51
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DeSantis ME, Cianfrocco MA, Htet ZM, Tran PT, Reck-Peterson SL, Leschziner AE. Lis1 Has Two Opposing Modes of Regulating Cytoplasmic Dynein. Cell 2017; 170:1197-1208.e12. [PMID: 28886386 DOI: 10.1016/j.cell.2017.08.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/08/2017] [Accepted: 08/21/2017] [Indexed: 11/28/2022]
Abstract
Regulation is central to the functional versatility of cytoplasmic dynein, a motor involved in intracellular transport, cell division, and neurodevelopment. Previous work established that Lis1, a conserved regulator of dynein, binds to its motor domain and induces a tight microtubule-binding state in dynein. The work we present here-a combination of biochemistry, single-molecule assays, and cryoelectron microscopy-led to the surprising discovery that Lis1 has two opposing modes of regulating dynein, being capable of inducing both low and high affinity for the microtubule. We show that these opposing modes depend on the stoichiometry of Lis1 binding to dynein and that this stoichiometry is regulated by the nucleotide state of dynein's AAA3 domain. The low-affinity state requires Lis1 to also bind to dynein at a novel conserved site, mutation of which disrupts Lis1's function in vivo. We propose a new model for the regulation of dynein by Lis1.
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Affiliation(s)
- Morgan E DeSantis
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zaw Min Htet
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biophysics Graduate Program, Harvard University, Boston, MA 92105, USA
| | - Phuoc Tien Tran
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Section of Cellular and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA.
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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52
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Laquerriere A, Maillard C, Cavallin M, Chapon F, Marguet F, Molin A, Sigaudy S, Blouet M, Benoist G, Fernandez C, Poirier K, Chelly J, Thomas S, Bahi-Buisson N. Neuropathological Hallmarks of Brain Malformations in Extreme Phenotypes Related to DYNC1H1 Mutations. J Neuropathol Exp Neurol 2017; 76:195-205. [PMID: 28395088 DOI: 10.1093/jnen/nlw124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dyneins play a critical role in a wide variety of cellular functions such as the movement of organelles and numerous aspects of mitosis, making it central player in neocortical neurogenesis and migration. Recently, cytoplasmic dynein-1, heavy chain-1 (DYNC1H1) mutations have been found to cause a wide spectrum of brain cortical malformations. We report on the detailed neuropathological features of brain lesions from 2 fetuses aged 36 and 22 weeks of gestation (WG), respectively, carrying de novo DYNC1H1 mutations, p.Arg2720Lys and p.Val3951Ala and presenting the most severe phenotype reported to date. Analysis using the Dictyostelium discoideum dynein motor crystal structure showed that the mutations are both predicted to have deleterious consequences on the function of the motor domain. Both fetuses showed a similar macroscopic and histological brain malformative complex associating bilateral fronto-parietal polymicrogyria (PMG), dysgenesis of the corpus callosum and of the cortico-spinal tracts, along with brainstem and cerebellar abnormalities. Both exhibited extremely severe disrupted cortical lamination. Immunohistochemical studies provided the evidence for defects in cell proliferation and postmitotic neuroblast ability to exit from the subventricular zone resulting in a failure of radial migration toward the cortical plate, thus providing new insights for the understanding of the pathophysiology in these cortical malformations.
