorly understood. Here, we sought to determine whether the microtubule-stabilizing effects (slower shrinking) of the β:T238A mutation we previously observed using yeast αβ-tubulin would generalize to mammalian microtubules. Using recombinant human microtubules as a model, we found that the mutation caused slow microtubule shrinking, indicating that this effect of the mutation is indeed conserved. However, unlike in yeast, β:T238A human microtubules grew faster than wild-type and the mutation did not appear to attenuate the conformational change associated with guanosine 5'-triphosphate (GTP) hydrolysis in the lattice. We conclude that the assembly-dependent conformational change in αβ-tubulin can contribute to determine the rates of microtubule growing as well as shrinking. Our results also suggest that an allosteric perturbation like the β:T238A mutation can alter the behavior of terminal subunits without accompanying changes in the conformation of fully surrounded subunits in the body of the microtubule.
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Affiliation(s)
- Xuecheng Ye
- UT Southwestern Medical Center, Departments of Biophysics and Biochemistry, Dallas, Texas, USA
| | - Tae Kim
- UT Southwestern Medical Center, Departments of Biophysics and Biochemistry, Dallas, Texas, USA
| | - Elisabeth A Geyer
- UT Southwestern Medical Center, Departments of Biophysics and Biochemistry, Dallas, Texas, USA
| | - Luke M Rice
- UT Southwestern Medical Center, Departments of Biophysics and Biochemistry, Dallas, Texas, USA
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38
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La Sala G, Olieric N, Sharma A, Viti F, de Asis Balaguer Perez F, Huang L, Tonra JR, Lloyd GK, Decherchi S, Díaz JF, Steinmetz MO, Cavalli A. Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes. Chem 2019. [DOI: 10.1016/j.chempr.2019.08.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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39
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Hemmat M, Castle BT, Sachs JN, Odde DJ. Multiscale Computational Modeling of Tubulin-Tubulin Lateral Interaction. Biophys J 2019; 117:1234-1249. [PMID: 31493861 DOI: 10.1016/j.bpj.2019.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022] Open
Abstract
Microtubules are multistranded polymers in eukaryotic cells that support key cellular functions such as chromosome segregation, motor-based cargo transport, and maintenance of cell polarity. Microtubules self-assemble via "dynamic instability," in which the dynamic plus ends switch stochastically between alternating phases of polymerization and depolymerization. A key question in the field is what are the atomistic origins of this switching, i.e., what is different between the GTP- and GDP-tubulin states that enables microtubule growth and shortening, respectively? More generally, a major challenge in biology is how to connect theoretical frameworks across length- and timescales, from atoms to cellular behavior. In this study, we describe a multiscale model by linking atomistic molecular dynamics (MD), molecular Brownian dynamics (BD), and cellular-level thermokinetic modeling of microtubules. Here, we investigated the underlying interaction energy when tubulin dimers associate laterally by performing all-atom MD simulations. We found that the lateral potential energy is not significantly different among three nucleotide states of tubulin, GTP, GDP, and GMPCPP and is estimated to be ≅ -11 kBT. Furthermore, using MD potential energy in our BD simulations of tubulin dimers confirms that the lateral bond is weak on its own, with a mean lifetime of ∼0.1 μs, implying that the longitudinal bond is required for microtubule assembly. We conclude that nucleotide-dependent lateral-bond strength is not the key mediator microtubule dynamic instability, implying that GTP acts elsewhere to exert its stabilizing influence on microtubule polymer. Furthermore, the estimated lateral-bond strength (ΔGlat0≅ -5 kBT) is well-aligned with earlier estimates based on thermokinetic modeling and light microscopy measurements. Thus, we have computationally connected atomistic-level structural information, obtained by cryo-electron microscopy, to cellular-scale microtubule assembly dynamics using a combination of MD, BD, and thermokinetic models to bridge from Ångstroms to micrometers and from femtoseconds to minutes.
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Affiliation(s)
- Mahya Hemmat
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Brian T Castle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.
