1
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Fleming PJ, Correia JJ, Fleming KG. Revisiting macromolecular hydration with HullRadSAS. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:215-224. [PMID: 36602579 DOI: 10.1007/s00249-022-01627-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023]
Abstract
Hydration of biological macromolecules is important for their stability and function. Historically, attempts have been made to describe the degree of macromolecular hydration using a single parameter over a narrow range of values. Here, we describe a method to calculate two types of hydration: surface shell water and entrained water. A consideration of these two types of hydration helps to explain the "hydration problem" in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and related macromolecular properties such as sedimentation and diffusion coefficients, intrinsic viscosities, and the concentration-dependent non-ideality identified with sedimentation velocity experiments.
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Affiliation(s)
- Patrick J Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
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2
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Tyukodi B, Mohajerani F, Hall DM, Grason GM, Hagan MF. Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries. ACS NANO 2022; 16:9077-9085. [PMID: 35638478 PMCID: PMC10362403 DOI: 10.1021/acsnano.2c00865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly toward a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of experimentally accessible parameters that control assembly driving forces and the magnitude of frustration. The results determine the parameter range where finite-temperature self-limiting assembly occurs, in which the equilibrium assembly size distribution is sharply peaked around a well-defined finite size. The simulations also identify two mechanisms by which the system can escape frustration and assemble to unlimited size, and determine the particle-scale properties of subunits that suppress unbounded growth.
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Affiliation(s)
- Botond Tyukodi
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Farzaneh Mohajerani
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Douglas M Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, United States
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3
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Benedetto A, Kelley EG. Absorption of the [bmim][Cl] Ionic Liquid in DMPC Lipid Bilayers across Their Gel, Ripple, and Fluid Phases. J Phys Chem B 2022; 126:3309-3318. [PMID: 35472281 PMCID: PMC9082605 DOI: 10.1021/acs.jpcb.2c00710] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Lipid bilayers are
a key component of cell membranes and play a
crucial role in life and in bio-nanotechnology. As a result, controlling
their physicochemical properties holds the promise of effective therapeutic
strategies. Ionic liquids (ILs)—a vast class of complex organic
electrolytes—have shown a high degree of affinity with lipid
bilayers and can be exploited in this context. However, the chemical
physics of IL absorption and partitioning into lipid bilayers is yet
to be fully understood. This work focuses on the absorption of the
model IL [bmim][Cl] into 1,2-dimyristoyl-sn-glycero-3-phosphocholine
(DMPC) lipid bilayers across their gel, ripple, and fluid phases.
Here, by small-angle neutron scattering, we show that (i) the IL cations
are absorbed in the lipid bilayer in all its thermodynamic phases
and (ii) the amount of IL inserted into the lipid phase increased
with increasing temperature, changing from three to four IL cations
per 10 lipids with increasing temperature from 10 °C in the gel
phase to 40 °C in the liquid phase, respectively. An explicative
hypothesis, based on the entropy gain coming from the IL hydration
water, is presented to explain the observed temperature trend. The
ability to control IL absorption with temperature can be used as a
handle to tune the effect of ILs on biomembranes and can be exploited
in bio-nanotechnological applications.
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Affiliation(s)
- Antonio Benedetto
- Department of Science, University of Roma Tre, 00146 Rome, Italy.,School of Physics, and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.,Laboratory for Neutron Scattering, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elizabeth G Kelley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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4
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Lee SC, Kim SH, Hoffmeister RA, Yoon MY, Kim SK. Novel Peptide-Based Inhibitors for Microtubule Polymerization in Phytophthora capsici. Int J Mol Sci 2019; 20:ijms20112641. [PMID: 31146360 PMCID: PMC6600545 DOI: 10.3390/ijms20112641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022] Open
Abstract
The plant disease Phytophthora blight, caused by the oomycete pathogen Phytophthora capsici, is responsible for major economic losses in pepper production. Microtubules have been an attractive target for many antifungal agents as they are involved in key cellular events such as cell proliferation, signaling, and migration in eukaryotic cells. In order to design a novel biocompatible inhibitor, we screened and identified inhibitory peptides against alpha- and beta-tubulin of P. capsici using a phage display method. The identified peptides displayed a higher binding affinity (nanomolar range) and improved specificity toward P. capsici alpha- and beta-tubulin in comparison to Homo sapiens tubulin as evaluated by fluorometric analysis. One peptide demonstrated the high inhibitory effect on microtubule formation with a nanomolar range of IC50 values, which were much lower than a well-known chemical inhibitor—benomyl (IC50 = 500 µM). Based on these results, this peptide can be employed to further develop promising candidates for novel antifungal agents against Phytophthora blight.
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Affiliation(s)
- Sang-Choon Lee
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | - Sang-Heon Kim
- Department of Chemistry and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Rachel A Hoffmeister
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK 74464, USA.
| | - Moon-Young Yoon
- Department of Chemistry and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Sung-Kun Kim
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK 74464, USA.
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5
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Liu C, Yao J, Yin J, Xue J, Zhang H. Recombinant α- and β-tubulin from Echinococcus granulosus: expression, purification and polymerization. ACTA ACUST UNITED AC 2018; 25:62. [PMID: 30516131 PMCID: PMC6280675 DOI: 10.1051/parasite/2018063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/19/2018] [Indexed: 12/29/2022]
Abstract
Echinococcosis, which causes a high disease burden and is of great public health significance, is caused by the larval stage of Echinococcus species. It has been suggested that tubulin is the target of benzimidazoles, the only drugs for the treatment of echinococcosis. This study evaluated the characteristics of tubulins from Echinococcus granulosus. The full-length cDNAs of E. granulosus α- and β-tubulin isoforms were cloned by reverse transcription PCR from protoscolex RNA. Then, these two tubulin isoforms (α9 and β4) were recombinantly expressed as insoluble inclusion bodies in Escherichia coli. Nickel affinity chromatography was used to purify and refold the contents of these inclusion bodies as active proteins. The polymerization of tubulins was monitored by UV spectrophotometry (A350) and confirmed by confocal microscopy and transmission electron microscopy (TEM). Nucleotide sequence analysis revealed that E. granulosus 1356 bp α9-tubulin and 1332 bp β4-tubulin encode corresponding proteins of 451 and 443 amino acids. The average yields of α9- and β4-tubulin were 2.0–3.0 mg/L and 3.5–5.0 mg/L of culture, respectively. Moreover, recombinant α9- and β4-tubulin were capable of polymerizing into microtubule-like structures under appropriate conditions in vitro. These recombinant tubulins could be helpful for screening anti-Echinococcus compounds targeting the tubulins of E. granulosus.
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Affiliation(s)
- Congshan Liu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, MOH, National Center for International Research on Tropical Diseases, WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Jiaqing Yao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, MOH, National Center for International Research on Tropical Diseases, WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Jianhai Yin
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, MOH, National Center for International Research on Tropical Diseases, WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Jian Xue
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, MOH, National Center for International Research on Tropical Diseases, WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Haobing Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, MOH, National Center for International Research on Tropical Diseases, WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, People's Republic of China
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6
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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] [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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7
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Abstract
Microtubules act as "railways" for motor-driven intracellular transport, interact with accessory proteins to assemble into larger structures such as the mitotic spindle, and provide an organizational framework to the rest of the cell. Key to these functions is the fact that microtubules are "dynamic." As with actin, the polymer dynamics are driven by nucleotide hydrolysis and influenced by a host of specialized regulatory proteins, including microtubule-associated proteins. However, microtubule turnover involves a surprising behavior-termed dynamic instability-in which individual polymers switch stochastically between growth and depolymerization. Dynamic instability allows microtubules to explore intracellular space and remodel in response to intracellular and extracellular cues. Here, we review how such instability is central to the assembly of many microtubule-based structures and to the robust functioning of the microtubule cytoskeleton.
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Affiliation(s)
- Holly V Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Erin M Jonasson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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8
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Bachand GD, Jain R, Ko R, Bouxsein NF, VanDelinder V. Inhibition of Microtubule Depolymerization by Osmolytes. Biomacromolecules 2018; 19:2401-2408. [PMID: 29689154 DOI: 10.1021/acs.biomac.7b01799] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microtubule dynamics play a critical role in the normal physiology of eukaryotic cells as well as a number of cancers and neurodegenerative disorders. The polymerization/depolymerization of microtubules is regulated by a variety of stabilizing and destabilizing factors, including microtubule-associated proteins and therapeutic agents (e.g., paclitaxel, nocodazole). Here we describe the ability of the osmolytes polyethylene glycol (PEG) and trimethylamine- N-oxide (TMAO) to inhibit the depolymerization of individual microtubule filaments for extended periods of time (up to 30 days). We further show that PEG stabilizes microtubules against both temperature- and calcium-induced depolymerization. Our results collectively suggest that the observed inhibition may be related to combination of the kosmotropic behavior and excluded volume/osmotic pressure effects associated with PEG and TMAO. Taken together with prior studies, our data suggest that the physiochemical properties of the local environment can regulate microtubule depolymerization and may potentially play an important role in in vivo microtubule dynamics.
