1
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Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers. Nat Methods 2021; 18:1247-1252. [PMID: 34608319 PMCID: PMC8490153 DOI: 10.1038/s41592-021-01261-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/04/2021] [Indexed: 02/08/2023]
Abstract
The quantification of membrane-associated biomolecular interactions is crucial to our understanding of various cellular processes. State-of-the-art single-molecule approaches rely largely on the addition of fluorescent labels, which complicates the quantification of the involved stoichiometries and dynamics because of low temporal resolution and the inherent limitations associated with labeling efficiency, photoblinking and photobleaching. Here, we demonstrate dynamic mass photometry, a method for label-free imaging, tracking and mass measurement of individual membrane-associated proteins diffusing on supported lipid bilayers. Application of this method to the membrane remodeling GTPase, dynamin-1, reveals heterogeneous mixtures of dimer-based oligomers, oligomer-dependent mobilities, membrane affinities and (dis)association of individual complexes. These capabilities, together with assay-based advances for studying integral membrane proteins, will enable the elucidation of biomolecular mechanisms in and on lipid bilayers.
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2
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Chafai DE, Sulimenko V, Havelka D, Kubínová L, Dráber P, Cifra M. Reversible and Irreversible Modulation of Tubulin Self-Assembly by Intense Nanosecond Pulsed Electric Fields. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1903636. [PMID: 31408579 DOI: 10.1002/adma.201903636] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/26/2019] [Indexed: 05/21/2023]
Abstract
Tubulin self-assembly into microtubules is a fascinating natural phenomenon. Its importance is not just crucial for functional and structural biological processes, but it also serves as an inspiration for synthetic nanomaterial innovations. The modulation of the tubulin self-assembly process without introducing additional chemical inhibitors/promoters or stabilizers has remained an elusive process. This work reports a versatile and vigorous strategy for controlling tubulin self-assembly by nanosecond electropulses (nsEPs). The polymerization assessed by turbidimetry is dependent on nsEPs dosage. The kinetics of microtubules formation is tightly linked to the nsEPs effects on structural properties of tubulin, and tubulin-solvent interface, assessed by autofluorescence, and the zeta potential. Moreover, the overall size of tubulin assessed by dynamic light scattering is affected as well. Additionally, atomic force microscopy imaging reveals the formation of different assemblies reflecting applied nsEPs. It is suggested that changes in C-terminal modification states alter tubulin polymerization-competent conformations. Although the assembled tubulin preserve their integral structure, they might exhibit a broad range of new properties important for their functions. Thus, these transient conformation changes of tubulin and their collective properties can result in new applications.
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Affiliation(s)
- Djamel Eddine Chafai
- Bioelectrodynamics Research Team, Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 51, Prague, Czech Republic
| | - Vadym Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Daniel Havelka
- Bioelectrodynamics Research Team, Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 51, Prague, Czech Republic
| | - Lucie Kubínová
- Department of Biomathematics, Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Pavel Dráber
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Michal Cifra
- Bioelectrodynamics Research Team, Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 51, Prague, Czech Republic
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3
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Abstract
Clathrin-mediated endocytosis (CME) is the major endocytic pathway in mammalian cells. It is responsible for the uptake of transmembrane receptors and transporters, for remodeling plasma membrane composition in response to environmental changes, and for regulating cell surface signaling. CME occurs via the assembly and maturation of clathrin-coated pits that concentrate cargo as they invaginate and pinch off to form clathrin-coated vesicles. In addition to the major coat proteins, clathrin triskelia and adaptor protein complexes, CME requires a myriad of endocytic accessory proteins and phosphatidylinositol lipids. CME is regulated at multiple steps-initiation, cargo selection, maturation, and fission-and is monitored by an endocytic checkpoint that induces disassembly of defective pits. Regulation occurs via posttranslational modifications, allosteric conformational changes, and isoform and splice-variant differences among components of the CME machinery, including the GTPase dynamin. This review summarizes recent findings on the regulation of CME and the evolution of this complex process.
