1
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Nelson AC, Rolls MM, Ciocanel MV, McKinley SA. Minimal Mechanisms of Microtubule Length Regulation in Living Cells. Bull Math Biol 2024; 86:58. [PMID: 38627264 DOI: 10.1007/s11538-024-01279-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/05/2024] [Indexed: 04/19/2024]
Abstract
The microtubule cytoskeleton is responsible for sustained, long-range intracellular transport of mRNAs, proteins, and organelles in neurons. Neuronal microtubules must be stable enough to ensure reliable transport, but they also undergo dynamic instability, as their plus and minus ends continuously switch between growth and shrinking. This process allows for continuous rebuilding of the cytoskeleton and for flexibility in injury settings. Motivated by in vivo experimental data on microtubule behavior in Drosophila neurons, we propose a mathematical model of dendritic microtubule dynamics, with a focus on understanding microtubule length, velocity, and state-duration distributions. We find that limitations on microtubule growth phases are needed for realistic dynamics, but the type of limiting mechanism leads to qualitatively different responses to plausible experimental perturbations. We therefore propose and investigate two minimally-complex length-limiting factors: limitation due to resource (tubulin) constraints and limitation due to catastrophe of large-length microtubules. We combine simulations of a detailed stochastic model with steady-state analysis of a mean-field ordinary differential equations model to map out qualitatively distinct parameter regimes. This provides a basis for predicting changes in microtubule dynamics, tubulin allocation, and the turnover rate of tubulin within microtubules in different experimental environments.
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Affiliation(s)
- Anna C Nelson
- Department of Mathematics, Duke University, Durham, NC, 27710, USA.
| | - Melissa M Rolls
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, 16801, USA
| | - Maria-Veronica Ciocanel
- Department of Mathematics, Duke University, Durham, NC, 27710, USA
- Department of Biology, Duke University, Durham, NC, 27710, USA
| | - Scott A McKinley
- Department of Mathematics, Tulane University, New Orleans, LA, 70118, USA
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Abstract
Tubulins are essential proteins, which are conserved across all eukaryotic species. They polymerize to form microtubules, cytoskeletal components of paramount importance for cellular mechanics. The microtubules combine an extraordinarily high flexural rigidity and a non-equilibrium behavior, manifested in their intermittent assembly and disassembly. These chemically fueled dynamics allow microtubules to generate significant pushing and pulling forces at their ends to reposition intracellular organelles, remodel membranes, bear compressive forces, and transport chromosomes during cell division. In this article, we review classical and recent studies, which have allowed the quantification of microtubule-generated forces. The measurements, to which we owe most of the quantitative information about microtubule forces, were carried out in biochemically reconstituted systems in vitro. We also discuss how mathematical and computational modeling has contributed to the interpretations of these results and shaped our understanding of the mechanisms of force production by tubulin polymerization and depolymerization.
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Affiliation(s)
- Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
- Pskov State University, Pskov, Russia
| | - Veronika V. Alexandrova
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
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4
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Luchniak A, Kuo YW, McGuinness C, Sutradhar S, Orbach R, Mahamdeh M, Howard J. Dynamic microtubules slow down during their shrinkage phase. Biophys J 2023; 122:616-623. [PMID: 36659852 PMCID: PMC9989939 DOI: 10.1016/j.bpj.2023.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/25/2022] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Microtubules are dynamic polymers that undergo stochastic transitions between growing and shrinking phases. The structural and chemical properties of these phases remain poorly understood. The transition from growth to shrinkage, termed catastrophe, is not a first-order reaction but rather a multistep process whose frequency increases with the growth time: the microtubule ages as the older microtubule tip becomes more unstable. Aging shows that the growing phase is not a single state but comprises several substates of increasing instability. To investigate whether the shrinking phase is also multistate, we characterized the kinetics of microtubule shrinkage following catastrophe using an in vitro reconstitution assay with purified tubulins. We found that the shrinkage speed is highly variable across microtubules and that the shrinkage speed of individual microtubules slows down over time by as much as several fold. The shrinkage slowdown was observed in both fluorescently labeled and unlabeled microtubules as well as in microtubules polymerized from tubulin purified from different species, suggesting that the shrinkage slowdown is a general property of microtubules. These results indicate that microtubule shrinkage, like catastrophe, is time dependent and that the shrinking microtubule tip passes through a succession of states of increasing stability. We hypothesize that the shrinkage slowdown is due to destabilizing events that took place during growth, which led to multistep catastrophe. This suggests that the aging associated with growth is also manifested during shrinkage, with the older, more unstable growing tip being associated with a faster depolymerizing shrinking tip.
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Affiliation(s)
- Anna Luchniak
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Yin-Wei Kuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Catherine McGuinness
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Sabyasachi Sutradhar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Ron Orbach
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Mohammed Mahamdeh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Jonathon Howard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
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6
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Sweet ES, Lange KR, Fenner MR, Tseng CY, Akum BF, Firestein BL. Cypin binds to tubulin heterodimers and microtubule protofilaments and regulates microtubule spacing in developing hippocampal neurons. Mol Cell Neurosci 2022; 123:103783. [PMID: 36208859 DOI: 10.1016/j.mcn.2022.103783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Cytosolic PSD-95 interactor (cypin) is a multifunctional, guanine deaminase that plays a major role in shaping the morphology of the dendritic arbor of hippocampal and cortical neurons. Cypin catalyzes the Zn2+-dependent deamination of guanine to xanthine, which is then metabolized to uric acid by xanthine oxidase. Cypin binds to tubulin heterodimers via its carboxyl terminal region (amino acids (aa) 350-454), which contains a collapsin response mediator protein (CRMP) homology domain (aa 350-403). Moreover, this region alone is not sufficient to facilitate microtubule polymerization; therefore, additional cypin regions must be involved in this process. Here, we asked whether cypin binds to fully formed microtubules and how overexpression of cypin regulates the microtubule cytoskeleton in dendrites of cultured hippocampal neurons. Protein-protein docking strategies confirm that the cypin homodimer binds to tubulin heterodimers via amino acids within aa 350-454. Biochemical pull-down data suggest that aa 1-220 are necessary for cypin binding to soluble tubulin heterodimers and to taxol-stabilized microtubules. Molecular docking of the cypin homodimer to soluble tubulin heterodimers reveals a consistently observed docking pose using aa 47-71, 113-118, 174-178, and 411-418, which is consistent with our biochemical data. Additionally, overexpression of cypin in hippocampal neurons results in decreased spacing between microtubules. Our results suggest that several protein domains facilitate cypin-mediated polymerization of tubulin heterodimers into microtubules, possibly through a mechanism whereby cypin dimers bind to multiple tubulin heterodimers.
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Affiliation(s)
- Eric S Sweet
- Department of Biology, West Chester University, West Chester, PA, United States of America
| | - Keith R Lange
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America; Molecular Biosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America
| | - Madeleine R Fenner
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America
| | - Chia-Yi Tseng
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America; Neurosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America
| | - Barbara F Akum
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America; Molecular Biosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America
| | - Bonnie L Firestein
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, United States of America.