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Affiliation(s)
- George D Bachand
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Rishi Jain
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Randy Ko
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Nathan F Bouxsein
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
| | - Virginia VanDelinder
- Center for Integrated Nanotechnologies , Sandia National Laboratories , P.O. Box 5800, MS 1303, Albuquerque , New Mexico 87185 , United States
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9
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Concha-Marambio L, Maldonado P, Lagos R, Monasterio O, Montecinos-Franjola F. Thermal adaptation of mesophilic and thermophilic FtsZ assembly by modulation of the critical concentration. PLoS One 2017; 12:e0185707. [PMID: 28982174 PMCID: PMC5628889 DOI: 10.1371/journal.pone.0185707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/18/2017] [Indexed: 01/16/2023] Open
Abstract
Cytokinesis is the last stage in the cell cycle. In prokaryotes, the protein FtsZ guides cell constriction by assembling into a contractile ring-shaped structure termed the Z-ring. Constriction of the Z-ring is driven by the GTPase activity of FtsZ that overcomes the energetic barrier between two protein conformations having different propensities to assemble into polymers. FtsZ is found in psychrophilic, mesophilic and thermophilic organisms thereby functioning at temperatures ranging from subzero to >100°C. To gain insight into the functional adaptations enabling assembly of FtsZ in distinct environmental conditions, we analyzed the energetics of FtsZ function from mesophilic Escherichia coli in comparison with FtsZ from thermophilic Methanocaldococcus jannaschii. Presumably, the assembly may be similarly modulated by temperature for both FtsZ orthologs. The temperature dependence of the first-order rates of nucleotide hydrolysis and of polymer disassembly, indicated an entropy-driven destabilization of the FtsZ-GTP intermediate. This destabilization was true for both mesophilic and thermophilic FtsZ, reflecting a conserved mechanism of disassembly. From the temperature dependence of the critical concentrations for polymerization, we detected a change of opposite sign in the heat capacity, that was partially explained by the specific changes in the solvent-accessible surface area between the free and polymerized states of FtsZ. At the physiological temperature, the assembly of both FtsZ orthologs was found to be driven by a small positive entropy. In contrast, the assembly occurred with a negative enthalpy for mesophilic FtsZ and with a positive enthalpy for thermophilic FtsZ. Notably, the assembly of both FtsZ orthologs is characterized by a critical concentration of similar value (1–2 μM) at the environmental temperatures of their host organisms. These findings suggest a simple but robust mechanism of adaptation of FtsZ, previously shown for eukaryotic tubulin, by adjustment of the critical concentration for polymerization.
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Affiliation(s)
- Luis Concha-Marambio
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Paula Maldonado
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail: (OM); (FMF)
| | - Felipe Montecinos-Franjola
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail: (OM); (FMF)
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10
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Mohapatra S, Saha A, Mondal P, Jana B, Ghosh S, Biswas A, Ghosh S. Synergistic Anticancer Effect of Peptide-Docetaxel Nanoassembly Targeted to Tubulin: Toward Development of Dual Warhead Containing Nanomedicine. Adv Healthc Mater 2017; 6. [PMID: 27782376 DOI: 10.1002/adhm.201600718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/12/2016] [Indexed: 01/09/2023]
Abstract
Microtubule dynamics play a crucial role in cancer cell division. Various drugs are developed to target microtubule. Although a few of them show potential in treatment of cancer, but success rate is limited due to their poor bioavailability and lack of specificity. Thus, development of highly bioavailable and target specific anticancer drug is extremely necessary. To address these key issues, here, a combination of approaches such as development of a dodecapeptide-docetaxel nanoassembly targeted to tubulin and MUC1 (mucin 1, cell surface associated glycoprotein) targeting oligonucleotide aptamer conjugated liposome for delivering peptide-docetaxel nanoassembly into the breast cancer cell have been demonstrated. These studies reveal that the peptide forms nanoassembly and entraps docetaxel drug. Further, the liposomal formulation of peptide-docetaxel exerts synergistic anticancer effect, activates key mitotic check point proteins, and inhibits bipolar spindle formation, metastatic cancer cell migration, and growth of tumor mimicking 3D multicellular spheroid.
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Affiliation(s)
- Saswat Mohapatra
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Indian Institute of Chemical Biology Campus; 4, Raja S. C. Mullick Road Kolkata 700 032 West Bengal India
| | - Abhijit Saha
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Indian Institute of Chemical Biology Campus; 4, Raja S. C. Mullick Road Kolkata 700 032 West Bengal India
| | - Batakrishna Jana
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Subhajit Ghosh
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Atanu Biswas
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division; Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB); 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700032 West Bengal India
- Academy of Scientific and Innovative Research (AcSIR); CSIR-Indian Institute of Chemical Biology Campus; 4, Raja S. C. Mullick Road Kolkata 700 032 West Bengal India
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11
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Schummel PH, Gao M, Winter R. Modulation of the Polymerization Kinetics of α/β-Tubulin by Osmolytes and Macromolecular Crowding. Chemphyschem 2016; 18:189-197. [DOI: 10.1002/cphc.201601032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
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12
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Vall-Sagarra A, McMicken B, Nonell S, Brancaleon L. Effects of Visible-Light Irradiation of Protoporphyrin IX on the Self-Assembly of Tubulin Heterodimers. Chemphyschem 2016; 17:3269-3282. [PMID: 27490308 PMCID: PMC5177992 DOI: 10.1002/cphc.201600629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Indexed: 11/10/2022]
Abstract
The formation and the effects of laser irradiation of the complex formed by protoporphyrin IX (PPIX) and tubulin was investigated. We have used tubulin as a model protein to investigate whether docked photoactive ligands can affect the structure and function of polypeptides upon exposure to visible light. We observed that laser irradiation in the Soret band prompts bleaching of the PPIX, which is accompanied by a sharp decrease in the intensity and average fluorescence lifetime of the protein (dominated by the four tryptophan residues of the tubulin monomer). The kinetics indicate non-trivial effects and suggest that the photosensitization of the PPIX bound to tubulin prompts structural alterations of the protein. These modifications were also observed through changes in the energy transfer between Trp residues and PPIX. The results suggest that laser irradiation produces localized partial unfolding of tubulin and that the changes prompt modification of the formation of microtubules in vitro. Measurements of singlet oxygen formation were inconclusive in determining whether the changes are prompted by reactive oxygen species or other excited state mechanisms.
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Affiliation(s)
- Alicia Vall-Sagarra
- Institut Quimic de Sarria, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, USA
| | - Brady McMicken
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, USA
| | - Santi Nonell
- Institut Quimic de Sarria, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Lorenzo Brancaleon
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX, USA.
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13
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Krieg E, Bastings MMC, Besenius P, Rybtchinski B. Supramolecular Polymers in Aqueous Media. Chem Rev 2016; 116:2414-77. [DOI: 10.1021/acs.chemrev.5b00369] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Pol Besenius
- Institute
of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Mainz 55128, Germany
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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14
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Ha NR, Lee SC, Hyun JW, Yoon MY. Development of inhibitory ssDNA aptamers for the FtsZ cell division protein from citrus canker phytopathogen. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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15
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Kononova O, Kholodov Y, Theisen KE, Marx KA, Dima RI, Ataullakhanov FI, Grishchuk EL, Barsegov V. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico. J Am Chem Soc 2014; 136:17036-45. [PMID: 25389565 PMCID: PMC4277772 DOI: 10.1021/ja506385p] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Microtubules,
the primary components of the chromosome segregation
machinery, are stabilized by longitudinal and lateral noncovalent
bonds between the tubulin subunits. However, the thermodynamics of
these bonds and the microtubule physicochemical properties are poorly
understood. Here, we explore the biomechanics of microtubule polymers
using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close
match between the simulated and experimental force–deformation
spectra enabled us to correlate the microtubule biomechanics with
dynamic structural transitions at the nanoscale. Our mechanical testing
revealed that the compressed MT behaves as a system of rigid elements
interconnected through a network of lateral and longitudinal elastic
bonds. The initial regime of continuous elastic deformation of the
microtubule is followed by the transition regime, during which the
microtubule lattice undergoes discrete structural changes, which include
first the reversible dissociation of lateral bonds followed by irreversible
dissociation of the longitudinal bonds. We have determined the free
energies of dissociation of the lateral (6.9 ± 0.4 kcal/mol)
and longitudinal (14.9 ± 1.5 kcal/mol) tubulin–tubulin
bonds. These values in conjunction with the large flexural rigidity
of tubulin protofilaments obtained (18,000–26,000 pN·nm2) support the idea that the disassembling microtubule is capable
of generating a large mechanical force to move chromosomes during
cell division. Our computational modeling offers a comprehensive quantitative
platform to link molecular tubulin characteristics with the physiological
behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration
of biomechanical properties of other cytoskeletal and multiprotein
assemblies.