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Affiliation(s)
- Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
| | - Ping-Hung Chen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
| | - Saipraveen Srinivasan
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
| | - Gaudenz Danuser
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , , .,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Sandra L Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , , , ,
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4
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Dar S, Pucadyil TJ. The pleckstrin-homology domain of dynamin is dispensable for membrane constriction and fission. Mol Biol Cell 2016; 28:152-160. [PMID: 28035046 PMCID: PMC5221619 DOI: 10.1091/mbc.e16-09-0640] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022] Open
Abstract
Classical dynamins engage in rapid vesicle release during synaptic vesicle recycling and contain a lipid-binding domain called the pleckstrin-homology domain (PHD). An analysis of a reengineered dynamin construct lacking the PHD shows that the PHD acts as a catalyst to enhance the rates of dynamin-induced membrane fission. Classical dynamins bind the plasma membrane–localized phosphatidylinositol-4,5-bisphosphate using the pleckstrin-homology domain (PHD) and engage in rapid membrane fission during synaptic vesicle recycling. This domain is conspicuously absent among extant bacterial and mitochondrial dynamins, however, where loop regions manage membrane recruitment. Inspired by the core design of bacterial and mitochondrial dynamins, we reengineered the classical dynamin by replacing its PHD with a polyhistidine or polylysine linker. Remarkably, when recruited via chelator or anionic lipids, respectively, the reengineered dynamin displayed the capacity to constrict and sever membrane tubes. However, when analyzed at single-event resolution, the tube-severing process displayed long-lived, highly constricted prefission intermediates that contributed to 10-fold reduction in bulk rates of membrane fission. Our results indicate that the PHD acts as a catalyst in dynamin-induced membrane fission and rationalize its adoption to meet the physiologic requirement of a fast-acting membrane fission apparatus.
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Affiliation(s)
- Srishti Dar
- Indian Institute of Science Education and Research, Pashan, Pune Maharashtra 411008, India
| | - Thomas J Pucadyil
- Indian Institute of Science Education and Research, Pashan, Pune Maharashtra 411008, India
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5
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Rong Y, Wang K, Shi R, Hou X, Dong CH. Expression, purification and characterization of ROP6 6-178 GTPase from Arabidopsis thaliana. Protein Expr Purif 2016; 131:1-6. [PMID: 27789389 DOI: 10.1016/j.pep.2016.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/14/2016] [Accepted: 10/23/2016] [Indexed: 11/25/2022]
Abstract
The unique type of GTPases in plants, termed ROPs, are the small GTP-binding proteins involved in signal transduction which play important roles in regulation of hormonal response pathway, cell polarity, defense from plant pathogens, etc. In order to explore the regulation mechanism of AtROPs involved in, the purified ROPs were needed to explore the interactions of ROP GTPases with their regulators and effectors. In this study, the first ROP GTPase from Arabidopsis thaliana, AtROP66-178 was successfully expressed in Escherichia coli and obtained in high quality and purity through affinity chromatography and gel-filtration chromatography. The resultant protein was identified as a single band of 19 kDa in SDS-PAGE and was confirmed to be active to interact with guanine nucleotides through the fluorescence-based assay. The intrinsic tryptophan fluorescence intensity of AtROP66-178 was enhanced upon interacting with either GDP or GTP. Meanwhile, the equilibrium dissociation constants of AtROP66-178 with fluorescent guanine nucleotide analogue mantGDP and mantGTP were determined to be 0.0721 μM and 0.0422 μM, respectively, based on fluorescence polarization.
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Affiliation(s)
- Yongheng Rong
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Kun Wang
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Renxing Shi
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaomin Hou
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
| | - Chun-Hai Dong
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
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6
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Srinivasan S, Dharmarajan V, Reed DK, Griffin PR, Schmid SL. Identification and function of conformational dynamics in the multidomain GTPase dynamin. EMBO J 2016; 35:443-57. [PMID: 26783363 DOI: 10.15252/embj.201593477] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 12/11/2015] [Indexed: 01/13/2023] Open
Abstract
Vesicle release upon endocytosis requires membrane fission, catalyzed by the large GTPase dynamin. Dynamin contains five domains that together orchestrate its mechanochemical activity. Hydrogen-deuterium exchange coupled with mass spectrometry revealed global nucleotide- and membrane-binding-dependent conformational changes, as well as the existence of an allosteric relay element in the α2(S) helix of the dynamin stalk domain. As predicted from structural studies, FRET analyses detect large movements of the pleckstrin homology domain (PHD) from a 'closed' conformation docked near the stalk to an 'open' conformation able to interact with membranes. We engineered dynamin constructs locked in either the closed or open state by chemical cross-linking or deletion mutagenesis and showed that PHD movements function as a conformational switch to regulate dynamin self-assembly, membrane binding, and fission. This PHD conformational switch is impaired by a centronuclear myopathy-causing disease mutation, S619L, highlighting the physiological significance of its role in regulating dynamin function. Together, these data provide new insight into coordinated conformational changes that regulate dynamin function and couple membrane binding, oligomerization, and GTPase activity during dynamin-catalyzed membrane fission.