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Affiliation(s)
- Annie Laquerriere
- Department of Pathology, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen University Hospital, NeoVasc Team, UNIROUEN, Inserm U1245, Rouen, France
| | - Camille Maillard
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris and INSERM UMR-1163, Embryology and Genetics of Congenital Malformations, Paris France
| | - Mara Cavallin
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris and INSERM UMR-1163, Embryology and Genetics of Congenital Malformations, Paris France.,Pediatric Neurology, Necker Enfants Malades University Paris Hospital, APHP, Paris, France
| | | | - Florent Marguet
- Department of Pathology, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen University Hospital, NeoVasc Team, UNIROUEN, Inserm U1245, Rouen, France
| | - Arnaud Molin
- Service de Génétique Pôle Biologie et Pharmacie Rouen University Hôpital, France
| | - Sabine Sigaudy
- Clinical Genetics, Hôpital de La Timone, APHM, Marseille University Hospital, Marseille France
| | - Marie Blouet
- Department of Radiology, Caen University Hospital, Caen France
| | - Guillaume Benoist
- Department of Obstetrics and Gynaecology, Caen University Hospital, Caen France
| | - Carla Fernandez
- Department of Pathology and Neuropathology, La Timone University Hospital, Marseille, France
| | - Karine Poirier
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Denis Diderot School of Medicine, Sorbonne-Paris Cité University, Paris, France
| | - Jamel Chelly
- IGBMC, INSERM U964, CNRS UMR 7104, Université de Strasbourg, Illkirch, France.,Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sophie Thomas
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris and INSERM UMR-1163, Embryology and Genetics of Congenital Malformations, Paris France
| | - Nadia Bahi-Buisson
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris and INSERM UMR-1163, Embryology and Genetics of Congenital Malformations, Paris France.,Pediatric Neurology, Necker Enfants Malades University Paris Hospital, APHP, Paris, France
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53
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Gutierrez PA, Ackermann BE, Vershinin M, McKenney RJ. Differential effects of the dynein-regulatory factor Lissencephaly-1 on processive dynein-dynactin motility. J Biol Chem 2017; 292:12245-12255. [PMID: 28576829 DOI: 10.1074/jbc.m117.790048] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/01/2017] [Indexed: 02/02/2023] Open
Abstract
Cytoplasmic dynein is the primary minus-end-directed microtubule motor protein in animal cells, performing a wide range of motile activities, including transport of vesicular cargos, mRNAs, viruses, and proteins. Lissencephaly-1 (LIS1) is a highly conserved dynein-regulatory factor that binds directly to the dynein motor domain, uncoupling the enzymatic and mechanical cycles of the motor and stalling dynein on the microtubule track. Dynactin, another ubiquitous dynein-regulatory factor, releases dynein from an autoinhibited state, leading to a dramatic increase in fast, processive dynein motility. How these opposing activities are integrated to control dynein motility is unknown. Here, we used fluorescence single-molecule microscopy to study the interaction of LIS1 with the processive dynein-dynactin-BicD2N (DDB) complex. Surprisingly, in contrast to the prevailing model for LIS1 function established in the context of dynein alone, we found that binding of LIS1 to DDB does not strongly disrupt processive motility. Motile DDB complexes bound up to two LIS1 dimers, and mutational analysis suggested that LIS1 binds directly to the dynein motor domains during DDB movement. Interestingly, LIS1 enhanced DDB velocity in a concentration-dependent manner, in contrast to observations of the effect of LIS1 on the motility of isolated dynein. Thus, LIS1 exerts concentration-dependent effects on dynein motility and can synergize with dynactin to enhance processive dynein movement. Our results suggest that the effect of LIS1 on dynein motility depends on both LIS1 concentration and the presence of other regulatory factors such as dynactin and may provide new insights into the mechanism of LIS1 haploinsufficiency in the neurodevelopmental disorder lissencephaly.
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Affiliation(s)
- Pedro A Gutierrez
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, California 95616
| | - Bryce E Ackermann
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, California 95616
| | - Michael Vershinin
- Department of Physics & Astronomy, University of Utah, Salt Lake City, Utah 84112; Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California-Davis, Davis, California 95616.