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Affiliation(s)
- Olga Kononova
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
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16
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Park HC, Gedi V, Cho JH, Hyun JW, Lee KJ, Kang J, So B, Yoon MY. Characterization and in vitro inhibition studies of Bacillus anthracis FtsZ: a potential antibacterial target. Appl Biochem Biotechnol 2014; 172:3263-70. [PMID: 24510482 DOI: 10.1007/s12010-014-0752-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/20/2014] [Indexed: 10/25/2022]
Abstract
FtsZ is an essential bacterial cell division protein that is an attractive target for the development of antibacterial agents. FtsZ is a homologue of eukaryotic tubulin, has GTPase activity, and forms a ring-type structure to initiate cell division. In this study, the FtsZ of Bacillus anthracis was cloned into a bacterial expression vector and overexpressed into Escherichia coli BL21 (DE3) cells. The overexpressed B. anthracis FtsZ was soluble and purified to homogeneity using Ni-His-tag affinity chromatography. Like other known FtsZs, the recombinant B. anthracis FtsZ also showed GTP-dependent polymerization, which was analyzed using both spectrophotometric and Transmission Electronic Microscopic (TEM) analysis. Using the purified FtsZ, we screened a naturally extracted chemical library to identify potent and novel inhibitors. The screening yielded three chemicals, SA-011, SA-059, and SA-069, that inhibited the in vitro polymerization activity of FtsZ in the micromolar range (IC50 of 55-168 μM). The inhibition potency was significantly comparable with that of berberine, a known potential inhibitor of FtsZ. Understanding the biochemical basis of the effect of these inhibitors on B. anthracis growth would provide a promising path for the development of new antianthracis drugs.
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Affiliation(s)
- Hae-Chul Park
- Department of Chemistry and Institute of Natural Science, Hanyang University, Seoul, 133-791, Republic of Korea
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17
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Lyons DF, Le V, Kramer WH, Bidwell GL, Lewis EA, Raucher D, Correia JJ. Effect of basic cell-penetrating peptides on the structural, thermodynamic, and hydrodynamic properties of a novel drug delivery vector, ELP[V5G3A2-150]. Biochemistry 2014; 53:1081-91. [PMID: 24450599 PMCID: PMC3985474 DOI: 10.1021/bi400955w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Elastin-like polypeptides (ELPs)
are large, nonpolar polypeptides
under investigation as components of a novel drug delivery system.
ELPs are soluble at low temperatures, but they desolvate and aggregate
above a transition temperature (TT). This
aggregation is being utilized for targeting systemically delivered
ELP–drug conjugates to heated tumors. We previously examined
the structural, thermodynamic, and hydrodynamic properties of ELP[V5G3A2-150] to understand its behavior
as a therapeutic agent. In this study, we investigate the effect that
adding basic cell-penetrating peptides (CPPs) to ELP[V5G3A2-150] has on the polypeptide’s solubility,
structure, and aggregation properties. CPPs are known to enhance the
uptake of ELP into cultured cells in vitro and into
tumor tissue in vivo. Interestingly, the asymmetric
addition of basic residues decreased the solubility of ELP[V5G3A2-150], although below the TT we still observed a low level of self-association that
increased with temperature. The ΔH of the aggregation
process correlates with solubility, suggesting that the basic CPPs
stabilize the aggregated state. This is potentially beneficial as
the decreased solubility will increase the fraction aggregated and
enhance drug delivery efficacy at a heated tumor. Otherwise, the basic
CPPs did not significantly alter the biophysical properties of ELP.
All constructs were monomeric at low temperatures but self-associate
with increasing temperature through an indefinite isodesmic association.
This self-association was coupled to a structural transition to type
II β-turns. All constructs reversibly aggregated in an endothermic
reaction, consistent with a reaction driven by the release of water.
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Affiliation(s)
- Daniel F Lyons
- Department of Biochemistry, University of Mississippi Medical Center , 2500 North State Street, Jackson, Mississippi 39216, United States
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18
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Structural and hydrodynamic analysis of a novel drug delivery vector: ELP[V5G3A2-150]. Biophys J 2013; 104:2009-21. [PMID: 23663844 DOI: 10.1016/j.bpj.2013.03.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/28/2013] [Accepted: 03/12/2013] [Indexed: 11/21/2022] Open
Abstract
The therapeutic potential of elastin-like polypeptide (ELP) conjugated to therapeutic compounds is currently being investigated as an approach to target drugs to solid tumors. ELPs are hydrophobic polymers that are soluble at low temperatures and cooperatively aggregate above a transition temperature (TT), allowing for thermal targeting of covalently attached drugs. They have been shown to cooperatively transition from a disordered structure to a repeating type II β-turn structure, forming a β-spiral above the TT. Here we present biophysical measurements of the structural, thermodynamic, and hydrodynamic properties of a specific ELP being investigated for drug delivery, ELP[V5G3A2-150]. We examine the biophysical properties below and above the TT to understand and predict the therapeutic potential of ELP-drug conjugates. We observed that below the TT, ELP[V5G3A2-150] is soluble, with an extended conformation consisting of both random coil and heterogeneous β structures. Sedimentation velocity experiments indicate that ELP[V5G3A2-150] undergoes weak self-association with increasing temperature, and above the TT the hydrophobic effect drives aggregation entropically. These experiments also reveal a previously unreported temperature-dependent critical concentration (Cc) that resembles a solubility constant. Labeling ELP[V5G3A2-150] with fluorescein lowers the TT by 3.5°C at 20 μM, whereas ELP[V5G3A2-150] dissolution in physiological media (fetal bovine serum) increases the TT by ∼2.2°C.
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19
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Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association. Biophys J 2013; 103:1363-9. [PMID: 22995509 DOI: 10.1016/j.bpj.2012.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 01/17/2023] Open
Abstract
Recent work has shown that the hydrophobic protein surfaces in aqueous solution sit near a drying transition. The tendency for these surfaces to expel water from their vicinity leads to self-assembly of macromolecular complexes. In this article, we show with a realistic model for a biologically pertinent system how this phenomenon appears at the molecular level. We focus on the association of the C-terminal domain (CA-C) of the human immunodeficiency virus capsid protein. By combining all-atom simulations with specialized sampling techniques, we measure the water density distribution during the approach of two CA-C proteins as a function of separation and amino acid sequence in the interfacial region. The simulations demonstrate that CA-C protein-protein interactions sit at the edge of a dewetting transition and that this mesoscopic manifestation of the underlying liquid-vapor phase transition can be readily manipulated by biology or protein engineering to significantly affect association behavior. Although the wild-type protein remains wet until contact, we identify a set of in silico mutations, in which three hydrophilic amino acids are replaced with nonpolar residues, that leads to dewetting before association. The existence of dewetting depends on the size and relative locations of substituted residues separated by nanometer length scales, indicating long-range cooperativity and a sensitivity to surface topography. These observations identify important details that are missing from descriptions of protein association based on buried hydrophobic surface area.