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Affiliation(s)
| | | | - Dana Kim Reed
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA
| | - Sandra L Schmid
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
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7
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Gao Y, Tan L, Dong CH, Hou X. Expression, purification and guanine nucleotide binding characterization of Arabidopsis RabE1d13-185 GTPase. Protein Expr Purif 2015; 119:57-62. [PMID: 26611608 DOI: 10.1016/j.pep.2015.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/03/2015] [Accepted: 11/15/2015] [Indexed: 01/27/2023]
Abstract
Arabidopsis RabE1d subclass plays important plant-specific functions in plant growth and development, response to ethylene and defence to plant pathogen, besides their basic cellular role in membrane trafficking. In this study, we present the expression, purification, and characterization of the recombinant core domain of AtRabE1d13-185. AtRabE1d13-185 was successfully expressed in Escherichia coli and purified via two-step nickel affinity chromatography followed by gel filtration, and identified single band in SDS-PAGE. The resultant protein was functionally active, as determined by interaction with guanine nucleotide by a fluorescence-based assay. The intrinsic tryptophan of AtRabE1d13-185 showed fluorescence resonance energy transfer (FRET) effect upon forming complex with fluorescent methylanthraniloyl (mant)-GDP, but quenched when binding with non-labelled guanine nucleotide. The association rate of mantGDP with AtRabE1d13-185 was determined to be 3.48 × 10(7) s(-1) M(-1). The dissociation rates of GDP and mantGDP from the complex with AtRabE1d13-185 were similar. The koff values were determined to be 4.02 × 10(-4) s(-1) based on the FRET effect for the AtRabE1d13-185:GDP and 5.41 × 10(-4) s(-1) for mantGDP excited directly.
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Affiliation(s)
- Yi Gao
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Lingling Tan
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Chun-Hai Dong
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaomin Hou
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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8
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González-Jamett AM, Haro-Acuña V, Momboisse F, Caviedes P, Bevilacqua JA, Cárdenas AM. Dynamin-2 in nervous system disorders. J Neurochem 2013; 128:210-23. [DOI: 10.1111/jnc.12455] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/04/2013] [Accepted: 09/12/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Arlek M. González-Jamett
- Centro Interdisciplinario de Neurociencia de Valparaíso; Facultad de Ciencias; Universidad de Valparaíso; Valparaíso Chile
| | - Valentina Haro-Acuña
- Centro Interdisciplinario de Neurociencia de Valparaíso; Facultad de Ciencias; Universidad de Valparaíso; Valparaíso Chile
| | - Fanny Momboisse
- Centro Interdisciplinario de Neurociencia de Valparaíso; Facultad de Ciencias; Universidad de Valparaíso; Valparaíso Chile
| | - Pablo Caviedes
- Programa de Farmacología Molecular y Clínica; Facultad de Medicina; Universidad de Chile; Santiago Chile
| | - Jorge A. Bevilacqua
- Departamento de Neurología y Neurocirugía; Hospital Clínico Universidad de Chile; and Programa de Anatomía y Biología del Desarrollo; ICBM; Facultad de Medicina; Universidad de Chile; Santiago Chile
| | - Ana M. Cárdenas
- Centro Interdisciplinario de Neurociencia de Valparaíso; Facultad de Ciencias; Universidad de Valparaíso; Valparaíso Chile
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Chappie JS, Dyda F. Building a fission machine--structural insights into dynamin assembly and activation. J Cell Sci 2013; 126:2773-84. [PMID: 23781021 DOI: 10.1242/jcs.108845] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Dynamin is a large multidomain GTPase that assembles into helical arrays around the necks of deeply invaginated clathrin-coated pits and catalyzes membrane fission during the final stages of endocytosis. Although it is well established that the function of dynamin in vivo depends on its oligomerization and its capacity for efficient GTP hydrolysis, the molecular mechanisms governing these activities have remained poorly defined. In recent years, there has been an explosion of structural data that has provided new insights into the architecture, organization and nucleotide-dependent conformational changes of the dynamin fission machine. Here, we review the key findings of these efforts and discuss the implications of each with regard to GTP hydrolysis, dynamin assembly and membrane fission.
