1
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Schleske JM, Hubrich J, Wirth JO, D'Este E, Engelhardt J, Hell SW. MINFLUX reveals dynein stepping in live neurons. Proc Natl Acad Sci U S A 2024; 121:e2412241121. [PMID: 39254993 DOI: 10.1073/pnas.2412241121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
Dynein is the primary molecular motor responsible for retrograde intracellular transport of a variety of cargoes, performing successive nanometer-sized steps within milliseconds. Due to the limited spatiotemporal precision of established methods for molecular tracking, current knowledge of dynein stepping is essentially limited to slowed-down measurements in vitro. Here, we use MINFLUX fluorophore localization to directly track CRISPR/Cas9-tagged endogenous dynein with nanometer/millisecond precision in living primary neurons. We show that endogenous dynein primarily takes 8 nm steps, including frequent sideways steps but few backward steps. Strikingly, the majority of direction reversals between retrograde and anterograde movement occurred on the time scale of single steps (16 ms), suggesting a rapid regulatory reversal mechanism. Tug-of-war-like behavior during pauses or reversals was unexpectedly rare. By analyzing the dwell time between steps, we concluded that a single rate-limiting process underlies the dynein stepping mechanism, likely arising from just one adenosine 5'-triphosphate hydrolysis event being required during each step. Our study underscores the power of MINFLUX localization to elucidate the spatiotemporal changes underlying protein function in living cells.
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Affiliation(s)
- Jonas M Schleske
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Jasmine Hubrich
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Jan Otto Wirth
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Elisa D'Este
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Johann Engelhardt
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg 69120, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
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Zimmermann N, Ishikawa T. Comparative structural study on axonemal and cytoplasmic dyneins. Cytoskeleton (Hoboken) 2024. [PMID: 39073294 DOI: 10.1002/cm.21897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
Axonemal dyneins are the driving force of motile cilia, while cytoplasmic dyneins play an essential role in minus-end oriented intracellular transport. Their molecular structure is indispensable for an understanding of the molecular mechanism of ciliary beating and cargo transport. After some initial structural analysis of cytoplasmic dyneins, which are easier to manipulate with genetic engineering, using X-ray crystallography and single-particle cryo-electron microscopy, a number of atomic and pseudo-atomic structural analyses of axonemal dyneins have been published. Currently, several structures of dyneins in the post-power stroke conformation as well as a few structures in the pre-power stroke conformation are available. It will be worth systematically comparing conformations of dynein motor proteins from different sources and at different states, to understand their role in biological function. In this review, we will overview published high- and intermediate-resolution structures of cytoplasmic and axonemal dyneins, compare the high-resolution structures of their core motor domains and overall tail conformations at various nucleotide states, and discuss their force generation mechanism.
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Affiliation(s)
- Noemi Zimmermann
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zürich, Switzerland
| | - Takashi Ishikawa
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zürich, Switzerland
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3
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Cuccurullo C, Cerulli Irelli E, Ugga L, Riva A, D'Amico A, Cabet S, Lesca G, Bilo L, Zara F, Iliescu C, Barca D, Fung F, Helbig K, Ortiz-Gonzalez X, Schelhaas HJ, Willemsen MH, van der Linden I, Canafoglia L, Courage C, Gommaraschi S, Gonzalez-Alegre P, Bardakjian T, Syrbe S, Schuler E, Lemke JR, Vari S, Roende G, Bak M, Huq M, Powis Z, Johannesen KM, Hammer TB, Møller RS, Rabin R, Pappas J, Zupanc ML, Zadeh N, Cohen J, Naidu S, Krey I, Saneto R, Thies J, Licchetta L, Tinuper P, Bisulli F, Minardi R, Bayat A, Villeneuve N, Molinari F, Salimi Dafsari H, Moller B, Le Roux M, Houdayer C, Vecchi M, Mammi I, Fiorini E, Proietti J, Ferri S, Cantalupo G, Battaglia DI, Gambardella ML, Contaldo I, Brogna C, Trivisano M, De Dominicis A, Bova SM, Gardella E, Striano P, Coppola A. Clinical features and genotype-phenotype correlations in epilepsy patients with de novo DYNC1H1 variants. Epilepsia 2024. [PMID: 38953796 DOI: 10.1111/epi.18054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
OBJECTIVE DYNC1H1 variants are involved on a disease spectrum from neuromuscular disorders to neurodevelopmental disorders. DYNC1H1-related epilepsy has been reported in small cohorts. We dissect the electroclinical features of 34 patients harboring de novo DYNC1H1 pathogenic variants, identify subphenotypes on the DYNC1H1-related epilepsy spectrum, and compare the genotype-phenotype correlations observed in our cohort with the literature. METHODS Patients harboring de novo DYNC1H1 pathogenic variants were recruited through international collaborations. Clinical data were retrospectively collected. Latent class analysis was performed to identify subphenotypes. Multivariable binary logistic regression analysis was applied to investigate the association with DYNC1H1 protein domains. RESULTS DYNC1H1-related epilepsy presented with infantile epileptic spasms syndrome (IESS) in 17 subjects (50%), and in 25% of these individuals the epileptic phenotype evolved into Lennox-Gastaut syndrome (LGS). In 12 patients (35%), focal onset epilepsy was defined. In two patients, the epileptic phenotype consisted of generalized myoclonic epilepsy, with a progressive phenotype in one individual harboring a frameshift variant. In approximately 60% of our cohort, seizures were drug-resistant. Malformations of cortical development were noticed in 79% of our patients, mostly on the lissencephaly-pachygyria spectrum, particularly with posterior predominance in a half of them. Midline and infratentorial abnormalities were additionally reported in 45% and 27% of subjects. We have identified three main classes of subphenotypes on the DYNC1H1-related epilepsy spectrum. SIGNIFICANCE We propose a classification in which pathogenic de novo DYNC1H1 variants feature drug-resistant IESS in half of cases with potential evolution to LGS (Class 1), developmental and epileptic encephalopathy other than IESS and LGS (Class 2), or less severe focal or genetic generalized epilepsy including a progressive phenotype (Class 3). We observed an association between stalk domain variants and Class 1 phenotypes. The variants p.Arg309His and p.Arg1962His were common and associated with Class 1 subphenotype in our cohort. These findings may aid genetic counseling of patients with DYNC1H1-related epilepsy.