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20
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Nakajima KI, Niisato N, Marunaka Y. Enhancement of tubulin polymerization by Cl(-)-induced blockade of intrinsic GTPase. Biochem Biophys Res Commun 2012; 425:225-9. [PMID: 22828510 DOI: 10.1016/j.bbrc.2012.07.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 07/14/2012] [Indexed: 01/03/2023]
Abstract
In growing neurite of neuronal cells, it is suggested that α/β-tubulin heterodimers assemble to form microtubule, and assembly of microtubule promotes neurite elongation. On the other hand, recent studies reveal importance of intracellular Cl(-) in regulation of various cellular functions such as cell cycle progression, differentiation, cell migration, and elongation of neurite in neuronal cells. In this study, we investigated effects of Cl(-) on in vitro tubulin polymerization. We found that efficiency of in vitro tubulin polymerization (the number of microtubule) was higher (3 to 5-fold) in Cl(-)-containing solutions than that in Cl(-)-free solutions containing Br(-) or NO(3)(-). On the other hand, GTPase activity of tubulin was lower (2/3-fold) in Cl(-)-containing solutions than that in Cl(-)-free solutions containing Br(-) or NO(3)(-). Efficiency of in vitro tubulin polymerization in solutions containing a non-hydrolyzable analogue of GTP (GpCpp) instead of GTP was much higher than that in the presence of GTP. Effects of replacement of GTP with GpCpp on in vitro tubulin polymerization was weaker in Cl(-) solutions (10-fold increases) than that in Br(-) or NO(3)(-) solutions (20-fold increases), although the efficiency of in vitro tubulin polymerization in Cl(-) solutions containing GpCpp was still higher than that in Br(-) or NO(3)(-) solutions containing GpCpp. Our results suggest that a part of stimulatory effects of Cl(-) on in vitro tubulin polymerization is mediated via an inhibitory effect on GTPase activity of tubulin, although Cl(-) would also regulate in vitro tubulin polymerization by factors other than an inhibitory effect on GTPase activity.
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Affiliation(s)
- Ken-ichi Nakajima
- Department of Molecular Cell Physiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
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21
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Bachand M, Bachand GD. Effects of potential environmental interferents on kinesin-powered molecular shuttles. NANOSCALE 2012; 4:3706-3710. [PMID: 22585042 DOI: 10.1039/c2nr30570d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biomolecular motor-powered active transport represents an alternate means for analyte processing in nanoscale biosensors and bioanalytical devices. For example, a prototype "smart dust" biosensor has recently been reported in which the motor protein kinesin processes antibody-functionalized microtubules (MTs) to capture and separate optically tagged protein analytes. A potential limitation of this technology, however, involves the inhibition of transport function by interfering compounds that may be present in raw samples. Here we characterized the response of kinesin-MT transport to a range of potential interferents including solvents, acids, oxidizers, and environmental contaminants. The results of kinesin motility assays suggest that, among the tested interferents, only acetic acid and sodium hypochlorite adversely affected MT transport, primarily due to depolymerization of MT filaments. While negative effects were not observed for the remaining compounds tested, enhancement in motility was observed in the presence of acetone, antifreeze, and organic matter. Overall, the data suggest that kinesin-MT transport is resilient against a variety of common interferents, but primarily susceptible to failure due to significant changes in pH or the presence of an oxidizer.
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Affiliation(s)
- Marlene Bachand
- Nanobiology Department, Sandia National Laboratories, PO Box 5800, Albuquerque, NM 87185, USA
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22
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Siva1 suppresses epithelial-mesenchymal transition and metastasis of tumor cells by inhibiting stathmin and stabilizing microtubules. Proc Natl Acad Sci U S A 2011; 108:12851-6. [PMID: 21768358 DOI: 10.1073/pnas.1017372108] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) enables epithelial cells to acquire motility and invasiveness that are characteristic of mesenchymal cells. It plays an important role in development and tumor cell metastasis. However, the mechanisms of EMT and their dysfunction in cancer cells are still not well understood. Here we report that Siva1 interacts with stathmin, a microtubule destabilizer. Siva1 inhibits stathmin's activity directly as well as indirectly through Ca(2+)/calmodulin-dependent protein kinase II-mediated phosphorylation of stathmin at Ser16. Via the inhibition of stathmin, Siva1 enhances the formation of microtubules and impedes focal adhesion assembly, cell migration, and EMT. Low levels of Siva1 and Ser16-phosphorylated stathmin correlate with high metastatic states of human breast cancer cells. In mouse models, knockdown of Siva1 promotes cancer dissemination, whereas overexpression of Siva1 inhibits it. These results suggest that microtubule dynamics are critical for EMT. Furthermore, they reveal an important role for Siva1 in suppressing cell migration and EMT and indicate that down-regulation of Siva1 may contribute to tumor cell metastasis.
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23
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Qi J, Blanden AR, Bane S, Kingston DGI. Design, synthesis and biological evaluation of a simplified fluorescently labeled discodermolide as a molecular probe to study the binding of discodermolide to tubulin. Bioorg Med Chem 2011; 19:5247-54. [PMID: 21802957 DOI: 10.1016/j.bmc.2011.06.082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 06/24/2011] [Accepted: 06/28/2011] [Indexed: 10/18/2022]
Abstract
The design, synthesis, and biological evaluation of a simplified fluorescently labeled discodermolide analogue possessing a dimethylaminobenzoyl fluorophore has been achieved. Stereoselective Suzuki coupling and Horner-Wadsworth-Emmons reaction comprised the key tactics for its construction. The analogue exhibited qualitatively similar activity to paclitaxel in a tubulin assembly assay, and it can thus be used as a fluorescent molecular probe to explore the local environment of the discodermolide binding site on tubulin. The results of fluorescence measurements on the tubulin-bound analogue are reported.
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Affiliation(s)
- Jun Qi
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA
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24
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Wang G, Gao X, Huang Y, Yao Z, Shi Q, Wu M. Nucleophosmin/B23 inhibits Eg5-mediated microtubule depolymerization by inactivating its ATPase activity. J Biol Chem 2010; 285:19060-7. [PMID: 20404347 DOI: 10.1074/jbc.m110.100396] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleophosmin/B23, an abundant nucleolar protein, plays multiple roles in cell growth and proliferation, and yet, little has been studied about its function in regulating dynamics of microtubules. Here, we report that B23 directly interacts with Eg5, a member of the kinesin family, in the cytosol. The DNA/RNA binding domain of B23 and the motor domain of Eg5 were found to be involved in their interaction. Both in vivo and in vitro evidences showed that B23 acts as an upstream regulator of Eg5 in promoting microtubule polymerization. Moreover, we further demonstrated that B23 regulates microtubule dynamics by directly inhibiting Eg5 ATPase activity.
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Affiliation(s)
- Guoxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
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25
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Valdez R, Johnson EM, Belcher JA, Fuini JF, Brancaleon L. Porphyrins affect the self-assembly of tubulin in solution. Biophys Chem 2009; 145:98-104. [PMID: 19819610 DOI: 10.1016/j.bpc.2009.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 09/16/2009] [Accepted: 09/16/2009] [Indexed: 10/20/2022]
Abstract
Self-assembly of tubulin heterodimers in solution has been studied in the past to predict the effects that ligands and/or conformational changes have on the formation of tubulin filaments. Self-assembly of tubulin in solution has produced formations similar to cellular microtubules (MTs). The present study reports on the effects that two porphyrins (protoporphyrin IX, PPIX and tetrakis(4-sulfonatophenyl)porphyrin, TPPS) produce on the self-assembly of tubulin alpha,beta-heterodimers in buffer solution. The study shows that, when incubated simultaneously with MT-stabilizing ligands (i.e., paclitaxel and guanosine triphosphate, GTP), porphyrins do not affect the ability of tubulin to form MT. However, if paclitaxel and GTP are added after tubulin has been allowed to self-assemble in the presence of either porphyrin, the ability to form MT-like structures is reduced or suppressed. We suggest that this effect is due to the formation of porphyrin-mediated aggregates that cannot be broken or elongated by the addition of GTP or paclitaxel.
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Affiliation(s)
- Rolando Valdez
- Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
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26
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Koo BS, Kalme S, Yeo SH, Lee SJ, Yoon MY. Molecular cloning and biochemical characterization of alpha- and beta-tubulin from potato plants (Solanum tuberosum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:761-768. [PMID: 19394244 DOI: 10.1016/j.plaphy.2009.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 05/27/2023]
Abstract
Few studies have investigated microtubules from plants that host pathogenic fungi. Considerable efforts are underway to find an antimitotic agent against plant pathogens like Phytophthora infestans. However, screening the effects of antifungal agents on plant tubulin in vivo or using purified native microtubule in vitro is a time consuming process. A recombinant, correctly folded, microtubule-like structure forming tubulin could accelerate research in this area. In this study, we cloned full length cDNAs isolated from potato leaves using reverse-transcribed polymerase chain reaction (RT-PCR). Solanum tuberosum (Stub) alpha-tubulin and beta-tubulin were predicted to encode 449 and 451 amino acid long proteins with molecular masses of 57 kDa and 60 kDa, respectively. Average yields of alpha- and beta-tubulin were 2.0-3.5 mg l(-1) and 1.3-3.0 mg l(-1) of culture, respectively. The amino acids, His6, Glu198, and Phe170 involved in benomyl sensitivity were conserved in Stub tubulin. The dimerization of tubulin monomers was confirmed by western blot analysis. When combined under appropriate conditions, these recombinant alpha- and beta-tubulins were capable of polymerizing into microtubules. Accessibility of cysteine residues of tubulin revealed that important ligand binding sites were folded correctly. This recombinant tubulin could serve as a control of phytotoxicity of selected antimitotic fungicide compounds during in vitro screening experiments.