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Affiliation(s)
- Joshua S Chappie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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10
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Two dynamin-2 genes are required for normal zebrafish development. PLoS One 2013; 8:e55888. [PMID: 23418470 PMCID: PMC3572173 DOI: 10.1371/journal.pone.0055888] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 01/07/2013] [Indexed: 01/28/2023] Open
Abstract
Dynamin-2 (DNM2) is a large GTPase involved in clathrin-mediated endocytosis and related trafficking pathways. Mutations in human DNM2 cause two distinct neuromuscular disorders: centronuclear myopathy and Charcot-Marie-Tooth disease. Zebrafish have been shown to be an excellent animal model for many neurologic disorders, and this system has the potential to inform our understanding of DNM2-related disease. Currently, little is known about the endogenous zebrafish orthologs to human DNM2. In this study, we characterize two zebrafish dynamin-2 genes, dnm2 and dnm2-like. Both orthologs are structurally similar to human DNM2 at the gene and protein levels. They are expressed throughout early development and in all adult tissues examined. Knockdown of dnm2 and dnm2-like gene products resulted in extensive morphological abnormalities during development, and expression of human DNM2 RNA rescued these phenotypes. Our findings suggest that dnm2 and dnm2-like are orthologs to human DNM2, and that they are required for normal zebrafish development.
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11
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Zarei Jaliani H, Riazi GH, Ghaffari SM, Karima O, Rahmani A. The effect of the crocus sativus L. Carotenoid, crocin, on the polymerization of microtubules, in vitro. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2013; 16:101-7. [PMID: 23638298 PMCID: PMC3637910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 08/15/2012] [Indexed: 10/25/2022]
Abstract
OBJECTIVE(S) Crocin, as the main carotenoid of saffron, has shown anti-tumor activity both in vitro and in vivo. Crocin might interact with cellular proteins and modulate their functions, but the exact target of this carotenoid and the other compounds of the saffron have not been discovered yet. Microtubular proteins, as one of the most important proteins inside the cells, have several functions in nearly all kinds of cellular processes. The aim of this study was to investigate whether crocin affects microtubule polymerization and tubulin structure. MATERIALS AND METHODS Microtubules were extracted from sheep brains after two cycles of temperature-dependant assembly-disassembly in the polymerization buffer (PMG). Then phosphocellulose P11 column was used to prepare MAP-free tubulin. Turbidimetric assay of microtubules was performed by incubation of tubulins at 37 ºC in PIPES buffer. To investigate the intrinsic fluorescence spectra of tubulins, the emission spectra of tryptophans was monitored. To test the interaction of crocin with tubulin in more details, ANS has been used. RESULTS Crocin extremely affected the tubulin polymerization and structure. Ultraviolet spectroscopy indicated that crocin increased polymerization of microtubules by nearly a factor of two. Fluorescence spectroscopic data also pointed to significant conformational changes of tubulin. CONCLUSION We showed that crocin increased tubulin polymerization and microtubule nucleation rate and this effect was concentration dependant. After entering cell, crocin can modulate cellular proteins and their functions. Concerning the results of this study, crocin would be able to affect several cell processes through interaction with tubulin proteins or microtubules.
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Affiliation(s)
- Hossein Zarei Jaliani
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran
| | - Gholam Hossein Riazi
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran,Corresponding author: Gholam Hossein Riazi, Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran. Tel: +98-21-61112473; Fax: +98-21-66404680;
| | - Seyyed Mahmoud Ghaffari
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran
| | - Oveis Karima
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), Tehran University, Tehran, Iran
| | - Abbas Rahmani
- School of Biology, University College of Sciences, University of Tehran, Tehran, Iran
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12
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Pattanayak GK, Venkataramani S, Hortensteiner S, Kunz L, Christ B, Moulin M, Smith AG, Okamoto Y, Tamiaki H, Sugishima M, Greenberg JT. Accelerated cell death 2 suppresses mitochondrial oxidative bursts and modulates cell death in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:589-600. [PMID: 21988537 PMCID: PMC3274588 DOI: 10.1111/j.1365-313x.2011.04814.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The Arabidopsis ACCELERATED CELL DEATH 2 (ACD2) protein protects cells from programmed cell death (PCD) caused by endogenous porphyrin-related molecules like red chlorophyll catabolite or exogenous protoporphyrin IX. We previously found that during bacterial infection, ACD2, a chlorophyll breakdown enzyme, localizes to both chloroplasts and mitochondria in leaves. Additionally, acd2 cells show mitochondrial dysfunction. In plants with acd2 and ACD2 (+) sectors, ACD2 functions cell autonomously, implicating a pro-death ACD2 substrate as being cell non-autonomous in promoting the spread of PCD. ACD2 targeted solely to mitochondria can reduce the accumulation of an ACD2 substrate that originates in chloroplasts, indicating that ACD2 substrate molecules are likely to be mobile within cells. Two different light-dependent reactive oxygen bursts in mitochondria play prominent and causal roles in the acd2 PCD phenotype. Finally, ACD2 can complement acd2 when targeted to mitochondria or chloroplasts, respectively, as long as it is catalytically active: the ability to bind substrate is not sufficient for ACD2 to function in vitro or in vivo. Together, the data suggest that ACD2 localizes dynamically during infection to protect cells from pro-death mobile substrate molecules, some of which may originate in chloroplasts, but have major effects on mitochondria.