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Affiliation(s)
- Claudia Cuccurullo
- Epilepsy Center, Department of Neuroscience, Reproductive and Odontostomatological Sciences, Federico II University of Naples, Naples, Italy
- Neurology and Stroke Unit, Ospedale del Mare Hospital, Naples, Italy
| | | | - Lorenzo Ugga
- Department of Advanced Biomedical Sciences, University Federico II, Naples, Italy
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- Medical Genetic Unit, Istituti di Ricovero e Cura a Carattere Scientifico Istituto Giannina Gaslini, Genoa, Italy
| | | | - Sara Cabet
- Pediatric and Fetal Imaging, Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Lyon, France
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Institut NeuroMyoGene, CNRS UMR5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Leonilda Bilo
- Epilepsy Center, Department of Neuroscience, Reproductive and Odontostomatological Sciences, Federico II University of Naples, Naples, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- Medical Genetic Unit, Istituti di Ricovero e Cura a Carattere Scientifico Istituto Giannina Gaslini, Genoa, Italy
| | - Catrinel Iliescu
- Department of Clinical Neurosciences, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Diana Barca
- Department of Pediatric Neurology, Expertise Center for Rare Diseases in Pediatric Neurology, member of the EpiCARE European Reference Network, "Prof. Dr. Alex. Obregia" Clinical Hospital, Bucharest, Romania
| | - France Fung
- Department of Pediatrics and Neurology, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Katherine Helbig
- Department of Pediatrics and Neurology, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xilma Ortiz-Gonzalez
- Department of Pediatrics and Neurology, Children's Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Inge van der Linden
- Department of Neurology, Epilepsy Center Kempenhaeghe, Heeze, the Netherlands
| | - Laura Canafoglia
- Integrated Diagnostics for Epilepsy, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Carolina Courage
- Folkhälsan Research Center, Helsinki, Finland
- Department of Biomedical and Clinical Science, University of Milan, Milan, Italy
| | - Samuele Gommaraschi
- Department of Biomedical and Clinical Science, University of Milan, Milan, Italy
| | - Pedro Gonzalez-Alegre
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, Philadelphia, USA
| | - Tanya Bardakjian
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, Philadelphia, USA
| | - Steffen Syrbe
- Division of Paediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Elisabeth Schuler
- Division of Paediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Johannes R Lemke
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Stella Vari
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, "G. Gaslini" Institute, University of Genoa, Genoa, Italy
| | - Gitte Roende
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshopitalet, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Mahbulul Huq
- Department of Pediatrics, Wayne State University, Detroit, Michigan, USA
| | - Zoe Powis
- Ambry Genetics, Department of Emerging Genetic Medicine, CGC 15 Argonaut, Aliso Viejo, California, USA
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
| | - Trine Bjørg Hammer
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
| | - Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU Grossman School of Medicine, New York, New York, USA
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU Grossman School of Medicine, New York, New York, USA
| | - Mary L Zupanc
- Children's Health of Orange County, Orange, California, USA
| | - Neda Zadeh
- Genetics Center and Division of Medical Genetics, Children's Hospital of Orange County, Orange, California, USA
| | - Julie Cohen
- Department of Neurology, Kennedy Krieger Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sakkubai Naidu
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Russell Saneto
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
| | - Jenny Thies
- Seattle Children's Research Institute, University of Washington, Seattle, Washington, USA
| | - Laura Licchetta
- IRCCS, Istituto Delle Scienze Neurologiche di Bologna, full member of the EpiCARE European Reference Network, Bologna, Italy
| | - Paolo Tinuper
- IRCCS, Istituto Delle Scienze Neurologiche di Bologna, full member of the EpiCARE European Reference Network, Bologna, Italy
| | - Francesca Bisulli
- IRCCS, Istituto Delle Scienze Neurologiche di Bologna, full member of the EpiCARE European Reference Network, Bologna, Italy
| | - Raffaella Minardi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Allan Bayat
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | | | - Florence Molinari
- Biolab, PolitoBIOMedLab, Department of Electronics and Telecommunications, Politecnico di Torino, Turin, Italy
| | - Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
- Department of Paediatric Neurology, Evelina's Children Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
- Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, King's College London, London, UK
| | - Birk Moller
- Department of Pediatrics, Faculty of Medicine, University of Cologne and University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marie Le Roux
- Department of Pediatric Neurology and Neurosurgery, CHU, Angers, France
| | - Clara Houdayer
- Service de Génétique Médicale, Université d'Angers, CHU d'Angers, Inserm, CNRS, MITOVASC, SFR ICAT, Angers, France
| | | | | | - Elena Fiorini
- Child Neuropsychiatry Unit, University Hospital of Verona, full member of the EpiCARE European Reference Network, Verona, Italy
- Center for Research on Epilepsy in Pediatric Age, University Hospital of Verona, Verona, Italy
| | - Jacopo Proietti
- Child Neuropsychiatry Unit, University Hospital of Verona, full member of the EpiCARE European Reference Network, Verona, Italy
- Center for Research on Epilepsy in Pediatric Age, University Hospital of Verona, Verona, Italy
| | - Sofia Ferri
- Child Neuropsychiatry Unit, University Hospital of Verona, full member of the EpiCARE European Reference Network, Verona, Italy
| | - Gaetano Cantalupo
- Child Neuropsychiatry Unit, University Hospital of Verona, full member of the EpiCARE European Reference Network, Verona, Italy
- Center for Research on Epilepsy in Pediatric Age, University Hospital of Verona, Verona, Italy
- Innovation Biomedicine Section, Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Domenica Immacolata Battaglia
- Pediatric Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Ilaria Contaldo
- Pediatric Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudia Brogna
- Pediatric Neurology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Neuropsychiatric Unit, ASL Avellino, Avellino, Italy
| | - Marina Trivisano
- Neurology, Epilepsy, and Movement Disorders, Bambino Gesù Children's Hospital, IRCCS, full member of the EpiCARE European Reference Network, Rome, Italy
| | | | | | - Elena Gardella
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, "G. Gaslini" Institute, University of Genoa, Genoa, Italy
| | - Antonietta Coppola
- Epilepsy Center, Department of Neuroscience, Reproductive and Odontostomatological Sciences, Federico II University of Naples, Naples, Italy
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Golcuk M, Yilmaz SZ, Yildiz A, Gur M. The mechanism and energetics of the dynein priming stroke. Structure 2024; 32:603-610.e4. [PMID: 38430911 DOI: 10.1016/j.str.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Dyneins are an AAA+ motor responsible for motility and force generation toward the minus end of microtubules. Dynein motility is powered by nucleotide-dependent transitions of its linker domain, which transitions between straight (post-powerstroke) and bent (pre-powerstroke) conformations. To understand the dynamics and energetics of the linker, we performed all-atom molecular dynamics simulations of human dynein-2 primed for its power stroke. Simulations revealed that the linker can adopt either a bent conformation or a semi-bent conformation, separated by a 5.7 kT energy barrier. The linker cannot switch back to its straight conformation in the pre-powerstroke state due to a steric clash with the AAA+ ring. Simulations also showed that an isolated linker has a free energy minimum near the semi-bent conformation in the absence of the AAA+ ring, indicating that the linker stores energy as it bends and releases this energy during the powerstroke.