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54
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Steinman JB, Santarossa CC, Miller RM, Yu LS, Serpinskaya AS, Furukawa H, Morimoto S, Tanaka Y, Nishitani M, Asano M, Zalyte R, Ondrus AE, Johnson AG, Ye F, Nachury MV, Fukase Y, Aso K, Foley MA, Gelfand VI, Chen JK, Carter AP, Kapoor TM. Chemical structure-guided design of dynapyrazoles, cell-permeable dynein inhibitors with a unique mode of action. eLife 2017; 6. [PMID: 28524820 PMCID: PMC5478271 DOI: 10.7554/elife.25174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/17/2017] [Indexed: 12/11/2022] Open
Abstract
Cytoplasmic dyneins are motor proteins in the AAA+ superfamily that transport cellular cargos toward microtubule minus-ends. Recently, ciliobrevins were reported as selective cell-permeable inhibitors of cytoplasmic dyneins. As is often true for first-in-class inhibitors, the use of ciliobrevins has in part been limited by low potency. Moreover, suboptimal chemical properties, such as the potential to isomerize, have hindered efforts to improve ciliobrevins. Here, we characterized the structure of ciliobrevins and designed conformationally constrained isosteres. These studies identified dynapyrazoles, inhibitors more potent than ciliobrevins. At single-digit micromolar concentrations dynapyrazoles block intraflagellar transport in the cilium and lysosome motility in the cytoplasm, processes that depend on cytoplasmic dyneins. Further, we find that while ciliobrevins inhibit both dynein's microtubule-stimulated and basal ATPase activity, dynapyrazoles strongly block only microtubule-stimulated activity. Together, our studies suggest that chemical-structure-based analyses can lead to inhibitors with improved properties and distinct modes of inhibition. DOI:http://dx.doi.org/10.7554/eLife.25174.001
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Affiliation(s)
- Jonathan B Steinman
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Cristina C Santarossa
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Rand M Miller
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Lola S Yu
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
| | - Anna S Serpinskaya
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Hideki Furukawa
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Sachie Morimoto
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Yuta Tanaka
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | | | - Moriteru Asano
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Ruta Zalyte
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alison E Ondrus
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Fan Ye
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Maxence V Nachury
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Yoshiyuki Fukase
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Kazuyoshi Aso
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Michael A Foley
- Tri-Institutitional Therapeutics Discovery Institute, New York, United States
| | - Vladimir I Gelfand
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Andrew P Carter
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, United States
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55
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Liu JJ. Regulation of dynein-dynactin-driven vesicular transport. Traffic 2017; 18:336-347. [PMID: 28248450 DOI: 10.1111/tra.12475] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 01/01/2023]
Abstract
Most of the long-range intracellular movements of vesicles, organelles and other cargoes are driven by microtubule (MT)-based molecular motors. Cytoplasmic dynein, a multisubunit protein complex, with the aid of dynactin, drives transport of a wide variety of cargoes towards the minus end of MTs. In this article, I review our current understanding of the mechanisms underlying spatiotemporal regulation of dynein-dynactin-driven vesicular transport with a special emphasis on the many steps of directional movement along MT tracks. These include the recruitment of dynein to MT plus ends, the activation and processivity of dynein, and cargo recognition and release by the motor complex at the target membrane. Furthermore, I summarize the most recent findings about the fine control mechanisms for intracellular transport via the interaction between the dynein-dynactin motor complex and its vesicular cargoes.
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Affiliation(s)
- Jia-Jia Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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56
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Mahale S, Kumar M, Sharma A, Babu A, Ranjan S, Sachidanandan C, Mylavarapu SVS. The Light Intermediate Chain 2 Subpopulation of Dynein Regulates Mitotic Spindle Orientation. Sci Rep 2016; 6:22. [PMID: 28003657 PMCID: PMC5431351 DOI: 10.1038/s41598-016-0030-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/03/2016] [Indexed: 12/11/2022] Open
Abstract
Cytoplasmic dynein 1 is a multi-protein intracellular motor essential for mediating several mitotic functions, including the establishment of proper spindle orientation. The functional relevance and mechanistic distinctions between two discrete dynein subpopulations distinguished only by Light Intermediate Chain (LIC) homologues, LIC1 and LIC2 is unknown during mitosis. Here, we identify LIC2-dynein as the major mediator of proper spindle orientation and uncover its underlying molecular mechanism. Cortically localized dynein, essential for maintaining correct spindle orientation, consists majorly of LIC2-dynein, which interacts with cortical 14-3-3 ε- ζ and Par3, conserved proteins required for orienting the spindle. LIC2-dynein is also responsible for the majority of dynein-mediated asymmetric poleward transport of NuMA, helping focus microtubule minus ends. In addition, LIC2-dynein dominates in equatorially aligning chromosomes at metaphase and in regulating mitotic spindle length. Key mitotic functions of LIC2 were remarkably conserved in and essential for early embryonic divisions and development in zebrafish. Thus LIC2-dynein exclusively engages with two major cortical pathways to govern spindle orientation. Overall, we identify a novel selectivity of molecular interactions between the two LICs in mitosis as the underlying basis for their uneven distribution of labour in ensuring proper spindle orientation.