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Affiliation(s)
- Gopal K. Pattanayak
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637
| | - Sujatha Venkataramani
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637
| | | | - Lukas Kunz
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Bastien Christ
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Michael Moulin
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB23EA, United Kingdom
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB23EA, United Kingdom
| | - Yukihiro Okamoto
- Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hitoshi Tamiaki
- Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Jean T. Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637
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Chappie JS, Mears JA, Fang S, Leonard M, Schmid SL, Milligan RA, Hinshaw JE, Dyda F. A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke. Cell 2011; 147:209-22. [PMID: 21962517 DOI: 10.1016/j.cell.2011.09.003] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/26/2011] [Accepted: 09/01/2011] [Indexed: 11/28/2022]
Abstract
The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process remain a mystery. We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. The structures reveal the position and connectivity of dynamin fragments in the assembled structure, showing that G domain dimers only form between tetramers in sequential rungs of the dynamin helix. Using chemical crosslinking, we demonstrate that dynamin tetramers are made of two dimers, in which the G domain of one molecule interacts in trans with the GED of another. Structural comparison of GG(GMPPCP) to the GG transition-state complex identifies a hydrolysis-dependent powerstroke that may play a role in membrane-remodeling events necessary for fission.
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Affiliation(s)
- Joshua S Chappie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
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14
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Abstract
Dynamin, best studied for its role in clathrin-mediated endocytosis, is the prototypical member of a family of multidomain GTPases involved in fission and remodeling of multiple organelles. Recent studies have shown that dynamin alone can catalyze fission of membrane tubules and vesicle formation from planar lipid templates. Thus, dynamin appears to be a self-sufficient fission machine. Here we review the biochemical activities and structural features of dynamin required for fission activity. As all changes in membrane topology require energetically unfavorable rearrangements of the lipid bilayer, we discuss the interplay between dynamin and its lipid substrates that are critical to defining a nonleaky pathway to membrane fission. We propose a two-stage model for dynamin-catalyzed fission. In stage one, dynamin's mechanochemical activities induce localized curvature stress and position its lipid-interacting pleckstrin homology domains to create a catalytic center that, in stage two, guides lipid remodeling through hemifission intermediates to drive membrane fission.
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Affiliation(s)
- Sandra L Schmid
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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15
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Koshiba T, Holman HA, Kubara K, Yasukawa K, Kawabata SI, Okamoto K, MacFarlane J, Shaw JM. Structure-function analysis of the yeast mitochondrial Rho GTPase, Gem1p: implications for mitochondrial inheritance. J Biol Chem 2011; 286:354-62. [PMID: 21036903 PMCID: PMC3012993 DOI: 10.1074/jbc.m110.180034] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/26/2010] [Indexed: 11/06/2022] Open
Abstract
Mitochondria undergo continuous cycles of homotypic fusion and fission, which play an important role in controlling organelle morphology, copy number, and mitochondrial DNA maintenance. Because mitochondria cannot be generated de novo, the motility and distribution of these organelles are essential for their inheritance by daughter cells during division. Mitochondrial Rho (Miro) GTPases are outer mitochondrial membrane proteins with two GTPase domains and two EF-hand motifs, which act as receptors to regulate mitochondrial motility and inheritance. Here we report that although all of these domains are biochemically active, only the GTPase domains are required for the mitochondrial inheritance function of Gem1p (the yeast Miro ortholog). Mutations in either of the Gem1p GTPase domains completely abrogated mitochondrial inheritance, although the mutant proteins retained half the GTPase activity of the wild-type protein. Although mitochondrial inheritance was not dependent upon Ca(2+) binding by the two EF-hands of Gem1p, a functional N-terminal EF-hand I motif was critical for stable expression of Gem1p in vivo. Our results suggest that basic features of Miro protein function are conserved from yeast to humans, despite differences in the cellular machinery mediating mitochondrial distribution in these organisms.