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Affiliation(s)
- Mert Golcuk
- Department of Mechanical Engineering, Istanbul Technical University (ITU), Istanbul 34437, Turkey
| | - Sema Zeynep Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University (ITU), Istanbul 34437, Turkey
| | - Ahmet Yildiz
- Physics Department, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University (ITU), Istanbul 34437, Turkey; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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5
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Kusakci E, Htet ZM, Zhao Y, Gillies JP, Reck-Peterson SL, Yildiz A. Lis1 slows force-induced detachment of cytoplasmic dynein from microtubules. Nat Chem Biol 2024; 20:521-529. [PMID: 37919547 PMCID: PMC11164236 DOI: 10.1038/s41589-023-01464-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/29/2023] [Indexed: 11/04/2023]
Abstract
Lis1 is a key cofactor for the assembly of active cytoplasmic dynein complexes that transport cargo along microtubules. Lis1 binds to the AAA+ ring and stalk of dynein and slows dynein motility, but the underlying mechanism has remained unclear. Using single-molecule imaging and optical trapping assays, we investigated how Lis1 binding affects the motility and force generation of yeast dynein in vitro. We showed that Lis1 slows motility by binding to the AAA+ ring of dynein, not by serving as a roadblock or tethering dynein to microtubules. Lis1 binding also does not affect force generation, but it induces prolonged stalls and reduces the asymmetry in the force-induced detachment of dynein from microtubules. The mutagenesis of the Lis1-binding sites on the dynein stalk partially recovers this asymmetry but does not restore dynein velocity. These results suggest that Lis1-stalk interaction slows the detachment of dynein from microtubules by interfering with the stalk sliding mechanism.
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Affiliation(s)
- Emre Kusakci
- Graduate Group in Biophysics, University of California Berkeley, Berkeley, CA, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Yuanchang Zhao
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Physics Department, University of California Berkeley, Berkeley, CA, USA
| | - John P Gillies
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ahmet Yildiz
- Graduate Group in Biophysics, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Physics Department, University of California Berkeley, Berkeley, CA, USA.
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6
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Singh K, Lau CK, Manigrasso G, Gama JB, Gassmann R, Carter AP. Molecular mechanism of dynein-dynactin complex assembly by LIS1. Science 2024; 383:eadk8544. [PMID: 38547289 PMCID: PMC7615804 DOI: 10.1126/science.adk8544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/09/2024] [Indexed: 04/02/2024]
Abstract
Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
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Affiliation(s)
- Kashish Singh
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Clinton K. Lau
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Giulia Manigrasso
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - José B. Gama
- Instituto de Investigação e Inovação em Saúde – i3S / Instituto de Biologia Molecular e Celular – IBMC, Universidade do Porto, 4200-135 Porto, Portugal
| | - Reto Gassmann
- Instituto de Investigação e Inovação em Saúde – i3S / Instituto de Biologia Molecular e Celular – IBMC, Universidade do Porto, 4200-135 Porto, Portugal
| | - Andrew P. Carter
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, CB2 0QH, UK
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Wang B, Lu Y. Collective Molecular Machines: Multidimensionality and Reconfigurability. NANO-MICRO LETTERS 2024; 16:155. [PMID: 38499833 PMCID: PMC10948734 DOI: 10.1007/s40820-024-01379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 03/20/2024]
Abstract
Molecular machines are key to cellular activity where they are involved in converting chemical and light energy into efficient mechanical work. During the last 60 years, designing molecular structures capable of generating unidirectional mechanical motion at the nanoscale has been the topic of intense research. Effective progress has been made, attributed to advances in various fields such as supramolecular chemistry, biology and nanotechnology, and informatics. However, individual molecular machines are only capable of producing nanometer work and generally have only a single functionality. In order to address these problems, collective behaviors realized by integrating several or more of these individual mechanical units in space and time have become a new paradigm. In this review, we comprehensively discuss recent developments in the collective behaviors of molecular machines. In particular, collective behavior is divided into two paradigms. One is the appropriate integration of molecular machines to efficiently amplify molecular motions and deformations to construct novel functional materials. The other is the construction of swarming modes at the supramolecular level to perform nanoscale or microscale operations. We discuss design strategies for both modes and focus on the modulation of features and properties. Subsequently, in order to address existing challenges, the idea of transferring experience gained in the field of micro/nano robotics is presented, offering prospects for future developments in the collective behavior of molecular machines.
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Affiliation(s)
- Bin Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, People's Republic of China.
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8
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Rao L, Gennerich A. Structure and Function of Dynein's Non-Catalytic Subunits. Cells 2024; 13:330. [PMID: 38391943 PMCID: PMC10886578 DOI: 10.3390/cells13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Dynein, an ancient microtubule-based motor protein, performs diverse cellular functions in nearly all eukaryotic cells, with the exception of land plants. It has evolved into three subfamilies-cytoplasmic dynein-1, cytoplasmic dynein-2, and axonemal dyneins-each differentiated by their cellular functions. These megadalton complexes consist of multiple subunits, with the heavy chain being the largest subunit that generates motion and force along microtubules by converting the chemical energy of ATP hydrolysis into mechanical work. Beyond this catalytic core, the functionality of dynein is significantly enhanced by numerous non-catalytic subunits. These subunits are integral to the complex, contributing to its stability, regulating its enzymatic activities, targeting it to specific cellular locations, and mediating its interactions with other cofactors. The diversity of non-catalytic subunits expands dynein's cellular roles, enabling it to perform critical tasks despite the conservation of its heavy chains. In this review, we discuss recent findings and insights regarding these non-catalytic subunits.
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Affiliation(s)
- Lu Rao
- Department of Biochemistry and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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9
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Sakato-Antoku M, Patel-King RS, Balsbaugh JL, King SM. Methylation of ciliary dynein motors involves the essential cytosolic assembly factor DNAAF3/PF22. Proc Natl Acad Sci U S A 2024; 121:e2318522121. [PMID: 38261620 PMCID: PMC10835030 DOI: 10.1073/pnas.2318522121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (Dynein Axonemal Assembly Factors; DNAAFs) are necessary for axonemal dynein assembly, although the detailed mechanisms involved remain very unclear. Here, we identify the essential assembly factor DNAAF3 as a structural ortholog of S-adenosylmethionine-dependent methyltransferases. We demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
| | - Ramila S. Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT06269
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT06030-3305
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10
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Kosugi T, Iida T, Tanabe M, Iino R, Koga N. Design of allosteric sites into rotary motor V 1-ATPase by restoring lost function of pseudo-active sites. Nat Chem 2023; 15:1591-1598. [PMID: 37414880 PMCID: PMC10624635 DOI: 10.1038/s41557-023-01256-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
Allostery produces concerted functions of protein complexes by orchestrating the cooperative work between the constituent subunits. Here we describe an approach to create artificial allosteric sites in protein complexes. Certain protein complexes contain subunits with pseudo-active sites, which are believed to have lost functions during evolution. Our hypothesis is that allosteric sites in such protein complexes can be created by restoring the lost functions of pseudo-active sites. We used computational design to restore the lost ATP-binding ability of the pseudo-active site in the B subunit of a rotary molecular motor, V1-ATPase. Single-molecule experiments with X-ray crystallography analyses revealed that binding of ATP to the designed allosteric site boosts this V1's activity compared with the wild-type, and the rotation rate can be tuned by modulating ATP's binding affinity. Pseudo-active sites are widespread in nature, and our approach shows promise as a means of programming allosteric control over concerted functions of protein complexes.
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Affiliation(s)
- Takahiro Kosugi
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki, Japan.
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Japan.
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Tatsuya Iida
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki, Japan
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Mikio Tanabe
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Ryota Iino
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki, Japan
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Nobuyasu Koga
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science (IMS), National Institutes of Natural Sciences (NINS), Okazaki, Japan.
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Japan.
- Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan.
- Institute for Protein Research (IPR), Osaka University, Suita, Japan.