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9
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Naghsh F, Monajjemi M. Thermodynamic Study of Assembling ↔ Disassembling of Microtubules via the Monte Carlo Simulation. Russ J Phys Chem 2022. [DOI: 10.1134/s0036024422070111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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10
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Abstract
The microtubule network of cardiac muscle cells has unique architectural and biophysical features to accommodate the demands of the working heart. Advances in live-cell imaging and in deciphering the 'tubulin code' have shone new light on this cytoskeletal network and its role in heart failure. Microtubule-based transport orchestrates the growth and maintenance of the contractile apparatus through spatiotemporal control of translation, while also organizing the specialized membrane systems required for excitation-contraction coupling. To withstand the high mechanical loads of the working heart, microtubules are post-translationally modified and physically reinforced. In response to stress to the myocardium, the microtubule network remodels, typically through densification, post-translational modification and stabilization. Under these conditions, physically reinforced microtubules resist the motion of the cardiomyocyte and increase myocardial stiffness. Accordingly, modified microtubules have emerged as a therapeutic target for reducing stiffness in heart failure. In this Review, we discuss the latest evidence on the contribution of microtubules to cardiac mechanics, the drivers of microtubule network remodelling in cardiac pathologies and the therapeutic potential of targeting cardiac microtubules in acquired heart diseases.
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Affiliation(s)
- Matthew A Caporizzo
- Department of Molecular Physiology and Biophysics, University of Vermont Larner College of Medicine, Burlington, VT, USA.,Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin L Prosser
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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11
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Cleary JM, Kim T, Cook ASI, McCormick LA, Hancock WO, Rice LM. Measurements and simulations of microtubule growth imply strong longitudinal interactions and reveal a role for GDP on the elongating end. eLife 2022; 11:75931. [PMID: 35420545 PMCID: PMC9064298 DOI: 10.7554/elife.75931] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
Microtubule polymerization dynamics result from the biochemical interactions of αβ-tubulin with the polymer end, but a quantitative understanding has been challenging to establish. We used interference reflection microscopy to make improved measurements of microtubule growth rates and growth fluctuations in the presence and absence of GTP hydrolysis. In the absence of GTP hydrolysis, microtubules grew steadily with very low fluctuations. These data were best described by a computational model implementing slow assembly kinetics, such that the rate of microtubule elongation is primarily limited by the rate of αβ-tubulin associations. With GTPase present, microtubules displayed substantially larger growth fluctuations than expected based on the no GTPase measurements. Our modeling showed that these larger fluctuations occurred because exposure of GDP-tubulin on the microtubule end transiently 'poisoned' growth, yielding a wider range of growth rates compared to GTP only conditions. Our experiments and modeling point to slow association kinetics (strong longitudinal interactions), such that drugs and regulatory proteins that alter microtubule dynamics could do so by modulating either the association or dissociation rate of tubulin from the microtubule tip. By causing slower growth, exposure of GDP tubulin at the growing microtubule end may be an important early event determining catastrophe.
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Affiliation(s)
- Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Tae Kim
- Departments of Biophysics and Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Annan S I Cook
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Lauren A McCormick
- Departments of Biophysics and Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, United States
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, The University of Texas Southwestern Medical Center, Dallas, United States
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12
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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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13
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Mahserejian SM, Scripture JP, Mauro AJ, Lawrence EJ, Jonasson EM, Murray KS, Li J, Gardner M, Alber M, Zanic M, Goodson HV. Quantification of Microtubule Stutters: Dynamic Instability Behaviors that are Strongly Associated with Catastrophe. Mol Biol Cell 2022; 33:ar22. [PMID: 35108073 PMCID: PMC9250389 DOI: 10.1091/mbc.e20-06-0348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Microtubules (MTs) are cytoskeletal fibers that undergo dynamic instability (DI), a remarkable process involving phases of growth and shortening separated by stochastic transitions called catastrophe and rescue. Dissecting DI mechanism(s) requires first characterizing and quantifying these dynamics, a subjective process that often ignores complexity in MT behavior. We present a Statistical Tool for Automated Dynamic Instability Analysis (STADIA) that identifies and quantifies not only growth and shortening, but also a category of intermediate behaviors that we term “stutters.” During stutters, the rate of MT length change tends to be smaller in magnitude than during typical growth or shortening phases. Quantifying stutters and other behaviors with STADIA demonstrates that stutters precede most catastrophes in our in vitro experiments and dimer-scale MT simulations, suggesting that stutters are mechanistically involved in catastrophes. Related to this idea, we show that the anticatastrophe factor CLASP2γ works by promoting the return of stuttering MTs to growth. STADIA enables more comprehensive and data-driven analysis of MT dynamics compared with previous methods. The treatment of stutters as distinct and quantifiable DI behaviors provides new opportunities for analyzing mechanisms of MT dynamics and their regulation by binding proteins.
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Affiliation(s)
- Shant M Mahserejian
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556.,Pacific Northwest National Laboratory, Richland, WA 99352
| | - Jared P Scripture
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556
| | - Ava J Mauro
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556.,Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst MA, 01003
| | - Elizabeth J Lawrence
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240
| | - Erin M Jonasson
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556.,Department of Natural Sciences, Saint Martin's University, Lacey, WA 98503
| | - Kristopher S Murray
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556
| | - Melissa Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Mark Alber
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556.,Department of Mathematics, University of California Riverside, Riverside, CA 92521
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37205
| | - Holly V Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556
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14
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Wijeratne SS, Marchan MF, Tresback JS, Subramanian R. Atomic force microscopy reveals distinct protofilament-scale structural dynamics in depolymerizing microtubule arrays. Proc Natl Acad Sci U S A 2022; 119:e2115708119. [PMID: 35101922 PMCID: PMC8812519 DOI: 10.1073/pnas.2115708119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/01/2022] Open
Abstract
One cannot help but marvel at the precise organization of microtubule polymers in cellular structures such as the axoneme and the spindle. However, our understanding of the biochemical mechanisms that sculpt these arrays comes largely from in vitro experiments with a small number (one or two) of microtubules. This is somewhat akin to studying the architecture of multilane highways by studying one-lane streets. Here, we directly visualize depolymerizing microtubule arrays at individual microtubule and protofilament resolution using atomic force microscopy. Our results reveal differences in microtubule depolymerase activity and provide insights into how these differences in enzymatic activity on the nanometer scale can result in the differential remodeling of multimicrotubule arrays on the micron-length scale. The dynamic reorganization of microtubule-based cellular structures, such as the spindle and the axoneme, fundamentally depends on the dynamics of individual polymers within multimicrotubule arrays. A major class of enzymes implicated in both the complete demolition and fine size control of microtubule-based arrays are depolymerizing kinesins. How different depolymerases differently remodel microtubule arrays is poorly understood. A major technical challenge in addressing this question is that existing optical or electron-microscopy methods lack the spatial-temporal resolution to observe the dynamics of individual microtubules within larger arrays. Here, we use atomic force microscopy (AFM) to image depolymerizing arrays at single-microtubule and protofilament resolution. We discover previously unseen modes of microtubule array destabilization by conserved depolymerases. We find that the kinesin-13 MCAK mediates asynchronous protofilament depolymerization and lattice-defect propagation, whereas the kinesin-8 Kip3p promotes synchronous protofilament depolymerization. Unexpectedly, MCAK can depolymerize the highly stable axonemal doublets, but Kip3p cannot. We propose that distinct protofilament-level activities underlie the functional dichotomy of depolymerases, resulting in either large-scale destabilization or length regulation of microtubule arrays. Our work establishes AFM as a powerful strategy to visualize microtubule dynamics within arrays and reveals how nanometer-scale substrate specificity leads to differential remodeling of micron-scale cytoskeletal structures.