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Affiliation(s)
- Takumi Koshiba
- Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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James NG, Ross JA, Stefl M, Jameson DM. Applications of phasor plots to in vitro protein studies. Anal Biochem 2010; 410:70-6. [PMID: 21078289 DOI: 10.1016/j.ab.2010.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 11/05/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
In a recent article, we described the application of phasor analysis to fluorescence intensity decay data on in vitro samples. As detailed in that article, this method provides researchers with a simple graphical method for viewing lifetime data that can be used to quantify individual components of a mixture as well as to identify excited state reactions. In the current article, we extend the use of in vitro phasor analysis to intrinsic protein fluorescence. We show how alterations in the excited state properties of tryptophan residues are easily visualized using the phasor method. Specifically, we demonstrate that protein-ligand and protein-protein interactions can result in unique shifts in the location of phasor points, indicative of protein conformational changes. Application of the method to a rapid kinetic experiment is also shown. Finally, we show that the unfolding of lysozyme with either urea or guanidine hydrochloride results in different phasor trajectories, indicative of unique denaturation pathways.
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Affiliation(s)
- Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
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17
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Pawlowski N. Dynamin self-assembly and the vesicle scission mechanism: how dynamin oligomers cleave the membrane neck of clathrin-coated pits during endocytosis. Bioessays 2010; 32:1033-9. [PMID: 20957720 DOI: 10.1002/bies.201000086] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recently, Gao et al. and Chappie et al. elucidated the crystal structures of the polytetrameric stalk domain of the dynamin-like virus resistance protein, MxA, and of the G-domain dimer of the large, membrane-deforming GTPase, dynamin, respectively. Combined, they provide a hypothetical oligomeric structure for the complete dynamin protein. Here, it is discussed how the oligomers are expected to form and how they participate in dynamin mediated vesicle fission during the process of endocytosis. The proposed oligomeric structure is compared with the novel mechanochemical model of dynamin function recently proposed by Bashkirov et al. and Pucadyil and Schmid. In conclusion, the new model of the dynamin oligomer has the potential to explain how short self-limiting fissogenic dynamin assemblies are formed and how concerted GTP hydrolysis is achieved. The oligomerisation of two other dynamin superfamily proteins, the guanylate binding proteins (GBPs) and the immunity-related GTPases (IRGs), is addressed briefly.
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Affiliation(s)
- Nikolaus Pawlowski
- Department of Cell Genetics, Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, Cologne, Germany.
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18
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Kenniston JA, Lemmon MA. Dynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients. EMBO J 2010; 29:3054-67. [PMID: 20700106 PMCID: PMC2944063 DOI: 10.1038/emboj.2010.187] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/14/2010] [Indexed: 01/18/2023] Open
Abstract
The large GTPase dynamin has an important membrane scission function in receptor-mediated endocytosis and other cellular processes. Self-assembly on phosphoinositide-containing membranes stimulates dynamin GTPase activity, which is crucial for its function. Although the pleckstrin-homology (PH) domain is known to mediate phosphoinositide binding by dynamin, it remains unclear how this promotes activation. Here, we describe studies of dynamin PH domain mutations found in centronuclear myopathy (CNM) that increase dynamin's GTPase activity without altering phosphoinositide binding. CNM mutations in the PH domain C-terminal α-helix appear to cause conformational changes in dynamin that alter control of the GTP hydrolysis cycle. These mutations either 'sensitize' dynamin to lipid stimulation or elevate basal GTPase rates by promoting self-assembly and thus rendering dynamin no longer lipid responsive. We also describe a low-resolution structure of dimeric dynamin from small-angle X-ray scattering that reveals conformational changes induced by CNM mutations, and defines requirements for domain rearrangement upon dynamin self-assembly at membrane surfaces. Our data suggest that changes in the PH domain may couple lipid binding to dynamin GTPase activation at sites of vesicle invagination.
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Affiliation(s)
- Jon A Kenniston
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Mark A Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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19
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Ramachandran R. Vesicle scission: dynamin. Semin Cell Dev Biol 2010; 22:10-7. [PMID: 20837154 DOI: 10.1016/j.semcdb.2010.09.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/03/2010] [Accepted: 09/03/2010] [Indexed: 11/17/2022]
Abstract
Dynamin is a large GTPase involved in endocytic vesicle formation, but its exact role and mechanism are subjects of long-standing debate. Despite recent advances in the structural analyses of isolated dynamin domains and the faithful reconstitution of dynamin-dependent membrane fission in model membrane systems, the mechanism of its action remains poorly understood at the molecular level. Here, I will review current progress in elucidating dynamin action in vesicle scission and highlight the most visible gaps in knowledge that limit the development of a coherent and complete model for its role in vesicle biogenesis. Coordinated functions of BAR domain-containing binding partners are also discussed.