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Affiliation(s)
- Sagar Mahale
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.,Affiliated to Manipal University, Manipal, Karnataka, 576104, India
| | - Megha Kumar
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India
| | - Amit Sharma
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.,Affiliated to Manipal University, Manipal, Karnataka, 576104, India
| | - Aswini Babu
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Shashi Ranjan
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi, 110025, India
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Sivaram V S Mylavarapu
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India. .,Affiliated to Manipal University, Manipal, Karnataka, 576104, India.
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57
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Mou L, Cui T, Liu W, Zhang H, Cai Z, Lu S, Gao G. Microsecond molecular dynamics simulations provide insight into the ATP-competitive inhibitor-induced allosteric protection of Akt kinase phosphorylation. Chem Biol Drug Des 2016; 89:723-731. [PMID: 27797456 DOI: 10.1111/cbdd.12895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/02/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
Akt is a serine/threonine protein kinase, a critical mediator of growth factor-induced survival in key cellular pathways. Allosteric signaling between protein intramolecular domains requires long-range communication mediated by hotspot residues, often triggered by ligand binding. Here, based on extensive 3 μs explicit solvent molecular dynamics (MD) simulations of Akt1 kinase domain in the unbound (apo) and ATP-competitive inhibitor, GDC-0068-bound states, we propose a molecular mechanism for allosteric regulation of Akt1 kinase phosphorylation by GDC-0068 binding to the ATP-binding site. MD simulations revealed that the apo Akt1 is flexible with two disengaged N- and C-lobes, equilibrated between the open and closed conformations. GDC-0068 occupancy of the ATP-binding site shifts the conformational equilibrium of Akt1 from the open conformation toward the closed conformation and stabilizes the closed state. This effect enables allosteric signal propagation from the GDC-0068 to the phosphorylated T308 (pT308) in the activation loop and restrains phosphatase access to pT308, thereby protecting the pT308 in the GDC-0068-bound Akt1. Importantly, functional hotspots involved in the allosteric communication from the GDC-0068 to the pT308 are identified. Our analysis of GDC-0068-induced allosteric protection of Akt kinase phosphorylation yields important new insights into the molecular mechanism of allosteric regulation of Akt kinase activity.
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Affiliation(s)
- Linkai Mou
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Tongwei Cui
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Weiguang Liu
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Hong Zhang
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhanxiu Cai
- Department of Electrical and Computer Engineering, College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong, China
| | - Shaoyong Lu
- Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Gao
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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58
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Abstract
Coiled‐coils are found in proteins throughout all three kingdoms of life. Coiled‐coil domains of some proteins are almost invariant in sequence and length, betraying a structural and functional role for amino acids along the entire length of the coiled‐coil. Other coiled‐coils are divergent in sequence, but conserved in length, thereby functioning as molecular spacers. In this capacity, coiled‐coil proteins influence the architecture of organelles such as centrioles and the Golgi, as well as permit the tethering of transport vesicles. Specialized coiled‐coils, such as those found in motor proteins, are capable of propagating conformational changes along their length that regulate cargo binding and motor processivity. Coiled‐coil domains have also been identified in enzymes, where they function as molecular rulers, positioning catalytic activities at fixed distances. Finally, while coiled‐coils have been extensively discussed for their potential to nucleate and scaffold large macromolecular complexes, structural evidence to substantiate this claim is relatively scarce.