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Affiliation(s)
- Bon-Sung Koo
- Fermentation and Food Processing Division, Department of Korean Food Research for Globalization, National Academy of Agricultural Science, Suwon 441 857, South Korea
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27
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Koo BS, Park H, Kalme S, Park HY, Han JW, Yeo YS, Yoon SH, Kim SJ, Lee CM, Yoon MY. α- and β-tubulin from Phytophthora capsici KACC 40483: molecular cloning, biochemical characterization, and antimicrotubule screening. Appl Microbiol Biotechnol 2009; 82:513-24. [DOI: 10.1007/s00253-008-1821-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 11/24/2008] [Accepted: 12/08/2008] [Indexed: 10/21/2022]
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Shanker N, Kingston DGI, Ganesh T, Yang C, Alcaraz AA, Geballe MT, Banerjee A, McGee D, Snyder JP, Bane S. Enhanced microtubule binding and tubulin assembly properties of conformationally constrained paclitaxel derivatives. Biochemistry 2007; 46:11514-27. [PMID: 17892304 DOI: 10.1021/bi700753y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Microtubule binding and tubulin assembly promotion by a series of conformationally restricted paclitaxel (PTX) derivatives was investigated. In these derivatives, the C-4 acetate of the taxane is tethered to the C-3' phenyl at ortho and meta positions with different length linkers. The apparent affinity of these derivatives for GMPCPP-stabilized microtubules was assessed by a competition assay, and their influence on microtubule polymerization was evaluated by measuring the critical concentration of GDP-tubulin in the presence of the respective molecule. In general, taxane derivatives with higher apparent affinity for microtubules induced tubulin assembly more efficiently. Among the derivatives, molecules with the shortest tether display the strongest affinity for microtubules. These derivatives exhibited enhanced microtubule stabilization properties and efficiently induced GDP-tubulin assembly into microtubules at low temperature of 12 degrees C and in the absence of Mg2+ ions in 0.1 M PIPES. Based on molecular dynamics simulations, we propose that the enhanced ability to assemble microtubules by these taxane derivatives is linked to their ability to effectively shape the conformation of the M-loop of tubulin for cross-protofilament interaction.
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Affiliation(s)
- Natasha Shanker
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
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29
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Munson KM, Mulugeta PG, Donhauser ZJ. Enhanced mechanical stability of microtubules polymerized with a slowly hydrolyzable nucleotide analogue. J Phys Chem B 2007; 111:5053-7. [PMID: 17441764 DOI: 10.1021/jp0716637] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic force microscopy (AFM) has been used to investigate the local mechanical and structural properties of microtubules polymerized using guanylyl-alpha-beta-methylene diphosphonate (GMPCPP), a slowly hydrolyzable analogue of guanosine triphosphate. Using a combination of AFM imaging and local force spectroscopy, GMPCPP-polymerized microtubules have been qualitatively and quantitatively compared to paclitaxel-stabilized microtubules. GMPCPP-polymerized microtubules qualitatively display a greater resistance to destruction by the AFM probe tip during imaging and during deformation measurements and maintain structural details after indentation. In addition, using force spectroscopy taken during the indentation and collapse of individual microtubules with the AFM probe tip, an effective spring constant of the microtubule wall (kMT) for both types of microtubules was determined. The average kMT of GMPCPP-polymerized microtubules, 0.172 N/m, is more than twice that of paclitaxel-stabilized microtubules. These results complement previously reported measurements of bending experiments on GMPCPP-polymerized and paclitaxel-stabilized microtubules.
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30
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31
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Lobert S, Ingram JW, Correia JJ. The thermodynamics of vinca alkaloid-induced tubulin spirals formation. Biophys Chem 2006; 126:50-8. [PMID: 16757093 DOI: 10.1016/j.bpc.2006.05.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 05/22/2006] [Accepted: 05/22/2006] [Indexed: 11/20/2022]
Abstract
Vinca alkaloids are antimitotic, anticancer agents that induce tubulin to form spiral polymers at physiological protein concentrations. We used sedimentation velocity to investigate the effects of six vinca alkaloids on tubulin spiraling. Fitting to a Wyman linkage model reveals a drug dependent change of over two orders of magnitude in spiraling potential, K(1)K(2). Thermodynamic analysis of LnK(1)K(2) data demonstrates large and positive DeltaS values, indicating that tubulin spiral formation is entropically-driven. From the curvature in van't Hoff plots of vinblastine data, we estimate DeltaC(p) for GTP and GDP conditions to be -439 and -396 cal/mol K. Partitioning of DeltaS into the hydrophobic effect, DeltaS(HE), change in rotational/translational freedom, DeltaS(RT) and change in protein conformation, DeltaS(other), demonstrates that the major driving force for tubulin spiral formation is burial of hydrophobic surfaces and that protein conformational changes do not make a significant contribution. Spiraling potential is an indicator of antimitotic activity in vivo, although turbidity studies indicate that there is no correlation between spiraling potential and microtubule inhibition in vitro. Mechanisms that explain this discrepancy are discussed.
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Affiliation(s)
- Sharon Lobert
- School of Nursing, University of Mississippi Medical Center, Jackson, MS 39216, USA
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32
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Boal AK, Tellez H, Rivera SB, Miller NE, Bachand GD, Bunker BC. The stability and functionality of chemically crosslinked microtubules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2006; 2:793-803. [PMID: 17193124 DOI: 10.1002/smll.200500381] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A variety of bifunctional crosslinking agents have been explored for stabilizing microtubule shuttles used for the active transport of nanomaterials in artificial environments. Crosslinking agents that target amine residues form intertubulin crosslinks that produce crosslinked microtubules (CLMTs) with structural and functional lifetimes that can be up to four times as long as those achieved with taxol stabilization. Such CLMTs are stable at temperatures down to -10 degrees C, are resistant to depolymerization induced by metal ions such as Ca2+, and yet continue to be adsorbed and transported by self-assembled monolayers containing the motor protein kinesin. However, crosslinkers that target cysteine residues depolymerize the MTs, probably by interfering with the guanosine triphosphate binding site. The impact of crosslink attributes, including terminal group chemistry, chain length, crosslink density, and specific location on the tubulin surface, on microtubule stability and functionality are discussed.
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Affiliation(s)
- Andrew K Boal
- Sandia National Laboratory, MS 1413, PO Box 5800, Albuquerque, NM 87185, USA
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33
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Banerjee M, Poddar A, Mitra G, Surolia A, Owa T, Bhattacharyya B. Sulfonamide drugs binding to the colchicine site of tubulin: thermodynamic analysis of the drug-tubulin interactions by isothermal titration calorimetry. J Med Chem 2005; 48:547-55. [PMID: 15658868 DOI: 10.1021/jm0494974] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discovery of several sulfonamide drugs paved the way toward the synthesis of 6 (N-[2-[(4-hydroxyphenyl)amino]-3-pyridinyl]-4-methoxybenzenesulfonamide, E7010) and 7 (N-(3-fluoro-4-methoxyphenyl)pentafluorobenzenesulfonamide, T138067), both of which inhibit tubulin polymerization and are under clinical development. A series of diarylsulfonamides containing an indole scaffold was also found to have antimitotic properties, but their mode of interactions with tubulin has remained unidentified so far. In this study, we demonstrate that these sulfonamide drugs bind to the colchicine site of tubulin in a reversible manner. They quenched intrinsic tryptophan fluorescence of tubulin presumably due to drug-induced conformational changes in the protein, but were unable to modulate GTPase activity of tubulin in contrast to colchicine that enhances the same enzymatic activity. Further investigation using isothermal titration calorimetry (ITC) revealed that 5 (N-(5-chloro-7-indolyl)-4-methoxybenzenesulfonamide) afforded a large positive value of heat capacity change (DeltaC(p)() = +264 cal mol(-1) K(-1)) on binding to tubulin, suggesting a substantial conformational transition in the protein along with partial enthalpy-entropy compensation. On the other hand, the 2-chloro regioisomer 2 gave a large negative value of DeltaC(p)() (-589 cal mol(-1) K(-1)) along with complete enthalpy-entropy compensation. This thermodynamic profile was thought to be attributable to a prominent contribution of van der Waals interaction and hydrogen bonding between specific groups in the drug-tubulin complex. These results indicate that a mere alteration in the position of a single substituent chlorine on the indole scaffold has a great influence on the drug-tubulin binding thermodynamics.