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40
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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: 264] [Impact Index Per Article: 52.8] [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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41
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Fedorov VA, Orekhov PS, Kholina EG, Zhmurov AA, Ataullakhanov FI, Kovalenko IB, Gudimchuk NB. Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability. PLoS Comput Biol 2019; 15:e1007327. [PMID: 31469822 PMCID: PMC6742422 DOI: 10.1371/journal.pcbi.1007327] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 09/12/2019] [Accepted: 08/08/2019] [Indexed: 11/18/2022] Open
Abstract
Thirteen tubulin protofilaments, made of αβ-tubulin heterodimers, interact laterally to produce cytoskeletal microtubules. Microtubules exhibit the striking property of dynamic instability, manifested in their intermittent growth and shrinkage at both ends. This behavior is key to many cellular processes, such as cell division, migration, maintenance of cell shape, etc. Although assembly and disassembly of microtubules is known to be linked to hydrolysis of a guanosine triphosphate molecule in the pocket of β-tubulin, detailed mechanistic understanding of corresponding conformational changes is still lacking. Here we take advantage of the recent generation of in-microtubule structures of tubulin to examine the properties of protofilaments, which serve as important microtubule assembly and disassembly intermediates. We find that initially straight tubulin protofilaments, relax to similar non-radially curved and slightly twisted conformations. Our analysis further suggests that guanosine triphosphate hydrolysis primarily affects the flexibility and conformation of the inter-dimer interface, without a strong impact on the shape or flexibility of αβ-heterodimer. Inter-dimer interfaces are significantly more flexible compared to intra-dimer interfaces. We argue that such a difference in flexibility could be key for distinct stability of the plus and minus microtubule ends. The higher flexibility of the inter-dimer interface may have implications for development of pulling force by curving tubulin protofilaments during microtubule disassembly, a process of major importance for chromosome motions in mitosis.
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Affiliation(s)
| | - Philipp S. Orekhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Sechenov University, Moscow, Russia
| | | | - Artem A. Zhmurov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Sechenov University, Moscow, Russia
| | - Fazoil I. Ataullakhanov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya B. Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Sechenov University, Moscow, Russia
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow, Russia
- Astrakhan State University, Astrakhan, Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
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42
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Erickson HP. Microtubule Assembly from Single Flared Protofilaments-Forget the Cozy Corner? Biophys J 2019; 116:2240-2245. [PMID: 31122668 DOI: 10.1016/j.bpj.2019.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/13/2019] [Accepted: 05/02/2019] [Indexed: 12/31/2022] Open
Abstract
A paradigm shift for models of MT assembly is suggested by a recent cryo-electron microscopy study of microtubules (MTs). Previous assembly models have been based on the two-dimensional lattice of the MT wall, where incoming subunits can add with longitudinal and lateral bonds. The new study of McIntosh et al. concludes that the growing ends of MTs separate into flared single protofilaments. This means that incoming subunits must add onto the end of single protofilaments, forming only a longitudinal bond. How can growth of single-stranded protofilaments exhibit cooperative assembly with a critical concentration? An answer is suggested by FtsZ, the bacterial tubulin homolog, which assembles into single-stranded protofilaments. Cooperative assembly of FtsZ is thought to be based on conformational changes that switch the longitudinal bond from low to high affinity when the subunit is incorporated in a protofilament. This novel mechanism may also apply to tubulin assembly and could be the primary mechanism for assembly onto single flared protofilaments.
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Affiliation(s)
- Harold P Erickson
- Departments of Cell Biology, Biochemistry, and Biomedical Engineering, Duke University Medical Center, Durham, North Carolina.
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43
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Abstract
Nucleation is one of the least understood steps of microtubule dynamics. It is a kinetically unfavorable process that is templated in the cell by the γ-tubulin ring complex or by preexisting microtubules; it also occurs in vitro from pure tubulin. Here we study the nucleation inhibition potency of natural or artificial proteins in connection with their binding mode to the longitudinal surface of α- or β-tubulin. The structure of tubulin-bound CopN, a Chlamydia protein that delays nucleation, suggests that this protein may interfere with two protofilaments at the (+) end of a nucleus. Designed ankyrin repeat proteins that share a binding mode similar to that of CopN also impede nucleation, whereas those that target only one protofilament do not. In addition, an αRep protein predicted to target two protofilaments at the (-) end does not delay nucleation, pointing to different behaviors at both ends of the nucleus. Our results link the interference with protofilaments at the (+) end and the inhibition of nucleation.
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44
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Orbach R, Howard J. The dynamic and structural properties of axonemal tubulins support the high length stability of cilia. Nat Commun 2019; 10:1838. [PMID: 31015426 PMCID: PMC6479064 DOI: 10.1038/s41467-019-09779-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/25/2019] [Indexed: 12/31/2022] Open
Abstract
Cilia and flagella play essential roles in cell motility, sensing and development. These organelles have tightly controlled lengths, and the axoneme, which forms the core structure, has exceptionally high stability. This is despite being composed of microtubules that are often characterized as highly dynamic. To understand how ciliary tubulin contribute to stability, we develop a procedure to differentially extract tubulins from different components of axonemes purified from Chlamydomonas reinhardtii, and characterize their properties. We find that the microtubules support length stability by two distinct mechanisms: low dynamicity, and unusual stability of the protofilaments. The high stability of the protofilaments manifests itself in the formation of curved tip structures, up to a few microns long. These structures likely reflect intrinsic curvature of GTP or GDP·Pi tubulin and provide structural insights into the GTP-cap. Together, our study provides insights into growth, stability and the role of post-translational modifications of axonemal microtubules. The axoneme in cilia and flagella has exceptionally high stability despite being composed of microtubules that are known to be highly dynamic. Here authors extract tubulin from different components of Chlamydomonas reinhardtii axonemes and characterize their properties.