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Affiliation(s)
- Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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59
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Schmidt H, Carter AP. Review: Structure and mechanism of the dynein motor ATPase. Biopolymers 2016; 105:557-67. [PMID: 27062277 PMCID: PMC4879348 DOI: 10.1002/bip.22856] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/21/2022]
Abstract
Dyneins are multiprotein complexes that move cargo along microtubules in the minus end direction. The largest individual component of the dynein complex is the heavy chain. Its C-terminal 3500 amino-acid residues form the motor domain, which hydrolyses ATP in its ring of AAA+ (ATPases associated with diverse cellular activities) domains to generate the force for movement. The production of force is synchronized with cycles of microtubule binding and release, another important prerequisite for efficient motility along the microtubule. Although the large scale conformational changes that lead to force production and microtubule affinity regulation are well established, it has been largely enigmatic how ATP-hydrolysis in the AAA+ ring causes these rearrangements. The past five years have seen a surge of high resolution information on the dynein motor domain that finally allowed unprecedented insights into this important open question. This review, part of the "ATP and GTP hydrolysis in Biology" special issue, will summarize our current understanding of the dynein motor mechanism with a special emphasis on the recently obtained crystal and EM structures. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 557-567, 2016.
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Affiliation(s)
- Helgo Schmidt
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Andrew P Carter
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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60
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Mahale SP, Sharma A, Mylavarapu SVS. Dynein Light Intermediate Chain 2 Facilitates the Metaphase to Anaphase Transition by Inactivating the Spindle Assembly Checkpoint. PLoS One 2016; 11:e0159646. [PMID: 27441562 PMCID: PMC4956306 DOI: 10.1371/journal.pone.0159646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/06/2016] [Indexed: 01/08/2023] Open
Abstract
The multi-functional molecular motor cytoplasmic dynein performs diverse essential roles during mitosis. The mechanistic importance of the dynein Light Intermediate Chain homologs, LIC1 and LIC2 is unappreciated, especially in the context of mitosis. LIC1 and LIC2 are believed to exist in distinct cytoplasmic dynein complexes as obligate subunits. LIC1 had earlier been reported to be required for metaphase to anaphase progression by inactivating the kinetochore-microtubule attachment-sensing arm of the spindle assembly checkpoint (SAC). However, the functional importance of LIC2 during mitosis remains elusive. Here we report prominent novel roles for the LIC2 subunit of cytoplasmic dynein in regulating the spindle assembly checkpoint. LIC2 depletion in mammalian cells led to prolonged metaphase arrest in the presence of an active SAC and also to stretched kinetochores, thus implicating it in SAC inactivation. Quantitative fluorescence microscopy of SAC components revealed accumulation of both attachment- and tension-sensing checkpoint proteins at metaphase kinetochores upon LIC2 depletion. These observations support a stronger and more diverse role in checkpoint inactivation for LIC2 in comparison to its close homolog LIC1. Our study uncovers a novel functional hierarchy during mitotic checkpoint inactivation between the closely related but homologous LIC subunits of cytoplasmic dynein. These subtle functional distinctions between dynein subpopulations could be exploited to study specific aspects of the spindle assembly checkpoint, which is a key mediator of fidelity in eukaryotic cell division.
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Affiliation(s)
- Sagar P. Mahale
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana, India
- Affiliated to Manipal University, Manipal, Karnataka, India
| | - Amit Sharma
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana, India
- Affiliated to Manipal University, Manipal, Karnataka, India
| | - Sivaram V. S. Mylavarapu
- Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana, India
- Affiliated to Manipal University, Manipal, Karnataka, India
- * E-mail:
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61
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Carter AP, Diamant AG, Urnavicius L. How dynein and dynactin transport cargos: a structural perspective. Curr Opin Struct Biol 2016; 37:62-70. [DOI: 10.1016/j.sbi.2015.12.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]
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62
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Bhabha G, Johnson GT, Schroeder CM, Vale RD. How Dynein Moves Along Microtubules. Trends Biochem Sci 2015; 41:94-105. [PMID: 26678005 DOI: 10.1016/j.tibs.2015.11.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 01/20/2023]
Abstract
Cytoplasmic dynein, a member of the AAA (ATPases Associated with diverse cellular Activities) family of proteins, drives the processive movement of numerous intracellular cargos towards the minus end of microtubules. Here, we summarize the structural and motile properties of dynein and highlight features that distinguish this motor from kinesin-1 and myosin V, two well-studied transport motors. Integrating information from recent crystal and cryoelectron microscopy structures, as well as high-resolution single-molecule studies, we also discuss models for how dynein biases its movement in one direction along a microtubule track, and present a movie that illustrates these principles.
