1
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Basu D, Dastidar SG. Molecular Dynamics and Machine Learning reveal distinguishing mechanisms of Competitive Ligands to perturb α,β-Tubulin. Comput Biol Chem 2024; 108:108004. [PMID: 38157659 DOI: 10.1016/j.compbiolchem.2023.108004] [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: 09/16/2023] [Revised: 11/25/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
The mechanisms of action of ligands competing for the Colchicine Binding Site (CBS) of the α,β-Tubulin are non-standard compared to the commonly witnessed ligand-induced inhibition of proteins. This is because their potencies are not solely judged by the binding affinity itself, but also by their capacity to bias the conformational states of the dimer. Regarding the latter requirement, it is observed that ligands competing for the same pocket that binds colchicine exhibit divergence in potential clinical outcomes. Molecular dynamics-based ∼5.2 µs sampling of α,β-Tubulin complexed with four different ligands has revealed that each ligand has its customized way of influencing the complex. Primarily, it is the proportion of twisting and/or bending characteristic of modes of the intrinsic dynamics which is revealed to be 'fundamental' to tune this variation in the mechanism. The milder influence of 'bending' makes a ligand (TUB092), better classifiable under the group of vascular disrupting agents (VDAs), which are phenotypically effective on cytoskeletons; whereas a stronger impact of 'bending' makes the classical ligand Colchicine (COL) a better Anti-Mitotic agent (AMA). Two other ligands BAL27862 (2RR) and Nocodazole (NZO) fall in the intermediate zone as they fail to explicitly induce bending modes. Random Forest Classification method and K-means Clustering is applied to reveal the efficiency of Machine Learning methods in classifying the Tubulin conformations according to their ligand-specific perturbations and to highlight the significance of specific amino acid residues, mostly positioned in the α-β and β-β interfaces involved in the mechanism. These key residues responsible to yield discriminative actions of the ligands are likely to be highly useful in future endeavours to design more precise inhibitors.
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Affiliation(s)
- Debadrita Basu
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India.
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2
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Cui YJ, Zhou Y, Zhang XW, Dou BK, Ma CC, Zhang J. The discovery of water-soluble indazole derivatives as potent microtubule polymerization inhibitors. Eur J Med Chem 2023; 262:115870. [PMID: 37890199 DOI: 10.1016/j.ejmech.2023.115870] [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: 08/23/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Taking a previously discovered indazole derivative 1 as a lead, systematic structural modifications were performed with an indazole core at the 1- and 6-positions to improve its aqueous solubility. Among the designed indazole derivatives, 6-methylpyridin-3-yl indazole derivative 8l and 1H-indol-4-yl indazole derivative 8m exhibited high potency in the low nanomolar range against A549, Huh-7, and T24 cancer cells, including Taxol-resistant variant cells (A549/Tax). As a hydrochloride salt, 8l exhibited much improved aqueous solubility, and its log P value fell into a favorable range. In mechanistic studies, 8l impeded tubulin polymerization through interacting with the colchicine site, resulting in cell cycle arrest and cellular apoptosis. In addition, compared to lead compound 1, 8l reduced cell migration and led to more potent inhibition of tumor growth in vivo without apparent toxicity. In summary, indazole derivative 8l could work as a potential anticancer agent and deserves further investigation for cancer therapy.
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Affiliation(s)
- Ying-Jie Cui
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
| | - Yi Zhou
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
| | - Xi-Wu Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
| | - Bao-Kai Dou
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China
| | - Chen-Chen Ma
- Central Laboratory, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250012, China.
| | - Jing Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250012, China.