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Affiliation(s)
- Ron Orbach
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathon Howard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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45
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van Haren J, Wittmann T. Microtubule Plus End Dynamics - Do We Know How Microtubules Grow?: Cells boost microtubule growth by promoting distinct structural transitions at growing microtubule ends. Bioessays 2019; 41:e1800194. [PMID: 30730055 PMCID: PMC7021488 DOI: 10.1002/bies.201800194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/22/2018] [Indexed: 12/31/2022]
Abstract
Microtubules form a highly dynamic filament network in all eukaryotic cells. Individual microtubules grow by tubulin dimer subunit addition and frequently switch between phases of growth and shortening. These unique dynamics are powered by GTP hydrolysis and drive microtubule network remodeling, which is central to eukaryotic cell biology and morphogenesis. Yet, our knowledge of the molecular events at growing microtubule ends remains incomplete. Here, recent ultrastructural, biochemical and cell biological data are integrated to develop a realistic model of growing microtubule ends comprised of structurally distinct but biochemically overlapping zones. Proteins that recognize microtubule lattice conformations associated with specific tubulin guanosine nucleotide states may independently control major structural transitions at growing microtubule ends. A model is proposed in which tubulin dimer addition and subsequent closure of the MT wall are optimized in cells to achieve rapid physiological microtubule growth.
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Affiliation(s)
- Jeffrey van Haren
- Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
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46
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Campanacci V, Urvoas A, Consolati T, Cantos-Fernandes S, Aumont-Nicaise M, Valerio-Lepiniec M, Surrey T, Minard P, Gigant B. Selection and Characterization of Artificial Proteins Targeting the Tubulin α Subunit. Structure 2019; 27:497-506.e4. [PMID: 30661854 PMCID: PMC6408325 DOI: 10.1016/j.str.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/08/2022]
Abstract
Microtubules are cytoskeletal filaments of eukaryotic cells made of αβ-tubulin heterodimers. Structural studies of non-microtubular tubulin rely mainly on molecules that prevent its self-assembly and are used as crystallization chaperones. Here we identified artificial proteins from an αRep library that are specific to α-tubulin. Turbidity experiments indicate that these αReps impede microtubule assembly in a dose-dependent manner and total internal reflection fluorescence microscopy further shows that they specifically block growth at the microtubule (−) end. Structural data indicate that they do so by targeting the α-tubulin longitudinal surface. Interestingly, in one of the complexes studied, the α subunit is in a conformation that is intermediate between the ones most commonly observed in X-ray structures of tubulin and those seen in the microtubule, emphasizing the plasticity of tubulin. These α-tubulin-specific αReps broaden the range of tools available for the mechanistic study of microtubule dynamics and its regulation. Selection of α-tubulin-specific artificial αRep proteins The αReps inhibit microtubule assembly and specifically block growth at the (−) end The αReps target the longitudinal surface of α-tubulin The αReps are useful tools for the mechanistic study of microtubule dynamics
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Affiliation(s)
- Valérie Campanacci
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Tanja Consolati
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Soraya Cantos-Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
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Nithianantham S, Cook BD, Beans M, Guo F, Chang F, Al-Bassam J. Structural basis of tubulin recruitment and assembly by microtubule polymerases with tumor overexpressed gene (TOG) domain arrays. eLife 2018; 7:38922. [PMID: 30422110 PMCID: PMC6251626 DOI: 10.7554/elife.38922] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022] Open
Abstract
XMAP215/Stu2/Alp14 proteins accelerate microtubule plus-end polymerization by recruiting tubulins via arrays of tumor overexpressed gene (TOG) domains, yet their mechanism remains unknown. Here, we describe the biochemical and structural basis for TOG arrays in recruiting and polymerizing tubulins. Alp14 binds four tubulins via dimeric TOG1-TOG2 subunits, in which each domain exhibits a distinct exchange rate for tubulin. X-ray structures revealed square-shaped assemblies composed of pseudo-dimeric TOG1-TOG2 subunits assembled head-to-tail, positioning four unpolymerized tubulins in a polarized wheel-like configuration. Crosslinking and electron microscopy show Alp14-tubulin forms square assemblies in solution, and inactivating their interfaces destabilize this organization without influencing tubulin binding. An X-ray structure determined using approach to modulate tubulin polymerization revealed an unfurled assembly, in which TOG1-TOG2 uniquely bind to two polymerized tubulins. Our findings suggest a new microtubule polymerase model in which TOG arrays recruit tubulins by forming square assemblies that then unfurl, facilitating their concerted polymerization into protofilaments.