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11
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Shvarev D, Scholz AI, Moeller A. Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis. mBio 2023; 14:e0189323. [PMID: 37737632 PMCID: PMC10653834 DOI: 10.1128/mbio.01893-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
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Affiliation(s)
- Dmitry Shvarev
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Alischa Ira Scholz
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Arne Moeller
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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12
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Sakato-Antoku M, Balsbaugh JL, King SM. N-Terminal Processing and Modification of Ciliary Dyneins. Cells 2023; 12:2492. [PMID: 37887336 PMCID: PMC10605206 DOI: 10.3390/cells12202492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Axonemal dyneins are highly complex microtubule motors that power ciliary motility. These multi-subunit enzymes are assembled at dedicated sites within the cytoplasm. At least nineteen cytosolic factors are specifically needed to generate dynein holoenzymes and/or for their trafficking to the growing cilium. Many proteins are subject to N-terminal processing and acetylation, which can generate degrons subject to the AcN-end rule, alter N-terminal electrostatics, generate new binding interfaces, and affect subunit stoichiometry through targeted degradation. Here, we have used mass spectrometry of cilia samples and electrophoretically purified dynein heavy chains from Chlamydomonas to define their N-terminal processing; we also detail the N-terminal acetylase complexes present in this organism. We identify four classes of dynein heavy chain based on their processing pathways by two distinct acetylases, one of which is dependent on methionine aminopeptidase activity. In addition, we find that one component of both the outer dynein arm intermediate/light chain subcomplex and the docking complex is processed to yield an unmodified Pro residue, which may provide a setpoint to direct the cytosolic stoichiometry of other dynein complex subunits that contain N-terminal degrons. Thus, we identify and describe an additional level of processing and complexity in the pathways leading to axonemal dynein formation in cytoplasm.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269, USA;
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;
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13
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Ton WD, Wang Y, Chai P, Beauchamp-Perez C, Flint NT, Lammers LG, Xiong H, Zhang K, Markus SM. Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Nat Struct Mol Biol 2023; 30:1365-1379. [PMID: 37322240 PMCID: PMC10590275 DOI: 10.1038/s41594-023-01010-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/28/2023] [Indexed: 06/17/2023]
Abstract
The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 binding is required for dynein activity, its unbinding prior to initiation of cargo transport is equally important, since preventing dissociation leads to dynein dysfunction. To understand whether and how dynein-LIS1 binding is modulated, we engineered dynein mutants locked in a microtubule-bound (MT-B) or microtubule-unbound (MT-U) state. Whereas the MT-B mutant exhibits low LIS1 affinity, the MT-U mutant binds LIS1 with high affinity, and as a consequence remains almost irreversibly associated with microtubule plus-ends. We find that a monomeric motor domain is sufficient to exhibit these opposing LIS1 affinities, and that this is evolutionarily conserved between yeast and humans. Three cryo-EM structures of human dynein with and without LIS1 reveal microtubule-binding induced conformational changes responsible for this regulation. Our work reveals key biochemical and structural insight into LIS1-mediated dynein activation.
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Affiliation(s)
- William D Ton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yue Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nicholas T Flint
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Lindsay G Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Hao Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
| | - Steven M Markus
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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14
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Ko S, Toda A, Tanaka H, Yu J, Kurisu G. Crystal structure of the stalk region of axonemal inner-arm dynein-d reveals unique features in the coiled-coil and microtubule-binding domain. FEBS Lett 2023; 597:2149-2160. [PMID: 37400274 DOI: 10.1002/1873-3468.14690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023]
Abstract
Axonemal dynein is an ATP-dependent microtubular motor protein responsible for cilia and flagella beating, and its dysfunction can cause diseases such as primary ciliary dyskinesia and sperm dysmotility. Despite its biological importance, structure-based mechanisms underlying axonemal dynein motors remain unclear. Here, we determined the X-ray crystal structure of the human inner-arm dynein-d (DNAH1) stalk region, which contains a long antiparallel coiled-coil and a microtubule-binding domain (MTBD), at 2.7 Å resolution. Notably, differences in the relative orientation of the coiled-coil and MTBD in comparison with other dyneins, as well as the diverse orientations of the MTBD flap region among various isoforms, lead us to propose a 'spike shoe model' with an altered stepping angle for the interaction between IAD-d and microtubules. Based on these findings, we discuss isoform-specific functions of the axonemal dynein stalk MTBDs.
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Affiliation(s)
- Seolmin Ko
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Akiyuki Toda
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Hideaki Tanaka
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Jian Yu
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
| | - Genji Kurisu
- Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
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15
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Halbi G, Fayer I, Aranovich D, Gat S, Pavan MJ, Nachmias D, Sanchez DS, Brik A, Granek R, Bernheim-Groswasser A. Smart design of universally decorated nanoparticles for drug delivery applications driven by active transport. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:74. [PMID: 37653248 DOI: 10.1140/epje/s10189-023-00331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Targeting the cell nucleus remains a challenge for drug delivery. Here, we present a universal platform for the smart design of nanoparticle (NP) decoration that is based on: (i) a spacer polymer, commonly biotin-polyethylene-glycol-thiol, whose grafting density and molecular weight can be tuned for optimized performance, and (ii) protein binding peptides, such as cell penetrating peptides (CPPs), cancer-targeting peptides, or nuclear localization signal (NLS) peptides, that are linked to the PEG free-end by universal chemistry. We manifested our platform with two different bromo-acetamide (Br-Ac) modified NLSs. We used cell extract-based and live cell assays to demonstrate the recruitment of dynein motor proteins, which drive the NP active transport toward the nucleus, and the enhancement of cellular and nuclear entry, manifesting the properties of NLS as a CPP. Our control of the NP decoration scheme, and the modularity of our platform, carry great advantages for nano-carrier design for drug delivery applications.
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Affiliation(s)
- Gal Halbi
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Itay Fayer
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Dina Aranovich
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Shachar Gat
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Mariela J Pavan
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Daniel Sevilla Sanchez
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, 3200008, Haifa, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Anne Bernheim-Groswasser
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
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16
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Rangan KJ, Reck-Peterson SL. RNA recoding in cephalopods tailors microtubule motor protein function. Cell 2023; 186:2531-2543.e11. [PMID: 37295401 PMCID: PMC10467349 DOI: 10.1016/j.cell.2023.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/05/2023] [Accepted: 04/24/2023] [Indexed: 06/12/2023]
Abstract
RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed "recoding." In cephalopods, most transcripts are recoded, and recoding is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. We investigated the function of cephalopod RNA recoding in the microtubule motor proteins kinesin and dynein. We found that squid rapidly employ RNA recoding in response to changes in ocean temperature, and kinesin variants generated in cold seawater displayed enhanced motile properties in single-molecule experiments conducted in the cold. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod kinesin and dynein. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and can inform the characterization of conserved non-cephalopod proteins.