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3
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Abbaali I, Truong D, Day SD, Mushayeed F, Ganesh B, Haro-Ramirez N, Isles J, Nag H, Pham C, Shah P, Tomar I, Manel-Romero C, Morrissette NS. The tubulin database: Linking mutations, modifications, ligands and local interactions. PLoS One 2023; 18:e0295279. [PMID: 38064432 PMCID: PMC10707541 DOI: 10.1371/journal.pone.0295279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Microtubules are polymeric filaments, constructed of α-β tubulin heterodimers that underlie critical subcellular structures in eukaryotic organisms. Four homologous proteins (γ-, δ-, ε- and ζ-tubulin) additionally contribute to specialized microtubule functions. Although there is an immense volume of publicly available data pertaining to tubulins, it is difficult to assimilate all potentially relevant information across diverse organisms, isotypes, and categories of data. We previously assembled an extensive web-based catalogue of published missense mutations to tubulins with >1,500 entries that each document a specific substitution to a discrete tubulin, the species where the mutation was described and the associated phenotype with hyperlinks to the amino acid sequence and citation(s) for research. This report describes a significant update and expansion of our online resource (TubulinDB.bio.uci.edu) to nearly 18,000 entries. It now encompasses a cross-referenced catalog of post-translational modifications (PTMs) to tubulin drawn from public datasets, primary literature, and predictive algorithms. In addition, tubulin protein structures were used to define local interactions with bound ligands (GTP, GDP and diverse microtubule-targeting agents) and amino acids at the intradimer interface, within the microtubule lattice and with associated proteins. To effectively cross-reference these datasets, we established a universal tubulin numbering system to map entries into a common framework that accommodates specific insertions and deletions to tubulins. Indexing and cross-referencing permitted us to discern previously unappreciated patterns. We describe previously unlinked observations of loss of PTM sites in the context of cancer cells and tubulinopathies. Similarly, we expanded the set of clinical substitutions that may compromise MAP or microtubule-motor interactions by collecting tubulin missense mutations that alter amino acids at the interface with dynein and doublecortin. By expanding the database as a curated resource, we hope to relate model organism data to clinical findings of pathogenic tubulin variants. Ultimately, we aim to aid researchers in hypothesis generation and design of studies to dissect tubulin function.
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Affiliation(s)
- Izra Abbaali
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Danny Truong
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Shania Deon Day
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Faliha Mushayeed
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Bhargavi Ganesh
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Nancy Haro-Ramirez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Juliet Isles
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Hindol Nag
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Catherine Pham
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Priya Shah
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Ishaan Tomar
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Carolina Manel-Romero
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
| | - Naomi S. Morrissette
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States of America
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4
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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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5
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Ganne A, Balasubramaniam M, Ayyadevara H, Kiaei L, Shmookler Reis RJ, Varughese KI, Kiaei M. In silico analysis of TUBA4A mutations in Amyotrophic Lateral Sclerosis to define mechanisms of microtubule disintegration. Sci Rep 2023; 13:2096. [PMID: 36747013 PMCID: PMC9902468 DOI: 10.1038/s41598-023-28381-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an inexorably progressive and degenerative disorder of motor neurons with no currently-known cure. Studies to determine the mechanism of neurotoxicity and the impact of ALS-linked mutations (SOD1, FUS, TARDP, C9ORF72, PFN1, TUBA4A and others) have greatly expanded our knowledge of ALS disease mechanisms and have helped to identify potential targets for ALS therapy. Cellular pathologies (e.g., aggregation of mutant forms of SOD1, TDP43, FUS, Ubiqulin2, PFN1, and C9ORF72), mitochondrial dysfunction, neuroinflammation, and oxidative damage are major pathways implicated in ALS. Nevertheless, the selective vulnerability of motor neurons remains unexplained. The importance of tubulins for long-axon infrastructure, and the special morphology and function of motor neurons, underscore the central role of the cytoskeleton. The recent linkage of mutations to the tubulin α chain, TUBA4A, to familial and sporadic cases of ALS provides a new investigative opportunity to shed light on both mechanisms of ALS and the vulnerability of motor neurons. In the current study we investigate TUBA4A, a structural microtubule protein with mutations causal to familial ALS, using molecular-dynamic (MD) modeling of protein structure to predict the effects of each mutation and its overall impact on GTP binding, chain stability, tubulin assembly, and aggregation propensity. These studies predict that each of the reported mutations will cause notable structural changes to the TUBA4A (α chain) tertiary protein structure, adversely affecting its physical properties and functions. Molecular docking and MD simulations indicate certain α chain mutations (e.g. K430N, R215C, and W407X) may cause structural deviations that impair GTP binding, and plausibly prevent or destabilize tubulin polymerization. Furthermore, several mutations (including R320C and K430N) confer a significant increase in predicted aggregation propensity of TUBA4A mutants relative to wild-type. Taken together, these in silico modeling studies predict structural perturbations and disruption of GTP binding, culminating in failure to form a stable tubulin heterocomplex, which may furnish an important pathogenic mechanism to trigger motor neuron degeneration in ALS.