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Affiliation(s)
- Gira Bhabha
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Graham T Johnson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA
| | - Courtney M Schroeder
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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63
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Structural Change in the Dynein Stalk Region Associated with Two Different Affinities for the Microtubule. J Mol Biol 2015; 428:1886-96. [PMID: 26585405 DOI: 10.1016/j.jmb.2015.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/08/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022]
Abstract
Dynein is a large microtubule-based motor complex that requires tight coupling of intra-molecular ATP hydrolysis with the generation of mechanical force and track-binding activity. However, the microtubule-binding domain is structurally separated by about 15nm from the nucleotide-binding sites by a coiled-coil stalk. Thus, long-range two-way communication is necessary for coordination between the catalytic cycle of ATP hydrolysis and dynein's track-binding affinities. To investigate the structural changes that occur in the dynein stalk region to produce two different microtubule affinities, here we improve the resolution limit of the previously reported structure of the entire stalk region and we investigate structural changes in the dynein stalk and strut/buttress regions by comparing currently available X-ray structures. In the light of recent crystal structures, the basis of the transition from the low-affinity to the high-affinity coiled-coil registry is discussed. A concerted movement model previously reported by Carter and Vale is modified more specifically, and we proposed it as the open zipper model.
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64
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Abstract
Torsin ATPases (Torsins) belong to the widespread AAA+ (ATPases associated with a variety of cellular activities) family of ATPases, which share structural similarity but have diverse cellular functions. Torsins are outliers in this family because they lack many characteristics of typical AAA+ proteins, and they are the only members of the AAA+ family located in the endoplasmic reticulum and contiguous perinuclear space. While it is clear that Torsins have essential roles in many, if not all metazoans, their precise cellular functions remain elusive. Studying Torsins has significant medical relevance since mutations in Torsins or Torsin-associated proteins result in a variety of congenital human disorders, the most frequent of which is early-onset torsion (DYT1) dystonia, a severe movement disorder. A better understanding of the Torsin system is needed to define the molecular etiology of these diseases, potentially enabling corrective therapy. Here, we provide a comprehensive overview of the Torsin system in metazoans, discuss functional clues obtained from various model systems and organisms and provide a phylogenetic and structural analysis of Torsins and their regulatory cofactors in relation to disease-causative mutations. Moreover, we review recent data that have led to a dramatically improved understanding of these machines at a molecular level, providing a foundation for investigating the molecular defects underlying the associated movement disorders. Lastly, we discuss our ideas on how recent progress may be utilized to inform future studies aimed at determining the cellular role(s) of these atypical molecular machines and their implications for dystonia treatment options.
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Affiliation(s)
- April E Rose
- a Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA and
| | - Rebecca S H Brown
- a Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA and
| | - Christian Schlieker
- a Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA and.,b Department of Cell Biology , Yale School of Medicine , New Haven , CT , USA
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65
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Cianfrocco MA, DeSantis ME, Leschziner AE, Reck-Peterson SL. Mechanism and regulation of cytoplasmic dynein. Annu Rev Cell Dev Biol 2015; 31:83-108. [PMID: 26436706 DOI: 10.1146/annurev-cellbio-100814-125438] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Until recently, dynein was the least understood of the cytoskeletal motors. However, a wealth of new structural, mechanistic, and cell biological data is shedding light on how this complicated minus-end-directed, microtubule-based motor works. Cytoplasmic dynein-1 performs a wide array of functions in most eukaryotes, both in interphase, in which it transports organelles, proteins, mRNAs, and viruses, and in mitosis and meiosis. Mutations in dynein or its regulators are linked to neurodevelopmental and neurodegenerative diseases. Here, we begin by providing a synthesis of recent data to describe the current model of dynein's mechanochemical cycle. Next, we discuss regulators of dynein, with particular focus on those that directly interact with the motor to modulate its recruitment to microtubules, initiate cargo transport, or activate minus-end-directed motility.