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15
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Kliuchnikov E, Klyshko E, Kelly MS, Zhmurov A, Dima RI, Marx KA, Barsegov V. Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue. Comput Struct Biotechnol J 2022; 20:953-974. [PMID: 35242287 PMCID: PMC8861655 DOI: 10.1016/j.csbj.2022.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/21/2022] Open
Abstract
Microtubules (MTs), a cellular structure element, exhibit dynamic instability and can switch stochastically from growth to shortening; but the factors that trigger these processes at the molecular level are not understood. We developed a 3D Microtubule Assembly and Disassembly DYnamics (MADDY) model, based upon a bead-per-monomer representation of the αβ-tubulin dimers forming an MT lattice, stabilized by the lateral and longitudinal interactions between tubulin subunits. The model was parameterized against the experimental rates of MT growth and shortening, and pushing forces on the Dam1 protein complex due to protofilaments splaying out. Using the MADDY model, we carried out GPU-accelerated Langevin simulations to access dynamic instability behavior. By applying Machine Learning techniques, we identified the MT characteristics that distinguish simultaneously all four kinetic states: growth, catastrophe, shortening, and rescue. At the cellular 25 μM tubulin concentration, the most important quantities are the MT length L , average longitudinal curvatureκ long , MT tip width w , total energy of longitudinal interactions in MT latticeU long , and the energies of longitudinal and lateral interactions required to complete MT to full cylinderU long add andU lat add . At high 250 μM tubulin concentration, the most important characteristics are L ,κ long , number of hydrolyzed αβ-tubulin dimersn hyd and number of lateral interactions per helical pitchn lat in MT lattice, energy of lateral interactions in MT latticeU lat , and energy of longitudinal interactions in MT tipu long . These results allow greater insights into what brings about kinetic state stability and the transitions between states involved in MT dynamic instability behavior.
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Affiliation(s)
| | - Eugene Klyshko
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Maria S. Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Artem Zhmurov
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
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16
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Rai A, Liu T, Katrukha EA, Estévez-Gallego J, Manka SW, Paterson I, Díaz JF, Kapitein LC, Moores CA, Akhmanova A. Lattice defects induced by microtubule-stabilizing agents exert a long-range effect on microtubule growth by promoting catastrophes. Proc Natl Acad Sci U S A 2021; 118:e2112261118. [PMID: 34916292 DOI: 10.1073/pnas.2112261118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Microtubules are major cytoskeletal filaments important for cell division, growth, and differentiation. Microtubules can rapidly switch between phases of growth and shortening, and this dynamic behavior is essential for shaping microtubule arrays. To obtain insights into mechanisms controlling microtubule dynamics, here we used microtubule-stabilizing agents such as Taxol and their fluorescent analogs to manipulate microtubule protofilament number and generate stable defects in microtubule lattices that can be visualized using fluorescence microscopy. We show that microtubule polymerization rate increases with protofilament number and that drug-induced microtubule lattice discontinuities can promote plus-end catastrophes at a distance of several micrometers. Our data indicate that structural defects in the microtubule wall can have long-range propagating effects on microtubule tip dynamics. Microtubules are dynamic cytoskeletal polymers that spontaneously switch between phases of growth and shrinkage. The probability of transitioning from growth to shrinkage, termed catastrophe, increases with microtubule age, but the underlying mechanisms are poorly understood. Here, we set out to test whether microtubule lattice defects formed during polymerization can affect growth at the plus end. To generate microtubules with lattice defects, we used microtubule-stabilizing agents that promote formation of polymers with different protofilament numbers. By employing different agents during nucleation of stable microtubule seeds and the subsequent polymerization phase, we could reproducibly induce switches in protofilament number and induce stable lattice defects. Such drug-induced defects led to frequent catastrophes, which were not observed when microtubules were grown in the same conditions but without a protofilament number mismatch. Microtubule severing at the site of the defect was sufficient to suppress catastrophes. We conclude that structural defects within the microtubule lattice can exert effects that can propagate over long distances and affect the dynamic state of the microtubule end.
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17
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Nasedkin A, Ermilova I, Swenson J. Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule. Eur Biophys J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Gudimchuk NB, McIntosh JR. Regulation of microtubule dynamics, mechanics and function through the growing tip. Nat Rev Mol Cell Biol 2021. [PMID: 34408299 DOI: 10.1038/s41580-021-00399-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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20
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Farmer V, Arpağ G, Hall SL, Zanic M. XMAP215 promotes microtubule catastrophe by disrupting the growing microtubule end. J Cell Biol 2021; 220:212518. [PMID: 34324632 PMCID: PMC8327381 DOI: 10.1083/jcb.202012144] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/11/2021] [Accepted: 07/08/2021] [Indexed: 01/13/2023] Open
Abstract
The GTP-tubulin cap is widely accepted to protect microtubules against catastrophe. The GTP-cap size is thought to increase with the microtubule growth rate, presumably endowing fast-growing microtubules with enhanced stability. It is unknown what GTP-cap properties permit frequent microtubule catastrophe despite fast growth. Here, we investigate microtubules growing in the presence and absence of the polymerase XMAP215. Using EB1 as a GTP-cap marker, we find that GTP-cap size increases regardless of whether growth acceleration is achieved by increasing tubulin concentration or by XMAP215. Despite increased mean GTP-cap size, microtubules grown with XMAP215 display increased catastrophe frequency, in contrast to microtubules grown with more tubulin, for which catastrophe is abolished. However, microtubules polymerized with XMAP215 have large fluctuations in growth rate; display tapered and curled ends; and undergo catastrophe at faster growth rates and with higher EB1 end-localization. Our results suggest that structural perturbations induced by XMAP215 override the protective effects of the GTP-cap, ultimately driving microtubule catastrophe.
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Affiliation(s)
- Veronica Farmer
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Göker Arpağ
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Sarah L Hall
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN.,Department of Biochemistry, Vanderbilt University, Nashville, TN
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21
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Abstract
Microtubules are dynamic cytoskeletal filaments composed of αβ-tubulin heterodimers. Historically, the dynamics of single tubulin interactions at the growing microtubule tip have been inferred from steady-state growth kinetics. However, recent advances in the production of recombinant tubulin and in high-resolution optical and cryo-electron microscopies have opened new windows into understanding the impacts of specific intermolecular interactions during growth. The microtubule lattice is held together by lateral and longitudinal tubulin-tubulin interactions, and these interactions are in turn regulated by the GTP hydrolysis state of the tubulin heterodimer. Furthermore, tubulin can exist in either an extended or a compacted state in the lattice. Growing evidence has led to the suggestion that binding of microtubule-associated proteins (MAPs) or motors can induce changes in tubulin conformation and that this information can be communicated through the microtubule lattice. Progress in understanding how dynamic tubulin-tubulin interactions control dynamic instability has benefitted from visualizing structures of growing microtubule plus ends and through stochastic biochemical models constrained by experimental data. Here, we review recent insights into the molecular basis of microtubule growth and discuss how MAPs and regulatory proteins alter tubulin-tubulin interactions to exert their effects on microtubule growth and stability.