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Affiliation(s)
- Akshatha Ganne
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Meenakshisundaram Balasubramaniam
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Central Arkansas Veterans Healthcare Service, McClellan Veterans Medical Center, Little Rock, AR, 72205, USA.,SiBioLead, LLC, Little Rock, AR, 72207, USA
| | | | - Lily Kiaei
- University of California, Los Angeles, Los Angeles, CA, 90095, USA.,RockGen Therapeutics, LLC, Little Rock, AR, 72205, USA
| | - Robert J Shmookler Reis
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Central Arkansas Veterans Healthcare Service, McClellan Veterans Medical Center, Little Rock, AR, 72205, USA.,SiBioLead, LLC, Little Rock, AR, 72207, USA
| | - Kottayil I Varughese
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Mahmoud Kiaei
- RockGen Therapeutics, LLC, Little Rock, AR, 72205, USA. .,Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA. .,Department of Neurology, University of Arkansas for Medical Sciences, 4301 W. Markham St., Slot 611 (BioMed 1, Rm B-306A), Little Rock, AR, 72205, USA.
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6
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Oliva M, Gago F, Kamimura S, Díaz JF. Alternative Approaches to Understand Microtubule Cap Morphology and Function. ACS OMEGA 2023; 8:3540-3550. [PMID: 36743020 PMCID: PMC9893253 DOI: 10.1021/acsomega.2c06926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Microtubules (MTs) are essential cellular machines built from concatenated αβ-tubulin heterodimers. They are responsible for two central and opposite functions from the dynamic point of view: scaffolding (static filaments) and force generation (dynamic MTs). These roles engage multiple physiological processes, including cell shape, polarization, division and movement, and intracellular long-distance transport. At the most basic level, the MT regulation is chemical because GTP binding and hydrolysis have the ability to promote assembly and disassembly in the absence of any other constraint. Due to the stochastic GTP hydrolysis, a chemical gradient from GTP-bound to GDP-bound tubulin is created at the MT growing end (GTP cap), which is translated into a cascade of structural regulatory changes known as MT maturation. This is an area of intense research, and several models have been proposed based on information mostly gathered from macromolecular crystallography and cryo-electron microscopy studies. However, these classical structural biology methods lack temporal resolution and can be complemented, as shown in this mini-review, by other approaches such as time-resolved fiber diffraction and computational modeling. Together with studies on structurally similar tubulins from the prokaryotic world, these inputs can provide novel insights on MT assembly, dynamics, and the GTP cap.