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Affiliation(s)
- Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Morgan E DeSantis
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093;
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66
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Filippova EV, Weigand S, Osipiuk J, Kiryukhina O, Joachimiak A, Anderson WF. Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG. J Mol Biol 2015; 427:3538-3553. [PMID: 26410587 DOI: 10.1016/j.jmb.2015.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/12/2023]
Abstract
The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulate their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligand-free form in three different conformational states: open, intermediate and closed. All structures were crystallized in C2 space group symmetry and contain six monomers in the asymmetric unit cell. Two hexamers related by crystallographic 2-fold symmetry form the SpeG dodecamer. The open and intermediate states have a unique open dodecameric ring. This SpeG dodecamer is asymmetric except for the one 2-fold axis and is unlike any known dodecameric structure. Using a fluorescence thermal shift assay, size-exclusion chromatography with multi-angle light scattering, small-angle X-ray scattering analysis, negative-stain electron microscopy and structural analysis, we demonstrate that this unique open dodecameric state exists in solution. Our combined results indicate that polyamines trigger conformational changes and induce the symmetric closed dodecameric state of the protein when they bind to their allosteric sites.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University , Chicago, IL 60611, USA
| | - Steven Weigand
- DuPont-Northwestern-Dow Collaborative Access Team, Northwestern University Synchrotron Research Center, Argonne, IL 60439, USA
| | - Jerzy Osipiuk
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Olga Kiryukhina
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University , Chicago, IL 60611, USA
| | - Andrzej Joachimiak
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Northwestern University , Chicago, IL 60611, USA.
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67
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Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proc Natl Acad Sci U S A 2015; 112:E4017-25. [PMID: 26170309 DOI: 10.1073/pnas.1500257112] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Members of the AAA family of ATPases assemble into hexameric double rings and perform vital functions, yet their molecular mechanisms remain poorly understood. Here, we report structures of the Pex1/Pex6 complex; mutations in these proteins frequently cause peroxisomal diseases. The structures were determined in the presence of different nucleotides by cryo-electron microscopy. Models were generated using a computational approach that combines Monte Carlo placement of structurally homologous domains into density maps with energy minimization and refinement protocols. Pex1 and Pex6 alternate in an unprecedented hexameric double ring. Each protein has two N-terminal domains, N1 and N2, structurally related to the single N domains in p97 and N-ethylmaleimide sensitive factor (NSF); N1 of Pex1 is mobile, but the others are packed against the double ring. The N-terminal ATPase domains are inactive, forming a symmetric D1 ring, whereas the C-terminal domains are active, likely in different nucleotide states, and form an asymmetric D2 ring. These results suggest how subunit activity is coordinated and indicate striking similarities between Pex1/Pex6 and p97, supporting the hypothesis that the Pex1/Pex6 complex has a role in peroxisomal protein import analogous to p97 in ER-associated protein degradation.
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68
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Alonso A, Greenlee M, Matts J, Kline J, Davis KJ, Miller RK. Emerging roles of sumoylation in the regulation of actin, microtubules, intermediate filaments, and septins. Cytoskeleton (Hoboken) 2015; 72:305-39. [PMID: 26033929 PMCID: PMC5049490 DOI: 10.1002/cm.21226] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/25/2015] [Accepted: 05/27/2015] [Indexed: 12/29/2022]
Abstract
Sumoylation is a powerful regulatory system that controls many of the critical processes in the cell, including DNA repair, transcriptional regulation, nuclear transport, and DNA replication. Recently, new functions for SUMO have begun to emerge. SUMO is covalently attached to components of each of the four major cytoskeletal networks, including microtubule-associated proteins, septins, and intermediate filaments, in addition to nuclear actin and actin-regulatory proteins. However, knowledge of the mechanisms by which this signal transduction system controls the cytoskeleton is still in its infancy. One story that is beginning to unfold is that SUMO may regulate the microtubule motor protein dynein by modification of its adaptor Lis1. In other instances, cytoskeletal elements can both bind to SUMO non-covalently and also be conjugated by it. The molecular mechanisms for many of these new functions are not yet clear, but are under active investigation. One emerging model links the function of MAP sumoylation to protein degradation through SUMO-targeted ubiquitin ligases, also known as STUbL enzymes. Other possible functions for cytoskeletal sumoylation are also discussed.