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Affiliation(s)
- Mithu Banerjee
- Department of Biochemistry, Centenary Campus, P1/12, CIT Scheme 7 M, Bose Institute, Calcutta 700 054, India
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34
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Devred F, Barbier P, Douillard S, Monasterio O, Andreu JM, Peyrot V. Tau induces ring and microtubule formation from alphabeta-tubulin dimers under nonassembly conditions. Biochemistry 2004; 43:10520-31. [PMID: 15301550 DOI: 10.1021/bi0493160] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tau is a neuronal microtubule-associated protein that plays a central role in many cellular processes, both physiological and pathological, such as axons stabilization and Alzheimer's disease. Despite extensive studies, very little is known about the detailed molecular basis of tau binding to microtubules. We used the four-repeat recombinant htau40 and tubulin dimers to show for the first time that tau is able to induce both microtubule and ring formation from 6S alphabeta tubulin in phosphate buffer without added magnesium (nonassembly conditions). The amount of microtubules or rings formed was protein concentration-, temperature-, and nucleotide-dependent. By means of biophysical approaches, we showed that tau binds to tubulin without global-folding change, detectable by circular dichroism. We also demonstrated that the tau-tubulin interaction follows a ligand-mediated elongation process, with two tau-binding site per tubulin dimer. Moreover, using a tubulin recombinant alpha-tubulin C-terminal fragment (404-451) and a beta-tubulin C-terminal fragment (394-445), we demonstrated the involvement of both of these tubulin regions in tau binding. From this model system, we gain new insight into the mechanisms by which tau binds to tubulin and induces microtubule formation.
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Affiliation(s)
- François Devred
- FRE 2737, ISPDCT, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
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35
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Synthesis and biological evaluation of fluorescently labeled epothilone analogs for tubulin binding studies. Tetrahedron 2003. [DOI: 10.1016/j.tet.2003.10.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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36
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Huecas S, Andreu JM. Energetics of the cooperative assembly of cell division protein FtsZ and the nucleotide hydrolysis switch. J Biol Chem 2003; 278:46146-54. [PMID: 12933789 DOI: 10.1074/jbc.m307128200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FtsZ is the first protein recruited to the bacterial division site, where it forms the cytokinetic Z ring. We have determined the functional energetics of FtsZ assembly, employing FtsZ from the thermophilic Archaea Methanococcus jannaschii bound to GTP, GMPCPP, GDP, or GMPCP, under different solution conditions. FtsZ oligomerizes in a magnesium-insensitive manner. FtsZ cooperatively assembles with magnesium and GTP or GMPCPP into large polymers, following a nucleated condensation polymerization mechanism, under nucleotide hydrolyzing and non-hydrolyzing conditions. The effect of temperature on the critical concentration indicates polymer elongation with an apparent heat capacity change of -800 +/- 100 cal mol-1 K-1 and positive enthalpy and entropy changes, compatible with axial hydrophobic contacts of each FtsZ in the polymer, and predicts optimal polymer stability near 75 degrees C. Assembly entails the binding of one medium affinity magnesium ion and the uptake of one proton per FtsZ. Interestingly, GDP- or GMPCP-liganded FtsZ cooperatively form helically curved polymers, with an elongation only 1-2 kcal mol-1 more unfavorable than the straight polymers formed with nucleotide triphosphate, suggesting a physiological requirement for FtsZ polymerization inhibitors. This GTP hydrolysis switch should provide the basic properties for FtsZ polymer disassembly and its functional dynamics.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
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37
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Ceres P, Zlotnick A. Weak protein-protein interactions are sufficient to drive assembly of hepatitis B virus capsids. Biochemistry 2002; 41:11525-31. [PMID: 12269796 DOI: 10.1021/bi0261645] [Citation(s) in RCA: 291] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is an enveloped DNA virus with a spherical capsid (or core). The capsid is constructed from 120 copies of the homodimeric capsid protein arranged with T = 4 icosahedral symmetry. We examined in vitro assembly of purified E. coli expressed HBV capsid protein. After equilibration, concentrations of capsid and dimer were evaluated by size exclusion chromatography. The extent of assembly increased as temperature and ionic strength increased. The concentration dependence of capsid assembly conformed to the equilibrium expression: K(capsid) = [capsid]/[dimer](120). Given the known geometry for HBV capsids and dimers, the per capsid assembly energy was partitioned into energy per subunit-subunit contact. We were able to make three major conclusions. (i) Weak interactions (from -2.9 kcal/mol at 21 degrees C in low salt to -4.4 kcal/mol at 37 degrees C in high salt) at each intersubunit contact result in a globally stable capsid; weak intersubunit interactions may be the basis for the phenomenon of capsid breathing. (ii) HBV assembly is characterized by positive enthalpy and entropy. The reaction is entropy-driven, consistent with the largely hydrophobic contacts found in the crystal structure. (iii) Increasing NaCl concentration increases the magnitude of free energy, enthalpy, and entropy, as if ionic strength were increasing the amount of hydrophobic surface buried by assembly. This last point leads us to suggest that salt acts by inducing a conformational change in the dimer from an assembly-inactive form to an assembly-active form. This model of conformational change linked to assembly is consistent with immunological differences between dimer and capsid.
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Affiliation(s)
- Pablo Ceres
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA
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38
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Pal D, Mahapatra P, Manna T, Chakrabarti P, Bhattacharyya B, Banerjee A, Basu G, Roy S. Conformational properties of alpha-tubulin tail peptide: implications for tail-body interaction. Biochemistry 2001; 40:15512-9. [PMID: 11747426 DOI: 10.1021/bi015677t] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The carboxy-terminal segments of the alpha/beta-tubulins are flexible regions rich in acidic amino acid residues. It is generally believed that these regions play crucial roles in tubulin polymerization and interaction with many ligands, including colchicine. Exactly how these effects are exerted are not known at present. One such interesting aspect is the pH dependence of colchicine-tubulin interaction and the influence of the alpha-tail on the binding interaction. We have investigated the location of the colchicine-binding site on tubulin by docking. It has been located on the alpha/beta interface on the N-terminal side, which is also supported by much of the solution data. This location is too far from the tail regions, suggesting that influence of the tail region is transmitted by a pH-dependent conformational change. Two-dimensional NMR studies indicate that at pH 7 a 13-residue peptide corresponding to alpha-tubulin tail shows little NOE constraints, suggesting extended conformation. On the contrary, at pH 5, a relatively compact structure was deduced from the interproton NOE constraints. Pulsed field gradient measurement of diffusion constant indicates that the peptide at pH 5 is substantially faster diffusing than at pH 7. The Perrin factors calculated from diffusion data indicates that the peptide structure at pH is significantly more compact than at pH 7. Temperature coefficients of several amide protons at pH 5 fall below 5 ppb/(o)K, indicating a degree of protection. A difference is also seen in the CD spectra obtained at different pHs, consistent with the NMR data. We have investigated the probable spatial organization of the tail of the alpha-subunit of tubulin, in the high pH extended form and the low pH compact form. On the basis of correlation of pH dependence of many properties of tubulin and the conformation of the alpha-tail peptide, we propose that the intrinsic conformational preference of the tail-region modulate the tail-body interaction, which in turn has important bearing on colchicine binding properties.