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Affiliation(s)
- Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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20
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Chappie JS, Acharya S, Leonard M, Schmid SL, Dyda F. G domain dimerization controls dynamin's assembly-stimulated GTPase activity. Nature 2010; 465:435-40. [PMID: 20428113 PMCID: PMC2879890 DOI: 10.1038/nature09032] [Citation(s) in RCA: 226] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 03/22/2010] [Indexed: 11/09/2022]
Abstract
Dynamin is an atypical GTPase that catalyzes membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin’s basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0Å resolution crystal structure of a minimal GTPase-GED fusion protein (GG) constructed from human dynamin 1, which has dimerized in the presence of the transition state mimic GDP.AlF4−. The structure reveals dynamin’s catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GG dimer provides new insight into the mechanisms underlying dynamin-catalyzed membrane fission.
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Affiliation(s)
- Joshua S Chappie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
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21
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Dynamin 2 and human diseases. J Mol Med (Berl) 2010; 88:339-50. [PMID: 20127478 DOI: 10.1007/s00109-009-0587-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 12/21/2009] [Accepted: 12/25/2009] [Indexed: 10/25/2022]
Abstract
Dynamin 2 (DNM2) mutations cause autosomal dominant centronuclear myopathy, a rare form of congenital myopathy, and intermediate and axonal forms of Charcot-Marie-Tooth disease, a peripheral neuropathy. DNM2 is a large GTPase mainly involved in membrane trafficking through its function in the formation and release of nascent vesicles from biological membranes. DNM2 participates in clathrin-dependent and clathrin-independent endocytosis and intracellular membrane trafficking (from endosomes and Golgi apparatus). Recent studies have also implicated DNM2 in exocytosis. DNM2 belongs to the machinery responsible for the formation of vesicles and regulates the cytoskeleton providing intracellular vesicle transport. In addition, DNM2 tightly interacts with and is involved in the regulation of actin and microtubule networks, independent from membrane trafficking processes. We summarize here the molecular, biochemical, and functional data on DNM2 and discuss the possible pathophysiological mechanisms via which DNM2 mutations can lead to two distinct neuromuscular disorders.
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22
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Mustafi D, Peng B, Foxley S, Makinen MW, Karczmar GS, Zamora M, Ejnik J, Martin H. New vanadium-based magnetic resonance imaging probes: clinical potential for early detection of cancer. J Biol Inorg Chem 2009; 14:1187-97. [PMID: 19572156 DOI: 10.1007/s00775-009-0562-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 06/18/2009] [Indexed: 12/25/2022]
Abstract
We have developed a magnetic resonance imaging (MRI) method for improved detection of cancer with a new class of cancer-specific contrast agents, containing vanadyl (VO(2+))-chelated organic ligands, specifically bis(acetylacetonato)oxovanadium(IV) [VO(acac)(2)]. Vanadyl compounds have been found to accumulate within cells, where they interact with intracellular glycolytic enzymes. Aggressive cancers are metabolically active and highly glycolytic; an MRI contrast agent that enters cells with high glycolytic activity could provide high-resolution functional images of tumor boundaries and internal structure, which cannot be achieved by conventional contrast agents. The present work demonstrates properties of VO(acac)(2) that may give it excellent specificity for cancer detection. A high dose of VO(acac)(2) did not cause any acute or short-term adverse reactions in murine subjects. Calorimetry and spectrofluorometric methods demonstrate that VO(acac)(2) is a blood pool agent that binds to serum albumin with a dissociation constant K (d) ~ 2.5 +/- 0.7 x 10(-7) M and a binding stoichiometry n = 1.03 +/- 0.04. Owing to its prolonged blood half-life and selective leakage from hyperpermeable tumor vasculature, a low dose of VO(acac)(2) (0.15 mmol/kg) selectively enhanced in vivo magnetic resonance images of tumors, providing high-resolution images of their interior structure. The kinetics of uptake and washout are consistent with the hypothesis that VO(acac)(2) preferentially accumulates in cancer cells. Although VO(acac)(2) has a lower relaxivity than gadolinium-based MRI contrast agents, its specificity for highly glycolytic cells may lead to an innovative approach to cancer detection since it has the potential to produce MRI contrast agents that are nontoxic and highly sensitive to cancer metabolism.
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Affiliation(s)
- Devkumar Mustafi
- Department of Biochemistry and Molecular Biology, Center for Integrative Science, The University of Chicago, Chicago, IL 60637, USA.