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Affiliation(s)
- Stanley Nithianantham
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Brian D Cook
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Madeleine Beans
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Fei Guo
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, United States
| | - Jawdat Al-Bassam
- Molecular Cellular Biology Department, University of California, Davis, United States
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Roostalu J, Rickman J, Thomas C, Nédélec F, Surrey T. Determinants of Polar versus Nematic Organization in Networks of Dynamic Microtubules and Mitotic Motors. Cell 2018; 175:796-808.e14. [PMID: 30340043 PMCID: PMC6198040 DOI: 10.1016/j.cell.2018.09.029] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/25/2018] [Accepted: 09/13/2018] [Indexed: 11/03/2022]
Abstract
During cell division, mitotic motors organize microtubules in the bipolar spindle into either polar arrays at the spindle poles or a "nematic" network of aligned microtubules at the spindle center. The reasons for the distinct self-organizing capacities of dynamic microtubules and different motors are not understood. Using in vitro reconstitution experiments and computer simulations, we show that the human mitotic motors kinesin-5 KIF11 and kinesin-14 HSET, despite opposite directionalities, can both organize dynamic microtubules into either polar or nematic networks. We show that in addition to the motor properties the natural asymmetry between microtubule plus- and minus-end growth critically contributes to the organizational potential of the motors. We identify two control parameters that capture system composition and kinetic properties and predict the outcome of microtubule network organization. These results elucidate a fundamental design principle of spindle bipolarity and establish general rules for active filament network organization.
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Affiliation(s)
| | - Jamie Rickman
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Claire Thomas
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - François Nédélec
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Shemesh A, Ginsburg A, Levi-Kalisman Y, Ringel I, Raviv U. Structure, Assembly, and Disassembly of Tubulin Single Rings. Biochemistry 2018; 57:6153-6165. [PMID: 30247898 DOI: 10.1021/acs.biochem.8b00560] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single and double tubulin rings were studied under a range of conditions and during microtubule (MT) assembly and disassembly. Here, tubulin was purified from porcine brain and used without any further modifications or additives that promote ring assembly. The structure of single GDP-rich tubulin rings was determined by cryo-transmission electron microscopy and synchrotron solution X-ray scattering. The scattering curves were fitted to atomic models, using our state-of-the-art analysis software, D+ . We found that there is a critical concentration for ring formation, which increased with GTP concentration with temperature. MT assembly or disassembly, induced by changes in temperature, was analyzed by time-resolved small-angle X-ray scattering. During MT assembly, the fraction of rings and unassembled dimers simultaneously decreased. During MT disassembly, the mass fraction of dimers increased. The increase in the concentration of rings was delayed until the fraction of dimers was sufficiently high. We verified that pure dimers, eluted via size-exclusion chromatography, could also form rings. Interestingly, X-ray radiation triggered tubulin ring disassembly. The concentration of disassembled rings versus exposure time followed a first-order kinetics. The disassembly rate constant and initial concentration were determined. X-ray radiation-triggered disassembly was used to determine the concentration of rings. We confirmed that following a temperature jump, the mass fraction of rings decreased and then stabilized at a constant value during the first stage of the MT assembly kinetics. This study sheds light on the most basic assembly and disassembly conditions for in vitro single GDP-rich tubulin rings and their relation to MT kinetics.
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Affiliation(s)
- Asaf Shemesh
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
| | - Avi Ginsburg
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Institute for Drug Research, School of Pharmacy , The Hebrew University of Jerusalem , Jerusalem 9112102 , Israel
| | - Yael Levi-Kalisman
- Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Institute of Life Sciences , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy , The Hebrew University of Jerusalem , Jerusalem 9112102 , Israel
| | - Uri Raviv
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel.,Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 9190401 , Israel
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50
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Martin HL, Bedford R, Heseltine SJ, Tang AA, Haza KZ, Rao A, McPherson MJ, Tomlinson DC. Non-immunoglobulin scaffold proteins: Precision tools for studying protein-protein interactions in cancer. N Biotechnol 2018; 45:28-35. [DOI: 10.1016/j.nbt.2018.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/08/2018] [Accepted: 02/18/2018] [Indexed: 02/08/2023]
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