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Affiliation(s)
- D Pal
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India
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39
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Chatterjee SK, Barron DM, Vos S, Bane S. Baccatin III induces assembly of purified tubulin into long microtubules. Biochemistry 2001; 40:6964-70. [PMID: 11389612 DOI: 10.1021/bi002816i] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Baccatin III is widely considered to be an inactive derivative of Taxol. We have reexamined its effect on in vitro assembly of tubulin under a variety of conditions. We found baccatin III to be active in all circumstances in which Taxol is active: it assembled GTP-tubulin, GDP-tubulin, and microtubule protein into normal microtubules and stabilized these polymers against cold-induced disassembly. The effect of baccatin III on in vitro microtubule assembly was quantitatively assessed through determination of critical concentrations, which can be used to obtain the apparent equilibrium constants for the addition of tubulin subunits to growing microtubules. The apparent equilibrium constants for the growth reaction for baccatin III-induced GTP-tubulin and GDP-tubulin assembly measured at 37 degrees C were 4.2-4.6-fold less than those measured for Taxol-induced GTP-tubulin and GDP-tubulin assembly. These data indicate that the entire Taxol side chain contributes only about -1 kcal/mol to the apparent standard free energy of microtubule growth at 37 degrees C regardless of the nature of the E site nucleotide. These data also support the idea that the majority of the interactions between Taxol and tubulin that affect this equilibrium occur between the baccatin portion of the molecule and the binding site. We have also observed a structural difference in microtubules formed using baccatin III and Taxol. Baccatin III-induced microtubules were routinely much longer than those assembled by Taxol, even when very high concentrations of baccatin III were employed. One interpretation of these data is that baccatin III and Taxol differ in their abilities to nucleate GTP-tubulin. This difference in activity may have bearing on the large disparity in cytotoxicity of the two molecules.
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Affiliation(s)
- S K Chatterjee
- Department of Chemistry, State University of New York, Binghamton, New York 13902-6016, USA
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40
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Abstract
The mechanism of T cell receptor signaling is unclear. Included among models for TCR signaling is ligand-induced oligomerization in a fashion analogous to other cell surface receptors. Published kinetic, saturation binding, and light scattering experiments have been interpreted to suggest a propensity for soluble alpha beta TCR/peptide/MHC ectodomain complexes to oligomerize. Upon performing these experiments with soluble ectodomains of human class I and class II restricted alpha beta TCRs, we find no evidence for dimerization or oligomerization of complexes. Apparently, oligomerization in solution to a detectable extent is not a general property of soluble alpha beta TCRs or their complexes with ligand. Our results suggest that membrane-anchored, fully assembled TCRs should be studied to determine the role oligomerization plays in T cell signaling.
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Affiliation(s)
- B M Baker
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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41
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Shah C, Xu CZ, Vickers J, Williams R. Properties of microtubules assembled from mammalian tubulin synthesized in Escherichia coli. Biochemistry 2001; 40:4844-52. [PMID: 11294652 DOI: 10.1021/bi002446y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
When isolated from tissues, the alpha beta-dimeric protein tubulin consists of multiple isoforms which originate from the expression and subsequent posttranslational modification of multiple polypeptide sequences. Microtubules studied in vitro consist of mixtures of these isoforms. It is therefore not known whether dimers composed of single sequences of alpha- and beta-tubulin can polymerize to form microtubules, or whether posttranslational modifications may be necessary for microtubule assembly. To initiate investigation of these questions, rabbit reticulocyte lysate, which contains the cytoplasmic chaperonin CCT and its cofactors, was employed to prepare substantial quantities (tens of micrograms) of active tubulin by in vitro folding of mouse alpha- and beta-tubulins recombinantly synthesized in E. coli. This recombinant tubulin is composed of only a single alpha-chain and a single beta-chain. When analyzed after folding by isoelectric focusing, each chain yielded only one band, indicating that neither was detectably posttranslationally modified in the course of the folding reaction. When subjected to assembly-promoting conditions, this tubulin formed microtubules without the addition of any exogenous protein. Electron microscopy showed them to be of normal morphology. Analysis of their protein composition showed that they are composed nearly entirely of recombinant tubulin. These results demonstrate that the naturally occurring mixtures of isoforms are not strictly required for the formation of microtubules. They also open a route to other studies, both biomedical and structural, of fully defined tubulin in vitro.
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Affiliation(s)
- C Shah
- Department of Biological Sciences, VU Station B 351634, Vanderbilt University, Nashville, Tennessee 37235-1634, USA
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42
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Mentré P, Hui Bon Hoa G. Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 201:1-84. [PMID: 11057830 DOI: 10.1016/s0074-7696(01)01001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.
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Affiliation(s)
- P Mentré
- Station INRA 806, Institut de Biologie Physico-Chimique, Paris, France
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43
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Affiliation(s)
- S Lobert
- School of Nursing, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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44
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Oxberry ME, Geary TG, Winterrowd CA, Prichard RK. Individual expression of recombinant alpha- and beta-tubulin from Haemonchus contortus: polymerization and drug effects. Protein Expr Purif 2001; 21:30-9. [PMID: 11162384 DOI: 10.1006/prep.2000.1347] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three tubulin isotypes from the parasitic nematode Haemonchus contortus were individually expressed in Escherichia coli, purified, and induced to polymerize into microtubules in the absence of microtubule-associated proteins. The effect of different conditions on the rate of polymerization of pure tubulin was assessed. This is the first time that recombinant alpha-tubulin has been shown to be capable of polymerization into microtubule-like structures when incubated with recombinant beta-tubulin. In addition, the present study has shown that: (1) microtubule-associated proteins are not required for tubulin polymerization; and (2) pure beta-tubulin isotype, beta12-16, alone was capable of forming microtubule-like structures in the absence of alpha-tubulin. Polymerization of the recombinant invertebrate tubulin, as measured by a spectrophotometric assay, was found to be enhanced by a concentration of tubulin >0.25 mg/mL; temperature > or =20 degrees C; 2 mM GTP; glycerol; EGTA; and Mg(2+). Polymerization was inhibited by GTP (>2 mM) and albendazole. Calcium ions and a pH range of 6 to 8.5 had no measurable effect on polymerization. Individual isotypes of tubulin polymerized to approximately the same extent as an alpha-/beta-tubulin mixture. Samples of tubulin assembled under the above conditions for 60 min were also examined under a transmission electron microscope. Although the spectrophotometric assay indicated polymerization, it did not predict the structure of the polymer. In many cases tubulin sheets, folded sheets, and rings were observed in addition to, or instead of, microtubule-like structures.
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Affiliation(s)
- M E Oxberry
- Molecular Immunology Laboratory, School of Biomedical Sciences, Perth, Western Australia, 6000, Australia
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45
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Díaz JF, Strobe R, Engelborghs Y, Souto AA, Andreu JM. Molecular recognition of taxol by microtubules. Kinetics and thermodynamics of binding of fluorescent taxol derivatives to an exposed site. J Biol Chem 2000; 275:26265-76. [PMID: 10818101 DOI: 10.1074/jbc.m003120200] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have determined the kinetic scheme and the reaction rates of binding to microtubules of two fluorescent taxoids, 7-O-[N-(4'-fluoresceincarbonyl)-l-alanyl]Taxol (Flutax-1) and 7-O-[N-(2,7-difluoro-4'-fluoresceincarbonyl)-l-alanyl]Taxol (Flutax-2). Flutax-1 and Flutax-2 bind to microtubules with high affinity (K(a) approximately 10(7) m(-1), 37 degrees C). The binding mechanism consists of a fast bimolecular reaction followed by at least two monomolecular rearrangements, which were characterized with stopped-flow techniques. The kinetic constants of the bimolecular reaction were 6.10 +/- 0.22 x 10(5) m(-1) s(-1) and 13.8 +/- 1.8 x 10(5) m(-1) s(-1) at 37 degrees C, respectively. A second slow binding step has been measured employing the change of fluorescence anisotropy of the probe. The reversal of this reaction is the rate-limiting step of dissociation. A third step has been detected using small angle x-ray scattering and involves a 2-nm increase in the diameter of microtubules. It is suggested that the first step entails the binding of the Taxol moiety and the second a relative immobilization of the fluorescent probe. The equilibrium and some kinetic measurements required the use of stabilized cross-linked microtubules, which preserved taxoid binding. The results indicate that the Taxol binding site is directly accessible, in contrast with its location at lumen in the current model of microtubules. An alternative structural model is considered in which the binding site is located between protofilaments, accessible from the microtubule surface.
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Affiliation(s)
- J F Díaz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, C/Velázquez, 144, 28006 Madrid, Spain.