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23
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Chappie JS, Acharya S, Liu YW, Leonard M, Pucadyil TJ, Schmid SL. An intramolecular signaling element that modulates dynamin function in vitro and in vivo. Mol Biol Cell 2009; 20:3561-71. [PMID: 19515832 DOI: 10.1091/mbc.e09-04-0318] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Dynamin exhibits a high basal rate of GTP hydrolysis that is enhanced by self-assembly on a lipid template. Dynamin's GTPase effector domain (GED) is required for this stimulation, though its mechanism of action is poorly understood. Recent structural work has suggested that GED may physically dock with the GTPase domain to exert its stimulatory effects. To examine how these interactions activate dynamin, we engineered a minimal GTPase-GED fusion protein (GG) that reconstitutes dynamin's basal GTPase activity and utilized it to define the structural framework that mediates GED's association with the GTPase domain. Chemical cross-linking of GG and mutagenesis of full-length dynamin establishes that the GTPase-GED interface is comprised of the N- and C-terminal helices of the GTPase domain and the C-terminus of GED. We further show that this interface is essential for structural stability in full-length dynamin. Finally, we identify mutations in this interface that disrupt assembly-stimulated GTP hydrolysis and dynamin-catalyzed membrane fission in vitro and impair the late stages of clathrin-mediated endocytosis in vivo. These data suggest that the components of the GTPase-GED interface act as an intramolecular signaling module, which we term the bundle signaling element, that can modulate dynamin function in vitro and in vivo.
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Affiliation(s)
- Joshua S Chappie
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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24
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Gheshlaghi ZN, Riazi GH, Ahmadian S, Ghafari M, Mahinpour R. Toxicity and interaction of titanium dioxide nanoparticles with microtubule protein. Acta Biochim Biophys Sin (Shanghai) 2008. [DOI: 10.1111/j.1745-7270.2008.00458.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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25
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Ramachandran R, Schmid SL. Real-time detection reveals that effectors couple dynamin's GTP-dependent conformational changes to the membrane. EMBO J 2007; 27:27-37. [PMID: 18079695 DOI: 10.1038/sj.emboj.7601961] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Accepted: 11/21/2007] [Indexed: 11/09/2022] Open
Abstract
The GTPase dynamin is a mechanochemical enzyme involved in membrane fission, but the molecular nature of its membrane interactions and their regulation by guanine nucleotides and protein effectors remain poorly characterized. Using site-directed fluorescence labeling and several independent fluorescence spectroscopic techniques, we have developed robust assays for the detection and real-time monitoring of dynamin-membrane and dynamin-dynamin interactions. We show that dynamin interacts preferentially with highly curved, PIP2-dense membranes and inserts partially into the lipid bilayer. Our kinetic measurements further reveal that cycles of GTP binding and hydrolysis elicit major conformational rearrangements in self-assembled dynamin that favor dynamin-membrane association and dissociation, respectively. Sorting nexin 9, an abundant dynamin partner, transiently stabilizes dynamin on the membrane at the onset of stimulated GTP hydrolysis and may function to couple dynamin's mechanochemical conformational changes to membrane destabilization. Amphiphysin I has the opposite effect. Thus, dynamin's mechanochemical properties on a membrane surface are dynamically regulated by its GTPase cycle and major binding partners.
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Affiliation(s)
- Rajesh Ramachandran
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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26
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Kim MV, Kasakov AS, Seit-Nebi AS, Marston SB, Gusev NB. Structure and properties of K141E mutant of small heat shock protein HSP22 (HspB8, H11) that is expressed in human neuromuscular disorders. Arch Biochem Biophys 2006; 454:32-41. [PMID: 16949546 DOI: 10.1016/j.abb.2006.07.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 07/24/2006] [Accepted: 07/25/2006] [Indexed: 11/16/2022]
Abstract
Some properties of the K141E mutant of human HSP22 that is expressed in distal hereditary motor neuropathy were investigated. This mutation slightly decreased intrinsic fluorescence of HSP22 and induced changes in the far UV CD spectra that correlate with increase of disordered structure. Destabilized K141E mutant was more susceptible to trypsinolysis than the wild type protein. Mutation K141E did not significantly affect the hydrophobic properties measured by bis-ANS binding and did not affect the quaternary structure of HSP22. With insulin as a substrate the chaperone-like activity of K141E mutant and the wild type protein were similar. However with alcohol dehydrogenase and rhodanese the chaperone-like activity of K141E mutant was remarkably lower than the corresponding activity of the wild type protein. It is concluded that K141E mutation induces destabilization of HSP22 structure and probably by this means diminish the chaperone-like activity of HSP22 with certain protein substrates.
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Affiliation(s)
- Maria V Kim
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
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