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Affiliation(s)
- Joseph M Cleary
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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22
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Ulyanov EV, Vinogradov DS, McIntosh JR, Gudimchuk NB. Brownian dynamics simulation of protofilament relaxation during rapid freezing. PLoS One 2021; 16:e0247022. [PMID: 33577570 PMCID: PMC7880439 DOI: 10.1371/journal.pone.0247022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/31/2021] [Indexed: 11/18/2022] Open
Abstract
Electron cryo-microscopy (Cryo-EM) is a powerful method for visualizing biological objects with up to near-angstrom resolution. Instead of chemical fixation, the method relies on very rapid freezing to immobilize the sample. Under these conditions, crystalline ice does not have time to form and distort structure. For many practical applications, the rate of cooling is fast enough to consider sample immobilization instantaneous, but in some cases, a more rigorous analysis of structure relaxation during freezing could be essential. This difficult yet important problem has been significantly under-reported in the literature, despite spectacular recent developments in Cryo-EM. Here we use Brownian dynamics modeling to examine theoretically the possible effects of cryo-immobilization on the apparent shapes of biological polymers. The main focus of our study is on tubulin protofilaments. These structures are integral parts of microtubules, which in turn are key elements of the cellular skeleton, essential for intracellular transport, maintenance of cell shape, cell division and migration. We theoretically examine the extent of protofilament relaxation within the freezing time as a function of the cooling rate, the filament's flexural rigidity, and the effect of cooling on water's viscosity. Our modeling suggests that practically achievable cooling rates are not rapid enough to capture tubulin protofilaments in conformations that are incompletely relaxed, suggesting that structures seen by cryo-EM are good approximations to physiological shapes. This prediction is confirmed by our analysis of curvatures of tubulin protofilaments, using samples, prepared and visualized with a variety of methods. We find, however, that cryofixation may capture incompletely relaxed shapes of more flexible polymers, and it may affect Cryo-EM-based measurements of their persistence lengths. This analysis will be valuable for understanding of structures of different types of biopolymers, observed with Cryo-EM.
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Affiliation(s)
- Evgeniy V. Ulyanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | | | - J. Richard McIntosh
- Department of MCD Biology, University of Colorado, Boulder, CO, United States of America
| | - Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of MCD Biology, University of Colorado, Boulder, CO, United States of America
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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23
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Hemmat M, Odde DJ. Atomistic Basis of Microtubule Dynamic Instability Assessed Via Multiscale Modeling. Ann Biomed Eng 2021; 49:1716-34. [PMID: 33537926 DOI: 10.1007/s10439-020-02715-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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24
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Stewman SF, Tsui KK, Ma A. Dynamic Instability from Non-equilibrium Structural Transitions on the Energy Landscape of Microtubule. Cell Syst 2020; 11:608-624.e9. [PMID: 33086051 DOI: 10.1016/j.cels.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 09/12/2019] [Accepted: 09/25/2020] [Indexed: 11/30/2022]
Abstract
Microtubules are the backbone of the cytoskeleton and vital to numerous cellular processes. The central dogma of microtubules is that all their functions are driven by dynamic instability, but its mechanism has remained unresolved for over 30 years because of conceptual difficulties inherent in the dominant GTP-cap framework. We present a physically rigorous structural mechanochemical model: dynamic instability is driven by non-equilibrium transitions between the bent (B), straight (S), and curved (C) forms of tubulin monomers and longitudinal interfaces in the two-dimensional lattice of microtubule. All the different phenomena (growth, shortening, catastrophe, rescue, and pausing) are controlled by the kinetic pathways for B↔S↔C transitions and corresponding energy landscapes. Different kinetics at minus end are due to different B↔S↔C pathways imposed by the polarity of microtubule lattice. This model enables us to reproduce all the observed phenomena of dynamic instability of purified tubulins in kinetic simulations.
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Affiliation(s)
- Shannon F Stewman
- Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
| | - Kenneth K Tsui
- Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA
| | - Ao Ma
- Department of Bioengineering, the University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607, USA.
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25
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Bajpai A, Li R, Chen W. The cellular mechanobiology of aging: from biology to mechanics. Ann N Y Acad Sci 2020; 1491:3-24. [PMID: 33231326 DOI: 10.1111/nyas.14529] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/10/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Aging is a chronic, complicated process that leads to degenerative physical and biological changes in living organisms. Aging is associated with permanent, gradual physiological cellular decay that affects all aspects of cellular mechanobiological features, including cellular cytoskeleton structures, mechanosensitive signaling pathways, and forces in the cell, as well as the cell's ability to sense and adapt to extracellular biomechanical signals in the tissue environment through mechanotransduction. These mechanobiological changes in cells are directly or indirectly responsible for dysfunctions and diseases in various organ systems, including the cardiovascular, musculoskeletal, skin, and immune systems. This review critically examines the role of aging in the progressive decline of the mechanobiology occurring in cells, and establishes mechanistic frameworks to understand the mechanobiological effects of aging on disease progression and to develop new strategies for halting and reversing the aging process. Our review also highlights the recent development of novel bioengineering approaches for studying the key mechanobiological mechanisms in aging.