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Affiliation(s)
- María
Ángela Oliva
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
| | - Federico Gago
- Department
of Biomedical Sciences and IQM-UAH Associate Unit, University of Alcalá, E-28805 Alcalá de Henares, Spain
| | - Shinji Kamimura
- Department
of Biological Sciences, Faculty of Science and Engineering, Chuo University, 112-8551 Tokyo, Japan
| | - J. Fernando Díaz
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
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7
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Estévez-Gallego J, Álvarez-Bernad B, Pera B, Wullschleger C, Raes O, Menche D, Martínez JC, Lucena-Agell D, Prota AE, Bonato F, Bargsten K, Cornelus J, Giménez-Abián JF, Northcote P, Steinmetz MO, Kamimura S, Altmann KH, Paterson I, Gago F, Van der Eycken J, Díaz JF, Oliva MÁ. Chemical modulation of microtubule structure through the laulimalide/peloruside site. Structure 2023; 31:88-99.e5. [PMID: 36462501 DOI: 10.1016/j.str.2022.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/23/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
Taxanes are microtubule-stabilizing agents used in the treatment of many solid tumors, but they often involve side effects affecting the peripheral nervous system. It has been proposed that this could be related to structural modifications on the filament upon drug binding. Alternatively, laulimalide and peloruside bind to a different site also inducing stabilization, but they have not been exploited in clinics. Here, we use a combination of the parental natural compounds and derived analogs to unravel the stabilization mechanism through this site. These drugs settle lateral interactions without engaging the M loop, which is part of the key and lock involved in the inter-protofilament contacts. Importantly, these drugs can modulate the angle between protofilaments, producing microtubules of different diameters. Among the compounds studied, we have found some showing low cytotoxicity and able to induce stabilization without compromising microtubule native structure. This opens the window of new applications for microtubule-stabilizing agents beyond cancer treatment.
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Affiliation(s)
- Juan Estévez-Gallego
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Beatriz Álvarez-Bernad
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Benet Pera
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Christoph Wullschleger
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences - ETH Zurich, Zürich 8093, Switzerland
| | - Olivier Raes
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - Dirk Menche
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Daniel Lucena-Agell
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Francesca Bonato
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Katja Bargsten
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Jelle Cornelus
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - Juan Francisco Giménez-Abián
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - Peter Northcote
- Ferrier Research Institute, University of Wellington, Lower Hutt 5010, New Zealand
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen 5232, Switzerland; University of Basel, Biozentrum, Basel 4056, Switzerland
| | - Shinji Kamimura
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo 192-0393, Japan
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences - ETH Zurich, Zürich 8093, Switzerland
| | - Ian Paterson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Federico Gago
- Department of Biomedical Sciences and Associated Unit IQM-UAH, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Johan Van der Eycken
- Department of Organic and Macromolecular Chemistry, Ghent University, Gent 9000, Belgium
| | - J Fernando Díaz
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - María Ángela Oliva
- Centro de Investigaciones Biológicas Margarita Salas - Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain.
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8
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Luo W, Demidov V, Shen Q, Girão H, Chakraborty M, Maiorov A, Ataullakhanov FI, Lin C, Maiato H, Grishchuk EL. CLASP2 recognizes tubulins exposed at the microtubule plus-end in a nucleotide state-sensitive manner. SCIENCE ADVANCES 2023; 9:eabq5404. [PMID: 36598991 PMCID: PMC9812398 DOI: 10.1126/sciadv.abq5404] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
CLASPs (cytoplasmic linker-associated proteins) are ubiquitous stabilizers of microtubule dynamics, but their molecular targets at the microtubule plus-end are not understood. Using DNA origami-based reconstructions, we show that clusters of human CLASP2 form a load-bearing bond with terminal non-GTP tubulins at the stabilized microtubule tip. This activity relies on the unconventional TOG2 domain of CLASP2, which releases its high-affinity bond with non-GTP dimers upon their conversion into polymerization-competent GTP-tubulins. The ability of CLASP2 to recognize nucleotide-specific tubulin conformation and stabilize the catastrophe-promoting non-GTP tubulins intertwines with the previously underappreciated exchange between GDP and GTP at terminal tubulins. We propose that TOG2-dependent stabilization of sporadically occurring non-GTP tubulins represents a distinct molecular mechanism to suppress catastrophe at the freely assembling microtubule ends and to promote persistent tubulin assembly at the load-bearing tethered ends, such as at the kinetochores in dividing cells.