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46
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Inoue YH, do Carmo Avides M, Shiraki M, Deak P, Yamaguchi M, Nishimoto Y, Matsukage A, Glover DM. Orbit, a novel microtubule-associated protein essential for mitosis in Drosophila melanogaster. J Cell Biol 2000; 149:153-66. [PMID: 10747094 PMCID: PMC2175100 DOI: 10.1083/jcb.149.1.153] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe a Drosophila gene, orbit, that encodes a conserved 165-kD microtubule-associated protein (MAP) with GTP binding motifs. Hypomorphic mutations in orbit lead to a maternal effect resulting in branched and bent mitotic spindles in the syncytial embryo. In the larval central nervous system, such mutants have an elevated mitotic index with some mitotic cells showing an increase in ploidy. Amorphic alleles show late lethality and greater frequencies of hyperploid mitotic cells. The presence of cells in the hypomorphic mutant in which the chromosomes can be arranged, either in a circular metaphase or an anaphase-like configuration on monopolar spindles, suggests that polyploidy arises through spindle and chromosome segregation defects rather than defects in cytokinesis. A role for the Orbit protein in regulating microtubule behavior in mitosis is suggested by its association with microtubules throughout the spindle at all mitotic stages, by its copurification with microtubules from embryonic extracts, and by the finding that the Orbit protein directly binds to MAP-free microtubules in a GTP-dependent manner.
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Affiliation(s)
- Yoshihiro H. Inoue
- Laboratory of Cell Biology, Aichi Cancer Center, Research Institute, Nagoya 464-8681, Japan
- Cell Cycle Genetics Research Group, Medical Sciences Institute, University of Dundee, Dundee DD1 4HN, Scotland
| | - Maria do Carmo Avides
- Cell Cycle Genetics Research Group, Medical Sciences Institute, University of Dundee, Dundee DD1 4HN, Scotland
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, England
| | - Michina Shiraki
- Laboratory of Cell Biology, Aichi Cancer Center, Research Institute, Nagoya 464-8681, Japan
| | - Peter Deak
- Cell Cycle Genetics Research Group, Medical Sciences Institute, University of Dundee, Dundee DD1 4HN, Scotland
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, England
| | - Masamitsu Yamaguchi
- Laboratory of Cell Biology, Aichi Cancer Center, Research Institute, Nagoya 464-8681, Japan
| | - Yoshio Nishimoto
- Laboratory of Cell Biology, Aichi Cancer Center, Research Institute, Nagoya 464-8681, Japan
| | - Akio Matsukage
- Laboratory of Cell Biology, Aichi Cancer Center, Research Institute, Nagoya 464-8681, Japan
| | - David M. Glover
- Cell Cycle Genetics Research Group, Medical Sciences Institute, University of Dundee, Dundee DD1 4HN, Scotland
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, England
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47
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Li Y, Edsall R, Jagtap PG, Kingston DG, Bane S. Equilibrium studies of a fluorescent paclitaxel derivative binding to microtubules. Biochemistry 2000; 39:616-23. [PMID: 10642187 DOI: 10.1021/bi992044u] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fluorescent derivative of paclitaxel, 3'-N-m-aminobenzamido-3'-N-debenzamidopaclitaxel (N-AB-PT), has been prepared in order to probe paclitaxel-microtubule interactions. Fluorescence spectroscopy was used to quantitatively assess the association of N-AB-PT with microtubules. N-AB-PT was found equipotent with paclitaxel in promoting microtubule polymerization. Paclitaxel and N-AB-PT underwent rapid exchange with each other on microtubules assembled from GTP-, GDP-, and GMPCPP-tubulin. The equilibrium binding parameters for N-AB-PT to microtubules assembled from GTP-tubulin were derived through fluorescence titration. N-AB-PT bound to two types of sites on microtubules (K(d1) = 61 +/- 7.0 nM and K(d2) = 3.3 +/- 0.54 microM). The stoichiometry of each site was less than one ligand per tubulin dimer in the microtubule (n(1) = 0.81 +/- 0.03 and n(2) = 0.44 +/- 0.02). The binding experiments were repeated after exchanging the GTP for GDP or for GMPCPP. It was found that N-AB-PT bound to a single site on microtubules assembled from GDP-tubulin with a dissociation constant of 2.5 +/- 0.29 microM, and that N-AB-PT bound to a single site on microtubules assembled from GMPCPP-tubulin with a dissociation constant of 15 +/- 4.0 nM. It therefore appears that microtubules contain two types of binding sites for paclitaxel and that the binding site affinity for paclitaxel depends on the nucleotide content of tubulin. It has been established that paclitaxel binding does not inhibit GTP hydrolysis and microtubules assembled from GTP-tubulin in the presence of paclitaxel contain almost exclusively GDP at the E-site. We propose that although all the subunits of the microtubule at steady state are the same "GDP-tubulin-paclitaxel", they are formed through two paths: paclitaxel binding to a tubulin subunit before its E-site GTP hydrolysis is of high affinity, and paclitaxel binding to a tubulin subunit containing hydrolyzed GDP at its E-site is of low affinity.
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Affiliation(s)
- Y Li
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, USA
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48
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Lu C, Reedy M, Erickson HP. Straight and curved conformations of FtsZ are regulated by GTP hydrolysis. J Bacteriol 2000; 182:164-70. [PMID: 10613876 PMCID: PMC94253 DOI: 10.1128/jb.182.1.164-170.2000] [Citation(s) in RCA: 238] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FtsZ assembles in vitro into protofilaments that can adopt two conformations-the straight conformation, which can assemble further into two-dimensional protofilament sheets, and the curved conformation, which forms minirings about 23 nm in diameter. Here, we describe the structure of FtsZ tubes, which are a variation of the curved conformation. In the tube the curved protofilament forms a shallow helix with a diameter of 23 nm and a pitch of 18 or 24 degrees. We suggest that this shallow helix is the relaxed structure of the curved protofilament in solution. We provide evidence that GTP favors the straight conformation while GDP favors the curved conformation. In particular, exclusively straight protofilaments and protofilament sheets are assembled in GMPCPP, a nonhydrolyzable GTP analog, or in GTP following chelation of Mg, which blocks GTP hydrolysis. Assembly in GDP produces exclusively tubes. The transition from straight protofilaments to the curved conformation may provide a mechanism whereby the energy of GTP hydrolysis is used to generate force for the constriction of the FtsZ ring in cell division.
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Affiliation(s)
- C Lu
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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49
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Vulevic B, Lobert S, Correia JJ. Role of guanine nucleotides in the vinblastine-induced self-association of tubulin: effects of guanosine alpha,beta-methylenetriphosphate and guanosine alpha,beta-methylenediphosphate. Biochemistry 1997; 36:12828-35. [PMID: 9335540 DOI: 10.1021/bi971120v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It is now well established that guanine nucleotides are allosteric effectors of the vinca alkaloid-induced self-association of tubulin. GDP enhances self-association for vinblastine-, vincristine- and vinorelbine-induced spiral assembly relative to GTP by 0.90 +/- 0.17 kcal/mol [Lobert et al. (1996) Biochemistry 35, 6806-6814]. Since chemical modifications of the vinca alkaloid structure are known to modulate the overall affinity of drug binding, it is very likely that, by Wyman linkage, chemical modifications of guanine nucleotide allosteric effectors also modulate drug binding. Here we compare the effects of the GTP and GDP alpha,beta-methylene analogues GMPCPP and GMPCP on vinblastine-induced tubulin association in 10 and 100 mM piperazine-N,N'-bis(2-ethanesulfonic acid) (Pipes), 1 mM MgSO4, and 2 mM [ethylenebis(oxyethylenenitrilo)]tetraacetic acid (EGTA), pH 6. 9, at different temperatures. We found that GMPCPP perfectly mimics GTP in its effect on spiral assembly under all ionic strength and temperature conditions. However, GMPCP in 10 mM Pipes behaves not as a GDP analogue, but as a GTP analogue. In 100 mM Pipes, GMPCP has characteristics that are intermediate between GDP and GTP. These data suggest that the alpha,beta methylene group in GMPCP and GMPCPP is sufficient to produce a GTP-like effect on vinblastine-induced tubulin self-assembly. This is consistent with previous observations that GMPCP-tubulin will assemble into microtubules in a 2 M glycerol and 100 mM Pipes buffer [Vulevic & Correia (1997) Biophys. J. 72, 1357-1375]. Our results demonstrate that an alpha,beta methylene modification of the guanine nucleotide phosphate moiety can induce a salt-dependent conformational change in the tubulin heterodimer that favors the GTP-tubulin structure. This has important implications for understanding allosteric interactions that occur in the binding of guanine nucleotides to tubulin.
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Affiliation(s)
- B Vulevic
- Department of Biochemistry and School of Nursing, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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