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Affiliation(s)
- Apratim Bajpai
- Department of Mechanical and Aerospace Engineering, Tandon School of Engineering, New York University, Brooklyn, New York
| | - Rui Li
- Department of Mechanical and Aerospace Engineering, Tandon School of Engineering, New York University, Brooklyn, New York.,Department of Biomedical Engineering, Tandon School of Engineering, New York University, Brooklyn, New York
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, Tandon School of Engineering, New York University, Brooklyn, New York.,Department of Biomedical Engineering, Tandon School of Engineering, New York University, Brooklyn, New York.,Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, New York
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26
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Sai KKS, Prabhakaran J, Damuka N, Craft S, Rajagopal SA, Mintz A, Mann J, Kumar D. Synthesis and Initial In Vivo Evaluations of [
11
C]WX‐132‐18B, a Microtubule PET Imaging Agent. ChemistrySelect 2020. [DOI: 10.1002/slct.202001827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Jaya Prabhakaran
- Department of PsychiatryColumbia University Irving Medical Center 1051 Riverside Drive New York 10032 USA
- Area of Molecular Imaging and neuropathologyNew York State Psychiatric Institute 1051 Riverside Drive New York 10032 USA
| | - Naresh Damuka
- Department of RadiologyWake Forest University School of Medicine Winston-Salem North Carolina 27157 USA
| | - Suzanne Craft
- Department of Internal MedicineWake Forest University School of Medicine Winston Salem North Carolina 27157 USA
| | - Shamyaa A. Rajagopal
- Department of RadiologyWake Forest University School of Medicine Winston-Salem North Carolina 27157 USA
| | - Akiva Mintz
- Department of RadiologyColumbia University Irving Medical Center New York 10032 USA
| | - John Mann
- Department of PsychiatryColumbia University Irving Medical Center 1051 Riverside Drive New York 10032 USA
- Area of Molecular Imaging and neuropathologyNew York State Psychiatric Institute 1051 Riverside Drive New York 10032 USA
- Department of RadiologyColumbia University Irving Medical Center New York 10032 USA
| | - Dileep Kumar
- Area of Molecular Imaging and neuropathologyNew York State Psychiatric Institute 1051 Riverside Drive New York 10032 USA
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27
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Khan MI, Hasan F, Mahmud KAHA, Adnan A. Recent Computational Approaches on Mechanical Behavior of Axonal Cytoskeletal Components of Neuron: A Brief Review. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s42493-020-00043-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Abstract
During dynamic instability, self-assembling microtubules (MTs) stochastically alternate between phases of growth and shrinkage. This process is driven by the presence of two distinct states of MT subunits, GTP- and GDP-bound tubulin dimers, that have different structural properties. Here, we use a combination of analysis and computer simulations to study the mechanical and kinetic regulation of dynamic instability in three-dimensional (3D) self-assembling MTs. Our model quantifies how the 3D structure and kinetics of the distinct states of tubulin dimers determine the mechanical stability of MTs. We further show that dynamic instability is influenced by the presence of quenched disorder in the state of the tubulin subunit as reflected in the fraction of non-hydrolysed tubulin. Our results connect the 3D geometry, kinetics and statistical mechanics of these tubular assemblies within a single framework, and may be applicable to other self-assembled systems where these same processes are at play.
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Affiliation(s)
- Thomas Ct Michaels
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
| | - Shuo Feng
- Department of Modern Mechanics, University of Science and Technology of China, Hefei, China.,IAT Chungu Joint Laboratory for Additive Manufacturing, Anhui Chungu 3D Institute of Intelligent Equipment and Industrial Technology, Wuhu, China
| | - Haiyi Liang
- Department of Modern Mechanics, University of Science and Technology of China, Hefei, China.,IAT Chungu Joint Laboratory for Additive Manufacturing, Anhui Chungu 3D Institute of Intelligent Equipment and Industrial Technology, Wuhu, China
| | - L Mahadevan
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States.,Department of Physics, Harvard University, Cambridge, United States.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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30
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J S A, Padinhateeri R, Das D. Regulation of microtubule disassembly by spatially heterogeneous patterns of acetylation. Soft Matter 2020; 16:3125-3136. [PMID: 32159199 DOI: 10.1039/c9sm02198a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microtubules (MTs) are bio-polymers, composed of tubulin proteins, involved in several functions such as cell division, transport of cargoes within cells, maintaining cellular structures etc. Their kinetics are often affected by chemical modifications on the filament known as Post Translational Modifications (PTMs). Acetylation is a PTM which occurs on the luminal surface of the MT lattice and has been observed to reduce the lateral interaction between tubulins on adjacent protofilaments. Depending on the properties of the acetylase enzyme αTAT1 and the structural features of MTs, the patterns of acetylation formed on MTs are observed to be quite diverse. In this study, we present a multi-protofilament model with spatially heterogeneous patterns of acetylation, and investigate how the local kinetic differences arising from heterogeneity affect the global kinetics of MT filaments. From the computational study we conclude that a filament with spatially uniform acetylation is least stable against disassembly, while ones with more clustered acetylation patterns may provide better resistance against disassembly. The increase in disassembly times for clustered pattern as compared to uniform pattern can be up to fifty percent for identical amounts of acetylation. Given that acetylated MTs affect several cellular functions as well as diseases such as cancer, our study indicates that spatial patterns of acetylation need to be focused on, apart from the overall amount of acetylation.
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Affiliation(s)
- Aparna J S
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Mumbai, India.
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31
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Diwe M, Gopalakrishnan M. Spatio-temporal correlations between catastrophe events in a microtubule bundle: a computational study. Eur Biophys J 2020; 49:215-22. [PMID: 32157375 DOI: 10.1007/s00249-020-01427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
We explore correlations between dynamics of different microtubules in a bundle, via numerical simulations, using a one-dimensional stochastic model of a microtubule. The guanosine triphosphate (GTP)-bound tubulins undergo diffusion-limited binding to the tip. Random hydrolysis events take place along the microtubule and converts the bound GTP in tubulin to guanosine diphosphate (GDP). The microtubule starts depolymerising when the monomer at the tip becomes GDP-bound; in this case, detachment of GDP-tubulin ensues and continues until either GTP-bound tubulin is exposed or complete depolymerisation is achieved. In the latter case, the microtubule is defined to have undergone a "catastrophe". Our results show that, in general, the dynamics of growth and catastrophe in different microtubules are coupled to each other; the closer the microtubules are, the stronger the coupling. In particular, all microtubules grow slower, on average, when brought closer together. The reduction in growth velocity also leads to more frequent catastrophes. More dramatically, catastrophe events in the different microtubules forming a bundle are found to be correlated; a catastrophe event in one microtubule is more likely to be followed by a similar event in the same microtubule. This propensity of bunching disappears when the microtubules move farther apart.
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32
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Hsu CJ, Brouhard GJ, François P. Numerical Parameter Space Compression and Its Application to Biophysical Models. Biophys J 2020; 118:1455-65. [PMID: 32070477 DOI: 10.1016/j.bpj.2020.01.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/07/2019] [Accepted: 01/14/2020] [Indexed: 11/20/2022] Open
Abstract
Physical models of biological systems can become difficult to interpret when they have a large number of parameters. But the models themselves actually depend on (i.e., are sensitive to) only a subset of those parameters. This phenomenon is due to parameter space compression (PSC), in which a subset of parameters emerges as "stiff" as a function of time or space. PSC has only been used to explain analytically solvable physics models. We have generalized this result by developing a numerical approach to PSC that can be applied to any computational model. We validated our method against analytically solvable models of a random walk with drift and protein production and degradation. We then applied our method to a simple computational model of microtubule dynamic instability. We propose that numerical PSC has the potential to identify the low-dimensional structure of many computational models in biophysics. The low-dimensional structure of a model is easier to interpret and identifies the mechanisms and experiments that best characterize the system.