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Affiliation(s)
- Wangxi Luo
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Demidov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
| | - Hugo Girão
- Chromosome Instability & Dynamics Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Manas Chakraborty
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aleksandr Maiorov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fazly I. Ataullakhanov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 119991 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russian Federation
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Helder Maiato
- Chromosome Instability & Dynamics Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Cell Division Group, Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Ekaterina L. Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Farmer VJ, Zanic M. Beyond the GTP-cap: Elucidating the molecular mechanisms of microtubule catastrophe. Bioessays 2023; 45:e2200081. [PMID: 36398561 PMCID: PMC10648283 DOI: 10.1002/bies.202200081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The "standard model" of microtubule dynamics implicates a "cap" of GTP-bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP-cap leads to microtubule "catastrophe," a switch-like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo-EM, and computational modeling approaches, challenge the simple GTP-cap model. Instead, a new perspective on the mechanisms of microtubule dynamics is emerging. In this view, highly dynamic transitions between different structural conformations of the growing microtubule end - which may or may not be directly linked to the nucleotide content at the microtubule end - ultimately drive microtubule catastrophe.
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Affiliation(s)
- Veronica J. Farmer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biomolecular and Chemical Engineering, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
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10
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Sun W, Liu J, Zhang X, Zhang X, Gao J, Chen X, Wang X, Qin W, Jin Z. Long Noncoding RNA and mRNA m6A Modification Analyses of Periodontal Ligament Stem Cells from the Periodontitis Microenvironment Exposed to Static Mechanical Strain. Stem Cells Int 2022; 2022:6243004. [PMID: 36483682 PMCID: PMC9726269 DOI: 10.1155/2022/6243004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 11/22/2023] Open
Abstract
Periodontal ligament stem cells (PDLSCs) play important roles in orthodontic tooth movement (OTM) and can respond to mechanical stress. Our previous study demonstrated that periodontal ligament stem cells derived from periodontitis tissue (pPDLSCs) are more sensitive to static mechanical strain (SMS) than those derived from healthy tissue (hPDLSCs) and reported the long noncoding RNA (lncRNA) expression profiles of pPDLSCs exposed to SMS. An increasing number of lncRNAs have been reported by various studies to be associated with the osteogenic differentiation of mesenchymal stem cells. Many studies have demonstrated that the n6-methyladenosine (m6A) modification exerts important effects on lncRNA and mRNA regulation of cell behaviors. However, the regulatory effects of lncRNA and mRNA m6A modification on PDLSCs have not been studied. Therefore, we performed an m6A microarray assay with pPLDSCs and hPDLSCs exposed to 12% SMS and found that 143 lncRNAs and 739 mRNAs were differentially methylated. These RNAs were thought to be involved in multiple differentiation and inflammatory responses. Moreover, we found that METTL3, an essential protein in the m6A system, was expressed at lower levels in the strain-exposed pPDLSCs than in strain-exposed hPLDSCs, and METTL3 promoted the osteogenic differentiation of pPDLSCs.
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Affiliation(s)
- Weifu Sun
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jia Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xu Zhang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xiaochen Zhang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jie Gao
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xin Chen
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xian Wang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wen Qin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zuolin Jin
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shanxi Clinical Research Center for Oral Diseases, Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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11
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High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol 2022; 5:360. [PMID: 35422073 PMCID: PMC9010423 DOI: 10.1038/s42003-022-03233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia. Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.
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12
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A Review of the Recent Developments of Molecular Hybrids Targeting Tubulin Polymerization. Int J Mol Sci 2022; 23:ijms23074001. [PMID: 35409361 PMCID: PMC8999808 DOI: 10.3390/ijms23074001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/17/2022] [Accepted: 03/29/2022] [Indexed: 12/17/2022] Open
Abstract
Microtubules are cylindrical protein polymers formed from αβ-tubulin heterodimers in the cytoplasm of eukaryotic cells. Microtubule disturbance may cause cell cycle arrest in the G2/M phase, and anomalous mitotic spindles will form. Microtubules are an important target for cancer drug action because of their critical role in mitosis. Several microtubule-targeting agents with vast therapeutic advantages have been developed, but they often lead to multidrug resistance and adverse side effects. Thus, single-target therapy has drawbacks in the effective control of tubulin polymerization. Molecular hybridization, based on the amalgamation of two or more pharmacophores of bioactive conjugates to engender a single molecular structure with enhanced pharmacokinetics and biological activity, compared to their parent molecules, has recently become a promising approach in drug development. The practical application of combined active scaffolds targeting tubulin polymerization inhibitors has been corroborated in the past few years. Meanwhile, different designs and syntheses of novel anti-tubulin hybrids have been broadly studied, illustrated, and detailed in the literature. This review describes various molecular hybrids with their reported structural–activity relationships (SARs) where it is possible in an effort to generate efficacious tubulin polymerization inhibitors. The aim is to create a platform on which new active scaffolds can be modeled for improved tubulin polymerization inhibitory potency and hence, the development of new therapeutic agents against cancer.