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Affiliation(s)
- Kavita J Rangan
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Samara L Reck-Peterson
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
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17
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Ge WR, Fu PP, Zhang WN, Zhang B, Ding YX, Yang G. Case report: Genotype and phenotype of DYNC1H1-related malformations of cortical development: a case report and literature review. Front Neurol 2023; 14:1163803. [PMID: 37181555 PMCID: PMC10167015 DOI: 10.3389/fneur.2023.1163803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Background Mutations in the dynein cytoplasmic 1 heavy chain 1 (DYNC1H1) gene are linked to malformations of cortical development (MCD), which may be accompanied by central nervous system (CNS) manifestations. Here, we present the case of a patient with MCD harboring a variant of DYNC1H1 and review the relevant literature to explore genotype-phenotype relationships. Case presentation A girl having infantile spasms, was unsuccessfully administered multiple antiseizure medications and developed drug-resistant epilepsy. Brain magnetic resonance imaging (MRI) at 14 months-of-age revealed pachygyria. At 4 years-of-age, the patient exhibited severe developmental delay and mental retardation. A de novo heterozygous mutation (p.Arg292Trp) in the DYNC1H1 gene was identified. A search of multiple databases, including PubMed and Embase, using the search strategy DYNC1H1 AND [malformations of cortical development OR seizure OR intellectual OR clinical symptoms] up to June 2022, identified 129 patients from 43 studies (including the case presented herein). A review of these cases showed that patients with DYNC1H1-related MCD had higher risks of epilepsy (odds ratio [OR] = 33.67, 95% confidence interval [CI] = 11.59, 97.84) and intellectual disability/developmental delay (OR = 52.64, 95% CI = 16.27, 170.38). Patients with the variants in the regions encoding the protein stalk or microtubule-binding domain had the most prevalence of MCD (95%). Conclusion MCD, particularly pachygyria, is a common neurodevelopmental disorder in patients with DYNC1H1 mutations. Literature searches reveales that most (95%) patients who carried mutations in the protein stalk or microtubule binding domains exhibited DYNC1H1-related MCD, whereas almost two-thirds of patients (63%) who carried mutations in the tail domain did not display MCD. Patients with DYNC1H1 mutations may experience central nervous system (CNS) manifestations due to MCD.
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Affiliation(s)
- Wen-Rong Ge
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Pei-Pei Fu
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wei-Na Zhang
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Bo Zhang
- Department of Neurology and ICCTR Biostatistics and Research Design Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Ying-Xue Ding
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Guang Yang
- Senior Department of Pediatrics, The Seventh Medical Center of People's Liberation Army General Hospital, Beijing, China
- Department of Pediatrics, The First Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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18
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Zimmermann N, Noga A, Obbineni JM, Ishikawa T. ATP-induced conformational change of axonemal outer dynein arms revealed by cryo-electron tomography. EMBO J 2023:e112466. [PMID: 37051721 DOI: 10.15252/embj.2022112466] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram averaging, and classification. These states of force generation depict the prepower stroke, postpower stroke, and intermediate state conformations. Comparison of these conformations to published in vitro atomic structures of cytoplasmic dynein, ODA, and the Shulin-ODA complex revealed differences in the orientation and position of the dynein head. Our analysis shows that in the absence of ATP, all dynein linkers interact with the AAA3/AAA4 domains, indicating that interactions with the adjacent microtubule doublet B-tubule direct dynein orientation. For the prepower stroke conformation, there were changes in the tail that is anchored on the A-tubule. We built models starting with available high-resolution structures to generate a best-fitting model structure for the in situ pre- and postpower stroke ODA conformations, thereby showing that ODA in a complex with Shulin adopts a similar conformation as the active prepower stroke ODA in the axoneme.
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Affiliation(s)
- Noemi Zimmermann
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
| | - Akira Noga
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
| | - Jagan Mohan Obbineni
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
- VIT School for Agricultural Innovations and Advanced, Learning (VAIAL), VIT, Vellore, India
| | - Takashi Ishikawa
- Paul Scherrer Institut (PSI), Laboratory of Nanoscale Biology, Villigen PSI, Switzerland
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19
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He S, Gillies JP, Zang JL, Córdoba-Beldad CM, Yamamoto I, Fujiwara Y, Grantham J, DeSantis ME, Shibuya H. Distinct dynein complexes defined by DYNLRB1 and DYNLRB2 regulate mitotic and male meiotic spindle bipolarity. Nat Commun 2023; 14:1715. [PMID: 36973253 PMCID: PMC10042829 DOI: 10.1038/s41467-023-37370-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Spindle formation in male meiosis relies on the canonical centrosome system, which is distinct from acentrosomal oocyte meiosis, but its specific regulatory mechanisms remain unknown. Herein, we report that DYNLRB2 (Dynein light chain roadblock-type-2) is a male meiosis-upregulated dynein light chain that is indispensable for spindle formation in meiosis I. In Dynlrb2 KO mouse testes, meiosis progression is arrested in metaphase I due to the formation of multipolar spindles with fragmented pericentriolar material (PCM). DYNLRB2 inhibits PCM fragmentation through two distinct pathways; suppressing premature centriole disengagement and targeting NuMA (nuclear mitotic apparatus) to spindle poles. The ubiquitously expressed mitotic counterpart, DYNLRB1, has similar roles in mitotic cells and maintains spindle bipolarity by targeting NuMA and suppressing centriole overduplication. Our work demonstrates that two distinct dynein complexes containing DYNLRB1 or DYNLRB2 are separately used in mitotic and meiotic spindle formations, respectively, and that both have NuMA as a common target.
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Affiliation(s)
- Shuwen He
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Juliana L Zang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carmen M Córdoba-Beldad
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - Io Yamamoto
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - Yasuhiro Fujiwara
- Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Tokyo, 113-0032, Japan
| | - Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41390, Gothenburg, Sweden.
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20
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Zavala-Vargas DI, Visoso-Carbajal G, Cedillo-Barrón L, Filisola-Villaseñor JG, Rosales-Ramirez R, Ludert JE, Morales-Ríos E. Interaction of the Zika virus with the cytoplasmic dynein-1. Virol J 2023; 20:43. [PMID: 36879270 PMCID: PMC9987375 DOI: 10.1186/s12985-023-01992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
Zika virus (ZIKV) infection is a major public health threat, making the study of its biology a matter of great importance. By analyzing the viral-host protein interactions, new drug targets may be proposed. In this work, we showed that human cytoplasmic dynein-1 (Dyn) interacts with the envelope protein (E) of ZIKV. Biochemical evidence indicates that the E protein and the dimerization domain of the heavy chain of Dyn binds directly without dynactin or any cargo adaptor. Analysis of this interactions in infected Vero cells by proximity ligation assay suggest that the E-Dyn interaction is dynamic and finely tuned along the replication cycle. Altogether, our results suggest new steps in the replication cycle of the ZIKV for virion transport and indicate a suitable molecular target to modulate infection by ZIKV.
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Affiliation(s)
- Dan Israel Zavala-Vargas
- Department of Biochemistry, Center for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | - Giovani Visoso-Carbajal
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | - Leticia Cedillo-Barrón
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | | | - Romel Rosales-Ramirez
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | - Juan E Ludert
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico
| | - Edgar Morales-Ríos
- Department of Biochemistry, Center for Research and Advanced Studies (Cinvestav), 07360, Mexico City, Mexico.