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33
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Dileep Kumar JS, Prabhakaran J, Damuka N, Hines JW, Norman S, Dodda M, John Mann J, Mintz A, Sai KKS. In vivo comparison of N- 11CH 3 vs O- 11CH 3 radiolabeled microtubule targeted PET ligands. Bioorg Med Chem Lett 2020; 30:126785. [PMID: 31753695 DOI: 10.1016/j.bmcl.2019.126785] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 11/22/2022]
Abstract
Altered dynamics of microtubules (MT) are implicated in the pathophysiology of a number of brain diseases. Therefore, radiolabeled MT targeted ligands that can penetrate the blood brain barrier (BBB) may offer a direct and sensitive approach for diagnosis, and assessing the clinical potential of MT targeted therapeutics using PET imaging. We recently reported two BBB penetrating radioligands, [11C]MPC-6827 and [11C]HD-800 as specific PET ligands for imaging MTs in brain. The major metabolic pathway of the above molecules is anticipated to be via the initial labeling site, O-methyl, compared to the N-methyl group. Herein, we report the radiosynthesis of N-11CH3-MPC-6827 and N-11CH3-HD-800 and a comparison of their in vivo binding with the corresponding O-11CH3 analogues using microPET imaging and biodistribution methods. Both O-11CH3 and N-11CH3 labeled MT tracers exhibit high specific binding and brain. The N-11CH3 labeled PET ligands demonstrated similar in vivo binding characteristics compared with the corresponding O-11CH3 labeled tracers, [11C]MPC-6827 and [11C]HD-800 respectively.
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34
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Coombes CE, Saunders HAJ, Mannava AG, Johnson-Schlitz DM, Reid TA, Parmar S, McClellan M, Yan C, Rogers SL, Parrish JZ, Wagenbach M, Wordeman L, Wildonger J, Gardner MK. Non-enzymatic Activity of the α-Tubulin Acetyltransferase αTAT Limits Synaptic Bouton Growth in Neurons. Curr Biol 2020; 30:610-623.e5. [PMID: 31928876 DOI: 10.1016/j.cub.2019.12.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 10/16/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022]
Abstract
Neuronal axons terminate as synaptic boutons that form stable yet plastic connections with their targets. Synaptic bouton development relies on an underlying network of both long-lived and dynamic microtubules that provide structural stability for the boutons while also allowing for their growth and remodeling. However, a molecular-scale mechanism that explains how neurons appropriately balance these two microtubule populations remains a mystery. We hypothesized that α-tubulin acetyltransferase (αTAT), which both stabilizes long-lived microtubules against mechanical stress via acetylation and has been implicated in promoting microtubule dynamics, could play a role in this process. Using the Drosophila neuromuscular junction as a model, we found that non-enzymatic dαTAT activity limits the growth of synaptic boutons by affecting dynamic, but not stable, microtubules. Loss of dαTAT results in the formation of ectopic boutons. These ectopic boutons can be similarly suppressed by resupplying enzyme-inactive dαTAT or by treatment with a low concentration of the microtubule-targeting agent vinblastine, which acts to suppress microtubule dynamics. Biophysical reconstitution experiments revealed that non-enzymatic αTAT1 activity destabilizes dynamic microtubules but does not substantially impact the stability of long-lived microtubules. Further, during microtubule growth, non-enzymatic αTAT1 activity results in increasingly extended tip structures, consistent with an increased rate of acceleration of catastrophe frequency with microtubule age, perhaps via tip structure remodeling. Through these mechanisms, αTAT enriches for stable microtubules at the expense of dynamic ones. We propose that the specific suppression of dynamic microtubules by non-enzymatic αTAT activity regulates the remodeling of microtubule networks during synaptic bouton development.
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Affiliation(s)
- Courtney E Coombes
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Harriet A J Saunders
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anirudh G Mannava
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Taylor A Reid
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sneha Parmar
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark McClellan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Connie Yan
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Stephen L Rogers
- Department of Biology, Integrative Program for Biological and Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, The University of Washington, Seattle, WA 98195, USA
| | - Linda Wordeman
- Department of Physiology and Biophysics, The University of Washington, Seattle, WA 98195, USA
| | - Jill Wildonger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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35
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Bollinger JA, Stevens MJ. Diverse balances of tubulin interactions and shape change drive and interrupt microtubule depolymerization. Soft Matter 2019; 15:8137-8146. [PMID: 31593193 DOI: 10.1039/c9sm01323g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microtubules are stiff biopolymers that self-assemble via the addition of GTP-tubulin (αβ-dimer bound to GTP), but hydrolysis of GTP- to GDP-tubulin within the tubules destabilizes them toward catastrophically-fast depolymerization. The molecular mechanisms and features of the individual tubulin proteins that drive such behavior are still not well-understood. Using molecular dynamics simulations of whole microtubules built from a coarse-grained model of tubulin, we demonstrate how conformational shape changes (i.e., deformations) in subunits that frustrate tubulin-tubulin binding within microtubules drive depolymerization of stiff tubules via unpeeling "ram's horns" consistent with experiments. We calculate the sensitivity of these behaviors to the length scales and strengths of binding attractions and varying degrees of binding frustration driven by subunit shape change, and demonstrate that the dynamic instability and mechanical properties of microtubules can be produced based on either balanced or imbalanced strengths of lateral and vertical binding attractions. Finally, we show how catastrophic depolymerization can be interrupted by small regions of the microtubule containing undeformed dimers, corresponding to incomplete lattice hydrolysis. The results demonstrate a mechanism by which microtubule rescue can occur.
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Affiliation(s)
- Jonathan A Bollinger
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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36
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Abstract
Microtubules (MTs) experience an effect called "catastrophe," which is the transition from the MT growth to a sudden dramatic shrinkage in length. The straight guanosine triphosphate (GTP)-tubulin cap at the filament tip and the intrinsic curvature of guanosine diphosphate (GDP)-tubulins are known to be the key thermodynamic factors that determine MT catastrophe, while the hydrolysis of this GTP-cap acts as the kinetic control of the process. Although several theoretical models have been developed, assuming the catastrophe occurs when the GTP-cap shrinks to a minimal stabilizing size, the structural effect of the GTP-cap and GDP-curvature is not explicitly included; thus, their influence on catastrophe kinetics remains less understood. To investigate this structural effect, we apply a single-protofilament model with one GTP-cap while assuming a random hydrolysis mechanism and take the occurrence of a crack in the lateral bonds between neighboring protofilaments as the onset of the catastrophe. Therein, we find the effective potential of the tip along the peel-off direction and formulate the catastrophe kinetics as a mean first-passage time problem, subject to thermal fluctuations. We consider cases with and without a compressive force on the MT tip, both of which give a quadratic effective potential, making MT catastrophe an Ornstein-Uhlenbeck process in our formalism. In the free-standing case, the mean catastrophe time has a sensitive tubulin-concentration dependence, similar to a double-exponential function, and agrees well with the experiment. For a compressed MT, we find a modified exponential function of force that shortens the catastrophe time.