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13
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Abstract
The mechanochemical basis of microtubule growth, which is essential for the normal function and division of eukaryotic cells, has remained elusive and controversial, despite extensive work. In particular, recent findings have created the paradox that the microtubule plus-end tips look very similar during both growing and shrinking phases, thereby challenging the traditional textbook picture. Our large-scale atomistic simulations resolve this paradox and explain microtubule growth and shrinkage dynamics as a process governed by energy barriers between protofilament conformations, the heights of which are in turn fine-tuned by different nucleotide states, thus implementing an information-driven Brownian ratchet. Microtubules (MTs), mesoscopic cellular filaments, grow primarily by the addition of GTP-bound tubulin dimers at their dynamic flaring plus-end tips. They operate as chemomechanical energy transducers with stochastic transitions to an astounding shortening motion upon hydrolyzing GTP to GDP. Time-resolved dynamics of the MT tip—a key determinant of this behavior—as a function of nucleotide state, internal lattice strain, and stabilizing lateral interactions have not been fully understood. Here we use atomistic simulations to study the spontaneous relaxation of complete GTP-MT and GDP-MT tip models from unfavorable straight to relaxed splayed conformations and to comprehensively characterize the elasticity of MT tips. Our simulations reveal the dominance of viscoelastic dynamics of MT protofilaments during the relaxation process, driven by the stored bending-torsional strain and counterbalanced by the interprotofilament interactions. We show that the posthydrolysis MT tip is exposed to higher activation energy barriers for straight lattice formation, which translates into its inability to elongate. Our study provides an information-driven Brownian ratchet mechanism for the elastic energy conversion and release by MT tips and offers insights into the mechanoenzymatics of MTs.
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14
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Krajka V, Vulinovic F, Genova M, Tanzer K, Jijumon AS, Bodakuntla S, Tennstedt S, Mueller-Fielitz H, Meier B, Janke C, Klein C, Rakovic A. H-ABC- and dystonia-causing TUBB4A mutations show distinct pathogenic effects. SCIENCE ADVANCES 2022; 8:eabj9229. [PMID: 35275727 PMCID: PMC8916731 DOI: 10.1126/sciadv.abj9229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Mutations in the brain-specific β-tubulin 4A (TUBB4A) gene cause a broad spectrum of diseases, ranging from dystonia (DYT-TUBB4A) to hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC). Currently, the mechanisms of how TUBB4A variants lead to this pleiotropic manifestation remain elusive. Here, we investigated whether TUBB4A mutations causing either DYT-TUBB4A (p.R2G and p.Q424H) or H-ABC (p.R2W and p.D249N) exhibit differential effects at the molecular and cellular levels. Using live-cell imaging of disease-relevant oligodendrocytes and total internal reflection fluorescence microscopy of whole-cell lysates, we observed divergent impact on microtubule polymerization and microtubule integration, partially reflecting the observed pleiotropy. Moreover, in silico simulations demonstrated that the mutants rarely adopted a straight heterodimer conformation in contrast to wild type. In conclusion, for most of the examined variants, we deciphered potential molecular disease mechanisms that may lead to the diverse clinical manifestations and phenotype severity across and within each TUBB4A-related disease.