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Affiliation(s)
- Annabel Alonso
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Matt Greenlee
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Jessica Matts
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Jake Kline
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Kayla J. Davis
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
| | - Rita K. Miller
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOklahoma
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69
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Xiang X, Qiu R, Yao X, Arst HN, Peñalva MA, Zhang J. Cytoplasmic dynein and early endosome transport. Cell Mol Life Sci 2015; 72:3267-80. [PMID: 26001903 DOI: 10.1007/s00018-015-1926-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 11/25/2022]
Abstract
Microtubule-based distribution of organelles/vesicles is crucial for the function of many types of eukaryotic cells and the molecular motor cytoplasmic dynein is required for transporting a variety of cellular cargos toward the microtubule minus ends. Early endosomes represent a major cargo of dynein in filamentous fungi, and dynein regulators such as LIS1 and the dynactin complex are both required for early endosome movement. In fungal hyphae, kinesin-3 and dynein drive bi-directional movements of early endosomes. Dynein accumulates at microtubule plus ends; this accumulation depends on kinesin-1 and dynactin, and it is important for early endosome movements towards the microtubule minus ends. The physical interaction between dynein and early endosome requires the dynactin complex, and in particular, its p25 component. The FTS-Hook-FHIP (FHF) complex links dynein-dynactin to early endosomes, and within the FHF complex, Hook interacts with dynein-dynactin, and Hook-early endosome interaction depends on FHIP and FTS.
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Affiliation(s)
- Xin Xiang
- Department of Biochemistry and Molecular Biology, F. Edward Hébert School of Medicine, The Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA,
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70
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Cytoplasmic dynein regulates its attachment to microtubules via nucleotide state-switched mechanosensing at multiple AAA domains. Proc Natl Acad Sci U S A 2015; 112:6371-6. [PMID: 25941405 DOI: 10.1073/pnas.1417422112] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cytoplasmic dynein is a homodimeric microtubule (MT) motor protein responsible for most MT minus-end-directed motility. Dynein contains four AAA+ ATPases (AAA: ATPase associated with various cellular activities) per motor domain (AAA1-4). The main site of ATP hydrolysis, AAA1, is the only site considered by most dynein motility models. However, it remains unclear how ATPase activity and MT binding are coordinated within and between dynein's motor domains. Using optical tweezers, we characterize the MT-binding strength of recombinant dynein monomers as a function of mechanical tension and nucleotide state. Dynein responds anisotropically to tension, binding tighter to MTs when pulled toward the MT plus end. We provide evidence that this behavior results from an asymmetrical bond that acts as a slip bond under forward tension and a slip-ideal bond under backward tension. ATP weakens MT binding and reduces bond strength anisotropy, and unexpectedly, so does ADP. Using nucleotide binding and hydrolysis mutants, we show that, although ATP exerts its effects via binding AAA1, ADP effects are mediated by AAA3. Finally, we demonstrate "gating" of AAA1 function by AAA3. When tension is absent or applied via dynein's C terminus, ATP binding to AAA1 induces MT release only if AAA3 is in the posthydrolysis state. However, when tension is applied to the linker, ATP binding to AAA3 is sufficient to "open" the gate. These results elucidate the mechanisms of dynein-MT interactions, identify regulatory roles for AAA3, and help define the interplay between mechanical tension and nucleotide state in regulating dynein motility.
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71
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Schmidt H. Dynein motors: How AAA+ ring opening and closing coordinates microtubule binding and linker movement. Bioessays 2015; 37:532-43. [DOI: 10.1002/bies.201400215] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Helgo Schmidt
- Medical Research Council Laboratory of Molecular Biology; Division of Structural Studies; Cambridge UK
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