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Affiliation(s)
- Cheng-Tai Lee
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Eugene M Terentjev
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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37
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Bordone MP, Salman MM, Titus HE, Amini E, Andersen JV, Chakraborti B, Diuba AV, Dubouskaya TG, Ehrke E, Espindola de Freitas A, Braga de Freitas G, Gonçalves RA, Gupta D, Gupta R, Ha SR, Hemming IA, Jaggar M, Jakobsen E, Kumari P, Lakkappa N, Marsh APL, Mitlöhner J, Ogawa Y, Paidi RK, Ribeiro FC, Salamian A, Saleem S, Sharma S, Silva JM, Singh S, Sulakhiya K, Tefera TW, Vafadari B, Yadav A, Yamazaki R, Seidenbecher CI. The energetic brain - A review from students to students. J Neurochem 2019; 151:139-165. [PMID: 31318452 DOI: 10.1111/jnc.14829] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
The past 20 years have resulted in unprecedented progress in understanding brain energy metabolism and its role in health and disease. In this review, which was initiated at the 14th International Society for Neurochemistry Advanced School, we address the basic concepts of brain energy metabolism and approach the question of why the brain has high energy expenditure. Our review illustrates that the vertebrate brain has a high need for energy because of the high number of neurons and the need to maintain a delicate interplay between energy metabolism, neurotransmission, and plasticity. Disturbances to the energetic balance, to mitochondria quality control or to glia-neuron metabolic interaction may lead to brain circuit malfunction or even severe disorders of the CNS. We cover neuronal energy consumption in neural transmission and basic ('housekeeping') cellular processes. Additionally, we describe the most common (glucose) and alternative sources of energy namely glutamate, lactate, ketone bodies, and medium chain fatty acids. We discuss the multifaceted role of non-neuronal cells in the transport of energy substrates from circulation (pericytes and astrocytes) and in the supply (astrocytes and microglia) and usage of different energy fuels. Finally, we address pathological consequences of disrupted energy homeostasis in the CNS.
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Affiliation(s)
- Melina Paula Bordone
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones Farmacológicas (ININFA), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mootaz M Salman
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Haley E Titus
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Elham Amini
- Department of Medicine, University Kebangsaan Malaysia Medical Centre (HUKM), Cheras, Kuala Lumpur, Malaysia
| | - Jens V Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Artem V Diuba
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatsiana G Dubouskaya
- Institute of Biophysics and Cell Engineering, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Eric Ehrke
- Centre for Biomolecular Interactions, University of Bremen, Bremen, Germany
| | - Andiara Espindola de Freitas
- Neurobiology Section, Biological Sciences Division, University of California, San Diego, La Jolla, California, USA
| | | | | | | | - Richa Gupta
- CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Sharon R Ha
- Baylor College of Medicine, Houston, Texas, USA
| | - Isabel A Hemming
- Brain Growth and Disease Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia.,School of Medicine and Pharmacology, The University of Western Australia, Crawley, Australia
| | - Minal Jaggar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Emil Jakobsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Punita Kumari
- Defense Institute of Physiology and allied sciences, Defense Research and Development Organization, Timarpur, Delhi, India
| | - Navya Lakkappa
- Department of Pharmacology, JSS college of Pharmacy, Ooty, India
| | - Ashley P L Marsh
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Jessica Mitlöhner
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Magdeburg, Germany
| | - Yuki Ogawa
- The Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | | | | | - Ahmad Salamian
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Suraiya Saleem
- CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sorabh Sharma
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Joana M Silva
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
| | - Shripriya Singh
- CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Kunjbihari Sulakhiya
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, India
| | - Tesfaye Wolde Tefera
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Behnam Vafadari
- Institute of environmental medicine, UNIKA-T, Technical University of Munich, Munich, Germany
| | - Anuradha Yadav
- CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Reiji Yamazaki
- Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.,Center for Behavioral Brain Sciences (CBBS), Otto von Guericke University, Magdeburg, Germany
| | - Constanze I Seidenbecher
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology Magdeburg, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Otto von Guericke University, Magdeburg, Germany
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38
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Abstract
Many previous studies of unbinding kinetics have focused on a two-state model, with fully bonded and free states, which may not extend to more complicated biopolymer dynamics involving other reactions. Here we address the kinetic rate of this process at the segment level, as it is influenced by a growing dangling end of the chain. We use the mean first-passage time approach and treat the polymer as a chain attached to a wall through a succession of spring potentials, with two distinct regions of bonded and free segments. The interaction between the wall and free-moving chain end adds an entropic repulsion to this process. We estimate the average monomer detachment rate K as a function of the free dangling length L. For a flexible polymer, we find an acceleration factor in the average detachment rate depending on L and the details of the spring bond; when L is long, this factor is a simple ratio of its breaking distance to the natural bond length. For a semiflexible filament, we examine the regime where L is shorter than persistence length L_{p}, as the limit opposite to that of the flexible chain. An enhancing factor also appears, speeding up the filament unbinding when the free length grows; for a long rigid rod, this factor becomes two, independently of the bond details. We also examine the total unbinding time of an irreversible detaching process by integrating (1/K) over polymer length and discover that its power-law scaling with chain length is smaller than one, over the commonly seen range of polymer size.
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Affiliation(s)
- Cheng-Tai Lee
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Eugene M Terentjev
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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39
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Wong TY, Chang SN, Jhong RC, Tseng CJ, Sun GC, Cheng PW. Closer to Nature Through Dynamic Culture Systems. Cells 2019; 8:E942. [PMID: 31438519 DOI: 10.3390/cells8090942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
Mechanics in the human body are required for normal cell function at a molecular level. It is now clear that mechanical stimulations play significant roles in cell growth, differentiation, and migration in normal and diseased cells. Recent studies have led to the discovery that normal and cancer cells have different mechanosensing properties. Here, we discuss the application and the physiological and pathological meaning of mechanical stimulations. To reveal the optimal conditions for mimicking an in vivo microenvironment, we must, therefore, discern the mechanotransduction occurring in cells.
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40
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Curr Opin Struct Biol 2019; 58:43-52. [PMID: 31226513 DOI: 10.1016/j.sbi.2019.05.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/13/2019] [Accepted: 05/19/2019] [Indexed: 01/19/2023]
Abstract
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.
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Affiliation(s)
- Anne E Hafner
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK
| | - Johannes Krausser
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK.
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44
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Abstract
Microtubules are cylindrical polymers of αβ-tubulin that play critical roles in fundamental processes such as chromosome segregation and vesicular transport. Microtubules display dynamic instability, switching stochastically between growth and rapid shrinking as a consequence of GTPase activity in the lattice. The molecular mechanisms behind microtubule catastrophe, the switch from growth to rapid shrinking, remain poorly defined. Indeed, two-state stochastic models that seek to describe microtubule dynamics purely in terms of the biochemical properties of GTP- and GDP-bound αβ-tubulin predict the concentration dependence of microtubule catastrophe incorrectly. Recent studies provide evidence for three distinct conformations of αβ-tubulin in the lattice that likely correspond to GTP, GDP.Pi, and GDP. The incommensurate lattices observed for these different conformations raise the possibility that in a mixed nucleotide state lattice, neighboring tubulin dimers might modulate each other’s conformations and hence each other’s biochemistry. We explored whether incorporating a GDP.Pi state or the likely effects of conformational accommodation can improve predictions of catastrophe. Adding a GDP.Pi intermediate did not improve the model. In contrast, adding neighbor-dependent modulation of tubulin biochemistry improved predictions of catastrophe. Because this conformational accommodation should propagate beyond nearest-neighbor contacts, our modeling suggests that long-range, through-lattice effects are important determinants of microtubule catastrophe.