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Affiliation(s)
- Victor Krajka
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Institute of Microtechnology (IMT), Technische Universität Braunschweig, Braunschweig 38124, Germany
| | - Franca Vulinovic
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Kerstin Tanzer
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - A. S. Jijumon
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Satish Bodakuntla
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Stephanie Tennstedt
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
- University Heart Center Lübeck, 23562 Lübeck, Germany
| | - Helge Mueller-Fielitz
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Britta Meier
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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15
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Liu J, Li L, Zou Y, Fu L, Ma X, Zhang H, Xu Y, Xu J, Zhang J, Li M, Hu X, Li Z, Wang X, Sun H, Zheng H, Zhu L, Guo J. Role of microtubule dynamics in Wallerian degeneration and nerve regeneration after peripheral nerve injury. Neural Regen Res 2022; 17:673-681. [PMID: 34380909 PMCID: PMC8504388 DOI: 10.4103/1673-5374.320997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Wallerian degeneration, the progressive disintegration of distal axons and myelin that occurs after peripheral nerve injury, is essential for creating a permissive microenvironment for nerve regeneration, and involves cytoskeletal reconstruction. However, it is unclear whether microtubule dynamics play a role in this process. To address this, we treated cultured sciatic nerve explants, an in vitro model of Wallerian degeneration, with the microtubule-targeting agents paclitaxel and nocodazole. We found that paclitaxel-induced microtubule stabilization promoted axon and myelin degeneration and Schwann cell dedifferentiation, whereas nocodazole-induced microtubule destabilization inhibited these processes. Evaluation of an in vivo model of peripheral nerve injury showed that treatment with paclitaxel or nocodazole accelerated or attenuated axonal regeneration, as well as functional recovery of nerve conduction and target muscle and motor behavior, respectively. These results suggest that microtubule dynamics participate in peripheral nerve regeneration after injury by affecting Wallerian degeneration. This study was approved by the Animal Care and Use Committee of Southern Medical University, China (approval No. SMU-L2015081) on October 15, 2015.
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Affiliation(s)
- Jingmin Liu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Lixia Li
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Ying Zou
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Lanya Fu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xinrui Ma
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Haowen Zhang
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yizhou Xu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University; Department of Spine Orthopedics, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiawei Xu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiaqi Zhang
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Mi Li
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xiaofang Hu
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zhenlin Li
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xianghai Wang
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
| | - Hao Sun
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
| | - Hui Zheng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong Province, China
| | - Lixin Zhu
- Department of Spine Orthopedics, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jiasong Guo
- Department of Histology and Embryology, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering; Department of Spine Orthopedics, Zhujiang Hospital of Southern Medical University; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory); Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong Province, China
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16
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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: 77] [Impact Index Per Article: 25.7] [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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17
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Chen J, Kholina E, Szyk A, Fedorov VA, Kovalenko I, Gudimchuk N, Roll-Mecak A. α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics. Dev Cell 2021; 56:2016-2028.e4. [PMID: 34022132 PMCID: PMC8476856 DOI: 10.1016/j.devcel.2021.05.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Microtubules are non-covalent polymers of αβ-tubulin dimers. Posttranslational processing of the intrinsically disordered C-terminal α-tubulin tail produces detyrosinated and Δ2-tubulin. Although these are widely employed as proxies for stable cellular microtubules, their effect (and of the α-tail) on microtubule dynamics remains uncharacterized. Using recombinant, engineered human tubulins, we now find that neither detyrosinated nor Δ2-tubulin affect microtubule dynamics, while the α-tubulin tail is an inhibitor of microtubule growth. Consistent with the latter, molecular dynamics simulations show the α-tubulin tail transiently occluding the longitudinal microtubule polymerization interface. The marked differential in vivo stabilities of the modified microtubule subpopulations, therefore, must result exclusively from selective effector recruitment. We find that tyrosination quantitatively tunes CLIP-170 density at the growing plus end and that CLIP170 and EB1 synergize to selectively upregulate the dynamicity of tyrosinated microtubules. Modification-dependent recruitment of regulators thereby results in microtubule subpopulations with distinct dynamics, a tenet of the tubulin code hypothesis.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Ekaterina Kholina
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Vladimir A Fedorov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Astrakhan State University, Astrakhan 414056, Russia; Sechenov University, Moscow 119991, Russia
| | - Nikita 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.