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21
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Kubo S, Bui KH. Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation. Sci Rep 2023; 13:1477. [PMID: 36702893 PMCID: PMC9879972 DOI: 10.1038/s41598-023-28026-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Intraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific to the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e., "tubulin code", for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the landing behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, H3A 0C7, Canada. .,Department of Biological Science, Grad. Sch. of Sci, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, H3A 0C7, Canada. .,Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, H3A 0C7, Canada.
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22
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Furuta A, Furuta K. Fast and Easy Transient Mammalian Cell Expression and Purification of Cytoplasmic Dynein. Methods Mol Biol 2023; 2623:157-173. [PMID: 36602685 DOI: 10.1007/978-1-0716-2958-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recombinant protein expression has been key to studying dynein's mechanochemistry and structure-function relationship. To gain further insight into the energy-converting mechanisms and interactions with an increasing variety of dynein cargos and regulators, rapid expression and purification of a variety of dynein proteins and fragments are important. Here we describe transient expression of cytoplasmic dynein in HEK293 cells and fast small-scale purification for high-throughput protein engineering. Mammalian cell expression might be generally considered to be a laborious process, but with recent technology and some simple inexpensive custom-built labware, dynein expression and purification from mammalian cells can be fast and easy.
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Affiliation(s)
- Akane Furuta
- Frontier Research Laboratory, Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, Japan
| | - Ken'ya Furuta
- Frontier Research Laboratory, Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, Japan.
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23
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Liu X, Rao L, Gennerich A. Measurements of the Force-Dependent Detachment Rates of Cytoplasmic Dynein from Microtubules. Methods Mol Biol 2023; 2623:221-238. [PMID: 36602689 PMCID: PMC9879306 DOI: 10.1007/978-1-0716-2958-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cytoplasmic dynein, the largest and most intricate cytoskeletal motor protein, powers the movement of numerous intracellular cargos toward the minus ends of microtubules (MT). Despite its essential roles in eukaryotic cells, dynein's molecular mechanism, the regulatory functions of its subunits and accessory proteins, and the consequences of human disease mutations on dynein force generation remain largely unclear. Recent work combining mutagenesis, single-molecule fluorescence, and optical tweezers-based force measurement have provided valuable insights into how dynein's multiple AAA+ ATPase domains regulate dynein's attachment to MTs. Here, we describe detailed protocols for the measurements of the force-dependent dynein-MT detachment rates. We provide updated and optimized protocols for the expression and purification of a tail-truncated single-headed Saccharomyces cerevisiae dynein, for polarity-marked MT polymerization, and for the non-covalent attachment of MTs to cover glass surfaces for the measurement of dynein-MT detachment forces.
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Affiliation(s)
- Xinglei Liu
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lu Rao
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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24
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Chaaban S, Carter AP. Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Nature 2022; 610:212-216. [PMID: 36071160 PMCID: PMC7613678 DOI: 10.1038/s41586-022-05186-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor1-3. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour4-6. Different coiled-coil adaptors are linked to different cargos7,8, and some share motifs known to contact sites on dynein and dynactin4,9-13. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos.
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Affiliation(s)
- Sami Chaaban
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew P Carter
- Division of Structural Studies, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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25
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Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M, Nakagaki T, Tamaoki N. Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists. Chemistry 2022; 28:e202200807. [DOI: 10.1002/chem.202200807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sampreeth Thayyil
- Research Institute for Electronic Science Hokkaido University Kita20, Nishi 10, Kita-ku Sapporo Hokkaido 001-0020 Japan
- Graduate School of Life Science Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Yukinori Nishigami
- Research Institute for Electronic Science Hokkaido University Kita20, Nishi 10, Kita-ku Sapporo Hokkaido 001-0020 Japan
- Graduate School of Life Science Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Md. Jahirul Islam
- Research Institute for Electronic Science Hokkaido University Kita20, Nishi 10, Kita-ku Sapporo Hokkaido 001-0020 Japan
- Graduate School of Life Science Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
- Current Address: Institute of Science and Technology Austria 3400 Klosterneuburg Austria
| | - P. K. Hashim
- Research Institute for Electronic Science Hokkaido University Kita20, Nishi 10, Kita-ku Sapporo Hokkaido 001-0020 Japan
- Graduate School of Life Science Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Ken'ya Furuta
- Advanced ICT Research Institute National Institute of Information and Communications Technology Kobe Hyogo 651-2492 Japan
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute National Institute of Information and Communications Technology Kobe Hyogo 651-2492 Japan
| | - Jian Yu
- Faculty of Advanced Life Science Hokkaido University North 10 West 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Min Yao
- Faculty of Advanced Life Science Hokkaido University North 10 West 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Toshiyuki Nakagaki
- Research Institute for Electronic Science Hokkaido University Kita20, Nishi 10, Kita-ku Sapporo Hokkaido 001-0020 Japan
- Graduate School of Life Science Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Nobuyuki Tamaoki
- Research Institute for Electronic Science Hokkaido University Kita20, Nishi 10, Kita-ku Sapporo Hokkaido 001-0020 Japan
- Graduate School of Life Science Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
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26
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Wonkam A, Adadey SM, Schrauwen I, Aboagye ET, Wonkam-Tingang E, Esoh K, Popel K, Manyisa N, Jonas M, deKock C, Nembaware V, Cornejo Sanchez DM, Bharadwaj T, Nasir A, Everard JL, Kadlubowska MK, Nouel-Saied LM, Acharya A, Quaye O, Amedofu GK, Awandare GA, Leal SM. Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes. Commun Biol 2022; 5:369. [PMID: 35440622 PMCID: PMC9019055 DOI: 10.1038/s42003-022-03326-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022] Open
Abstract
We investigated hearing impairment (HI) in 51 families from Ghana with at least two affected members that were negative for GJB2 pathogenic variants. DNA samples from 184 family members underwent whole-exome sequencing (WES). Variants were found in 14 known non-syndromic HI (NSHI) genes [26/51 (51.0%) families], five genes that can underlie either syndromic HI or NSHI [13/51 (25.5%)], and one syndromic HI gene [1/51 (2.0%)]. Variants in CDH23 and MYO15A contributed the most to HI [31.4% (16/51 families)]. For DSPP, an autosomal recessive mode of inheritance was detected. Post-lingual expression was observed for a family segregating a MARVELD2 variant. To our knowledge, seven novel candidate HI genes were identified (13.7%), with six associated with NSHI (INPP4B, CCDC141, MYO19, DNAH11, POTEI, and SOX9); and one (PAX8) with Waardenburg syndrome. MYO19 and DNAH11 were replicated in unrelated Ghanaian probands. Six of the novel genes were expressed in mouse inner ear. It is known that Pax8-/- mice do not respond to sound, and depletion of Sox9 resulted in defective vestibular structures and abnormal utricle development. Most variants (48/60; 80.0%) have not previously been associated with HI. Identifying seven candidate genes in this study emphasizes the potential of novel HI genes discovery in Africa.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kalinka Popel
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Mario Jonas
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Carmen deKock
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Diana M Cornejo Sanchez
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon-si, Republic of Korea
| | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Magda K Kadlubowska
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Geoffrey K Amedofu
- Department of Eye, Ear, Nose, and Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Centre, New York, NY, 10032, USA.