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Affiliation(s)
- Tae Kim
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Luke M Rice
- Departments of Biophysics and Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mickolajczyk KJ, Geyer EA, Kim T, Rice LM, Hancock WO. Direct observation of individual tubulin dimers binding to growing microtubules. Proc Natl Acad Sci U S A 2019; 116:7314-22. [PMID: 30804205 DOI: 10.1073/pnas.1815823116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biochemical basis of microtubule growth has remained elusive for over 30 years despite being fundamental for both cell division and associated chemotherapy strategies. Here, we combine interferometric scattering microscopy with recombinant tubulin to monitor individual tubulins binding to and dissociating from growing microtubule tips. We make direct, single-molecule measurements of tubulin association and dissociation rates. We detect two populations of transient dwell times and determine via binding-interface mutants that they are distinguished by the formation of one interprotofilament bond. Applying a computational model, we find that slow association kinetics with strong interactions along protofilaments best recapitulate our data and, furthermore, predicts plus-end tapering. Overall, we provide the most direct and complete experimental quantification of how microtubules grow to date.
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Lawrence EJ, Zanic M. Rescuing microtubules from the brink of catastrophe: CLASPs lead the way. Curr Opin Cell Biol 2019; 56:94-101. [PMID: 30453184 PMCID: PMC6370552 DOI: 10.1016/j.ceb.2018.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/12/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023]
Abstract
Microtubules are cytoskeletal polymers that dynamically remodel to perform essential cellular functions. Individual microtubules alternate between phases of growth and shrinkage via sudden transitions called catastrophe and rescue, driven by losing and regaining a stabilizing cap at the dynamic microtubule end. New in vitro studies now show that a conserved family of CLASP proteins specifically modulate microtubule catastrophe and rescue transitions. Further, recent cryo-electron microscopy approaches have elucidated new structural features of the stabilizing cap. Together, these new advances provide a clearer view on the complexity of the microtubule end and its regulation.
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Affiliation(s)
- E J Lawrence
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, United States
| | - M Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, United States; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, United States; Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, United States.
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48
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Abstract
The development of cryo-electron microscopy (cryo-EM) allowed microtubules to be captured in their solution-like state, enabling decades of insight into their dynamic mechanisms and interactions with binding partners. Cryo-EM micrographs provide 2D visualization of microtubules, and these 2D images can also be used to reconstruct the 3D structure of the polymer and any associated binding partners. In this way, the binding sites for numerous components of the microtubule cytoskeleton-including motor domains from many kinesin motors, and the microtubule-binding domains of dynein motors and an expanding collection of microtubule associated proteins-have been determined. The effects of various microtubule-binding drugs have also been studied. High-resolution cryo-EM structures have also been used to probe the molecular basis of microtubule dynamic instability, driven by the GTPase activity of β-tubulin. These studies have shown the conformational changes in lattice-confined tubulin dimers in response to steps in the tubulin GTPase cycle, most notably lattice compaction at the longitudinal inter-dimer interface. Although work is ongoing to define a complete structural model of dynamic instability, attention has focused on the role of gradual destabilization of lateral contacts between tubulin protofilaments, particularly at the microtubule seam. Furthermore, lower resolution cryo-electron tomography 3D structures are shedding light on the heterogeneity of microtubule ends and how their 3D organization contributes to dynamic instability. The snapshots of these polymers captured using cryo-EM will continue to provide critical insights into their dynamics, interactions with cellular components, and the way microtubules contribute to cellular functions in diverse physiological contexts.
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Affiliation(s)
- Szymon W Manka
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, U.K.
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, U.K
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49
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Chaaban S, Jariwala S, Hsu CT, Redemann S, Kollman JM, Müller-Reichert T, Sept D, Bui KH, Brouhard GJ. The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Dev Cell 2018; 47:191-204.e8. [PMID: 30245157 DOI: 10.1016/j.devcel.2018.08.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/06/2018] [Accepted: 08/23/2018] [Indexed: 01/04/2023]
Abstract
The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and responses to GTP hydrolysis. Therefore, we do not know what limits microtubule growth, what determines microtubule structure, or whether the mechanisms of dynamic instability are universal. Here, we studied microtubules from the nematode C. elegans, which have strikingly fast growth rates and non-canonical lattices in vivo. Using a reconstitution approach, we discovered that C. elegans microtubules combine intrinsically fast growth with very frequent catastrophes. We solved the structure of C. elegans microtubules to 4.8 Å and discovered sequence divergence in the lateral contact loops, one of which is ordered in C. elegans but unresolved in other species. We provide direct evidence that C. elegans tubulin has a higher free energy in solution and propose a model wherein the ordering of lateral contact loops activates tubulin for growth.
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Affiliation(s)
- Sami Chaaban
- Department of Biology, 1205 Avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Chieh-Ting Hsu
- Department of Biology, 1205 Avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada
| | - Stefanie Redemann
- Experimental Center, Technische Universität Dresden, Faculty of Medicine, Fiedlerstraße 42, 01307 Dresden, Germany; Center for Membrane & Cell Physiology, University of Virginia and Department of Molecular Physiology & Biological Physics, 480 Ray C. Hung Drive, Charlottesville, VA 22903, USA
| | - Justin M Kollman
- Department of Biochemistry, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Thomas Müller-Reichert
- Experimental Center, Technische Universität Dresden, Faculty of Medicine, Fiedlerstraße 42, 01307 Dresden, Germany
| | - David Sept
- Department of Biomedical Engineering, 2200 Bonisteel Boulevard, Ann Arbor, MI 48109, USA
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, 3640 Rue University, Montréal, QC H3A 0C7, Canada
| | - Gary J Brouhard
- Department of Biology, 1205 Avenue Docteur Penfield, Montréal, QC H3A 1B1, Canada.
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50
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Manka SW, Moores CA. The role of tubulin-tubulin lattice contacts in the mechanism of microtubule dynamic instability. Nat Struct Mol Biol 2018; 25:607-15. [PMID: 29967541 DOI: 10.1038/s41594-018-0087-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/01/2018] [Indexed: 11/08/2022]
Abstract
Microtubules form from longitudinally and laterally assembling tubulin α-β dimers. The assembly induces strain in tubulin, resulting in cycles of microtubule catastrophe and regrowth. This 'dynamic instability' is governed by GTP hydrolysis that renders the microtubule lattice unstable, but it is unclear how. We used a human microtubule nucleating and stabilizing neuronal protein, doublecortin, and high-resolution cryo-EM to capture tubulin's elusive hydrolysis intermediate GDP•Pi state, alongside the prehydrolysis analog GMPCPP state and the posthydrolysis GDP state with and without an anticancer drug, Taxol. GTP hydrolysis to GDP•Pi followed by Pi release constitutes two distinct structural transitions, causing unevenly distributed compressions of tubulin dimers, thereby tightening longitudinal and loosening lateral interdimer contacts. We conclude that microtubule catastrophe is triggered because the lateral contacts can no longer counteract the strain energy stored in the lattice, while reinforcement of the longitudinal contacts may support generation of force.
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