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA; Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, Bethesda, MD 20892, USA.
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18
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Atomistic Basis of Microtubule Dynamic Instability Assessed Via Multiscale Modeling. Ann Biomed Eng 2021; 49:1716-1734. [PMID: 33537926 PMCID: PMC8302526 DOI: 10.1007/s10439-020-02715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023]
Abstract
Microtubule “dynamic instability,” the abrupt switching from assembly to disassembly caused by the hydrolysis of GTP to GDP within the β subunit of the αβ-tubulin heterodimer, is necessary for vital cellular processes such as mitosis and migration. Despite existing high-resolution structural data, the key mechanochemical differences between the GTP and GDP states that mediate dynamic instability behavior remain unclear. Starting with a published atomic-level structure as an input, we used multiscale modeling to find that GTP hydrolysis results in both longitudinal bond weakening (~ 4 kBT) and an outward bending preference (~ 1.5 kBT) to both drive dynamic instability and give rise to the microtubule tip structures previously observed by light and electron microscopy. More generally, our study provides an example where atomic level structural information is used as the sole input to predict cellular level dynamics without parameter adjustment.
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19
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Wall KP, Hart H, Lee T, Page C, Hawkins TL, Hough LE. C-Terminal Tail Polyglycylation and Polyglutamylation Alter Microtubule Mechanical Properties. Biophys J 2020; 119:2219-2230. [PMID: 33137305 DOI: 10.1016/j.bpj.2020.09.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 09/20/2020] [Accepted: 09/25/2020] [Indexed: 11/13/2022] Open
Abstract
Microtubules are biopolymers that perform diverse cellular functions. Microtubule behavior regulation occurs in part through post-translational modification of both the α- and β-subunits of tubulin. One class of modifications is the heterogeneous addition of glycine and/or glutamate residues to the disordered C-terminal tails (CTTs) of tubulin. Because of their prevalence in stable, high-stress cellular structures such as cilia, we sought to determine if these modifications alter microtubules' intrinsic stiffness. Here, we describe the purification and characterization of differentially modified pools of tubulin from Tetrahymena thermophila. We found that post-translational modifications do affect microtubule stiffness but do not affect the number of protofilaments incorporated into microtubules. We measured the spin dynamics of nuclei in the CTT backbone by NMR spectroscopy to explore the mechanism of this change. Our results show that the α-tubulin CTT does not protrude out from the microtubule surface, as is commonly depicted in models, but instead interacts with the dimer's surface. This suggests that the interactions of the α-tubulin CTT with the tubulin body contributes to the stiffness of the assembled microtubule, thus providing insight into the mechanism by which polyglycylation and polyglutamylation can alter microtubule mechanical properties.
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Affiliation(s)
- Kathryn P Wall
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Harold Hart
- Physics Department, University of Wisconsin La Crosse, La Crosse, Wisconsin
| | - Thomas Lee
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Cynthia Page
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Taviare L Hawkins
- Physics Department, University of Wisconsin La Crosse, La Crosse, Wisconsin
| | - Loren E Hough
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado; Department of Physics, University of Colorado Boulder, Boulder, Colorado.
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20
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Igaev M, Grubmüller H. Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Comput Biol 2020; 16:e1008132. [PMID: 32877399 PMCID: PMC7467311 DOI: 10.1371/journal.pcbi.1008132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Tubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These changes render the MT lattice unstable, but it is unclear exactly how they affect lattice energetics and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond stability, the stored elastic energy results in more strongly confined and correlated dynamics of GDP-tubulins, thereby entropically destabilizing the MT lattice.
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Affiliation(s)
- Maxim Igaev
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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21
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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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22
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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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23
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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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