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27
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Spinal muscular atrophy with predominant lower extremity (SMA-LED) with no signs other than pure motor symptoms at the intersection of multiple overlap syndrome. Brain Dev 2022; 44:294-298. [PMID: 34974950 DOI: 10.1016/j.braindev.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mutations in the cytoplasmic dynein 1 heavy chain gene (DYNC1H1) have been associated with spinal muscular atrophy with predominant lower extremity involvement (SMA-LED), Charcot-Marie-Tooth 2O (CMT2O) disease, cortical migration anomalies, and autosomal dominant mental retardation13. SMA-LED phenotype-related mutation was found in the DYNC1H1 gene in the patient who applied with the complaint of gait disturbance. METHODS Pathogenic heterozygous c.1678G > A (p.Val560Met) mutation was detected in the DYNC1H1 gene by next-generation targeted gene analysis in the patient who had no phenotypic findings except delayed motor milestones, lumbar lordosis, and lower extremity muscle weakness. The patient's creatinine phosphokinase enzyme level and brain magnetic resonance imaging (MRI) were normal. Electromyography (EMG) had pure motor findings. CONCLUSION It should be kept in mind that DYNC1H1 mutation, which we are accustomed to seeing with accompanying findings such as orthopedic and ocular dysmorphic findings, sensorineural EMG findings, and intellectual disability, can also observe with pure motor findings such as muscular dystrophy examination findings.
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28
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Abstract
Cilia are tail-like organelles responsible for motility, transportation, and sensory functions in eukaryotic cells. Cilia research has been providing multifaceted questions, attracting biologists of various areas and inducing interdisciplinary studies. In this chapter, we mainly focus on efforts to elucidate the molecular mechanism of ciliary beating motion, a field of research that has a long history and is still ongoing. We also overview topics closely related to the motility mechanism, such as ciliogenesis, cilia-related diseases, and sensory cilia. Subnanometer-scale to submillimeter-scale 3D imaging of the axoneme and the basal body resulted in a wide variety of insights into these questions.
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Affiliation(s)
- Takashi Ishikawa
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.
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29
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Halbi G, Fayer I, Aranovich D, Gat S, Bar S, Erukhimovitch V, Granek R, Bernheim-Groswasser A. Nano-Particles Carried by Multiple Dynein Motors Self-Regulate Their Number of Actively Participating Motors. Int J Mol Sci 2021; 22:ijms22168893. [PMID: 34445598 PMCID: PMC8396316 DOI: 10.3390/ijms22168893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
Intra-cellular active transport by native cargos is ubiquitous. We investigate the motion of spherical nano-particles (NPs) grafted with flexible polymers that end with a nuclear localization signal peptide. This peptide allows the recruitment of several mammalian dynein motors from cytoplasmic extracts. To determine how motor–motor interactions influenced motility on the single microtubule level, we conducted bead-motility assays incorporating surface adsorbed microtubules and combined them with model simulations that were based on the properties of a single dynein. The experimental and simulation results revealed long time trajectories: when the number of NP-ligated motors Nm increased, run-times and run-lengths were enhanced and mean velocities were somewhat decreased. Moreover, the dependence of the velocity on run-time followed a universal curve, regardless of the system composition. Model simulations also demonstrated left- and right-handed helical motion and revealed self-regulation of the number of microtubule-bound, actively transporting dynein motors. This number was stochastic along trajectories and was distributed mainly between one, two, and three motors, regardless of Nm. We propose that this self-regulation allows our synthetic NPs to achieve persistent motion that is associated with major helicity. Such a helical motion might affect obstacle bypassing, which can influence active transport efficiency when facing the crowded environment of the cell.
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Affiliation(s)
- Gal Halbi
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Itay Fayer
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Dina Aranovich
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Shachar Gat
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Shay Bar
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Vitaly Erukhimovitch
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- Correspondence: (R.G.); (A.B.-G.)
| | - Anne Bernheim-Groswasser
- The Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (G.H.); (D.A.); (S.G.); (S.B.); (V.E.)
- The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- Correspondence: (R.G.); (A.B.-G.)
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30
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Abstract
Axonemal dyneins power the beating of motile cilia and flagella. These massive multimeric motor complexes are assembled in the cytoplasm, and subsequently trafficked to cilia and incorporated into the axonemal superstructure. Numerous cytoplasmic factors are required for the dynein assembly process, and, in mammals, defects lead to primary ciliary dyskinesia, which results in infertility, bronchial problems and failure to set up the left-right body axis correctly. Liquid-liquid phase separation (LLPS) has been proposed to underlie the formation of numerous membrane-less intracellular assemblies or condensates. In multiciliated cells, cytoplasmic assembly of axonemal dyneins also occurs in condensates that exhibit liquid-like properties, including fusion, fission and rapid exchange of components both within condensates and with bulk cytoplasm. However, a recent extensive meta-analysis suggests that the general methods used to define LLPS systems in vivo may not readily distinguish LLPS from other mechanisms. Here, I consider the time and length scales of axonemal dynein heavy chain synthesis, and the possibility that during translation of dynein heavy chain mRNAs, polysomes are crosslinked via partially assembled proteins. I propose that axonemal dynein factory formation in the cytoplasm may be a direct consequence of the sheer scale and complexity of the assembly process itself.
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Affiliation(s)
- Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030-3305, USA
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31
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Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility. Proc Natl Acad Sci U S A 2021; 118:2101391118. [PMID: 34326255 PMCID: PMC8346880 DOI: 10.1073/pnas.2101391118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dynein, a dimeric motor protein, moves along microtubules through adenosine 5′-triphosphate- and thermal-driven motions of two large ring domains (AAA rings) and small microtubule-binding domains (MTBDs) separated by a long coiled-coil. Previous single-molecule studies have tracked the positions of the AAA rings during motility, but not the MTBDs. Here, we tracked the relative positions of both MTBDs and one AAA ring by three-color, nanometer-resolution imaging. The observation of both MTBDs provided a direct measurement of how dynein steps on the tubulin subunits, and the simultaneous observation of three fiducial markers revealed extraordinary flexibility and previously unknown conformational states of the motor during motility. The techniques presented here can be used to explore conformational dynamics of many other macromolecular complexes. The motor protein dynein undergoes coordinated conformational changes of its domains during motility along microtubules. Previous single-molecule studies analyzed the motion of the AAA rings of the dynein homodimer, but not the distal microtubule-binding domains (MTBDs) that step along the track. Here, we simultaneously tracked with nanometer precision two MTBDs and one AAA ring of a single dynein as it underwent hundreds of steps using three-color imaging. We show that the AAA ring and the MTBDs do not always step simultaneously and can take differently sized steps. This variability in the movement between the AAA ring and MTBDs results in an unexpectedly large number of conformational states of dynein during motility. Extracting data on conformational transition biases, we could accurately model dynein stepping in silico. Our results reveal that the flexibility between major dynein domains is critical for dynein motility.
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32
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Tati S, Alisaraie L. Analysis of the Structural Mechanism of ATP Inhibition at the AAA1 Subunit of Cytoplasmic Dynein-1 Using a Chemical "Toolkit". Int J Mol Sci 2021; 22:ijms22147704. [PMID: 34299323 PMCID: PMC8304172 DOI: 10.3390/ijms22147704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 11/28/2022] Open
Abstract
Dynein is a ~1.2 MDa cytoskeletal motor protein that carries organelles via retrograde transport in eukaryotic cells. The motor protein belongs to the ATPase family of proteins associated with diverse cellular activities and plays a critical role in transporting cargoes to the minus end of the microtubules. The motor domain of dynein possesses a hexameric head, where ATP hydrolysis occurs. The presented work analyzes the structure–activity relationship (SAR) of dynapyrazole A and B, as well as ciliobrevin A and D, in their various protonated states and their 46 analogues for their binding in the AAA1 subunit, the leading ATP hydrolytic site of the motor domain. This study exploits in silico methods to look at the analogues’ effects on the functionally essential subsites of the motor domain of dynein 1, since no similar experimental structural data are available. Ciliobrevin and its analogues bind to the ATP motifs of the AAA1, namely, the walker-A (W-A) or P-loop, the walker-B (W-B), and the sensor I and II. Ciliobrevin A shows a better binding affinity than its D analogue. Although the double bond in ciliobrevin A and D was expected to decrease the ligand potency, they show a better affinity to the AAA1 binding site than dynapyrazole A and B, lacking the bond. In addition, protonation of the nitrogen atom in ciliobrevin A and D, as well as dynapyrazole A and B, at the N9 site of ciliobrevin and the N7 of the latter increased their binding affinity. Exploring ciliobrevin A geometrical configuration suggests the E isomer has a superior binding profile over the Z due to binding at the critical ATP motifs. Utilizing the refined structure of the motor domain obtained through protein conformational search in this study exhibits that Arg1852 of the yeast cytoplasmic dynein could involve in the “glutamate switch” mechanism in cytoplasmic dynein 1 in lieu of the conserved Asn in AAA+ protein family.
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Goldtzvik Y, Thirumalai D. Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin. J Chem Theory Comput 2021; 17:5358-5368. [PMID: 34251798 DOI: 10.1021/acs.jctc.1c00317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conventional kinesin, a motor protein that transports cargo within cells, walks by taking multiple steps toward the plus end of the microtubule (MT). While significant progress has been made in understanding the details of the walking mechanism of kinesin, there are many unresolved issues. From a computational perspective, a central challenge is the large size of the system, which limits the scope of time scales accessible in standard computer simulations. Here, we create a general multiscale coarse-grained model for motors that enables us to simulate the stepping process of motors on polar tracks (actin and MT) with a focus on kinesin. Our approach greatly shortens the computation times without a significant loss in detail, thus allowing us to better describe the molecular basis of the stepping kinetics. The small number of parameters, which are determined by fitting to experimental data, allows us to develop an accurate method that may be adopted to simulate stepping in other molecular motors. The model enables us to simulate a large number of steps, which was not possible previously. We show in agreement with experiments that due to the docking of the neck linker (NL) of kinesin, sometimes deemed as the power stroke, the space explored diffusively by the tethered head is severely restricted, allowing the step to be completed in tens of microseconds. We predict that increasing the interaction strength between the NL and the motor head, achievable by mutations in the NL, decreases the stepping time but reaches a saturation value. Furthermore, the full three-dimensional dynamics of the cargo are fully resolved in our model, contributing to the predictive power and allowing us to study the important aspects of cargo-motor interactions.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
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Dutta M, Jana B. Computational modeling of dynein motor proteins at work. Chem Commun (Camb) 2021; 57:272-283. [PMID: 33332489 DOI: 10.1039/d0cc05857b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Along with various experimental methods, a combination of theoretical and computational methods is essential to explore different length-scale and time-scale processes in the biological system. The functional mechanism of a dynein, an ATP-fueled motor protein, working in a multiprotein complex, involves a wide range of length/time-scale events. It generates mechanical force from chemical energy and moves on microtubules towards the minus end direction while performing a large number of biological processes including ciliary beating, intracellular material transport, and cell division. Like in the cases of other conventional motor proteins, a combination of experimental techniques including X-crystallography, cryo-electron microscopy, and single molecular assay have provided a wealth of information about the mechanochemical cycle of a dynein. Dyneins have a large and complex structural architecture and therefore, computational modeling of different aspects of a dynein is extremely challenging. As the process of dynein movement involves varying length and timescales, it demands, like in experiments, a combination of computational methods covering such a wide range of processes for the comprehensive investigation of the mechanochemical cycle. In this review article, we will summarize how the use of state-of-the-art computational methods can provide a detailed molecular understanding of the mechanochemical cycle of the dynein. We implemented all-atom molecular dynamics simulations and hybrid quantum-mechanics/molecular-mechanics simulations to explore the ATP hydrolysis mechanisms at the primary ATPase site (AAA1) of dynein. To investigate the large-scale conformational changes we employed coarse-grained structure-based molecular dynamics simulations to capture the domain motions. Here we explored the conformational changes upon binding of ATP at AAA1, nucleotide state-dependent regulation of the mechanochemical cycle, and inter-head coordination by inter-head tension. Additionally, implementing a phenomenological theoretical model we explore the force-dependent detachment rate of a motorhead from the microtubule and the principle of multi-dynein cooperation during cargo transport.
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Affiliation(s)
- Mandira Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata - 700032, India.
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Abstract
Dyneins make up a family of AAA+ motors that move toward the minus end of microtubules. Cytoplasmic dynein is responsible for transporting intracellular cargos in interphase cells and mediating spindle assembly and chromosome positioning during cell division. Other dynein isoforms transport cargos in cilia and power ciliary beating. Dyneins were the least studied of the cytoskeletal motors due to challenges in the reconstitution of active dynein complexes in vitro and the scarcity of high-resolution methods for in-depth structural and biophysical characterization of these motors. These challenges have been recently addressed, and there have been major advances in our understanding of the activation, mechanism, and regulation of dyneins. This review synthesizes the results of structural and biophysical studies for each class of dynein motors. We highlight several outstanding questions about the regulation of bidirectional transport along microtubules and the mechanisms that sustain self-coordinated oscillations within motile cilia.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA;
| | - Ruensern Tan
- Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA
| | - Emre Kusakci
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA;
| | - Jonathan Fernandes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, USA.,Physics Department, University of California, Berkeley, California 94720, USA
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Santarossa CC, Mickolajczyk KJ, Steinman JB, Urnavicius L, Chen N, Hirata Y, Fukase Y, Coudray N, Ekiert DC, Bhabha G, Kapoor TM. Targeting allostery in the Dynein motor domain with small molecule inhibitors. Cell Chem Biol 2021; 28:1460-1473.e15. [PMID: 34015309 DOI: 10.1016/j.chembiol.2021.04.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/24/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
Cytoplasmic dyneins are AAA (ATPase associated with diverse cellular activities) motor proteins responsible for microtubule minus-end-directed intracellular transport. Dynein's unusually large size, four distinct nucleotide-binding sites, and conformational dynamics pose challenges for the design of potent and selective chemical inhibitors. Here we use structural approaches to develop a model for the inhibition of a well-characterized S. cerevisiae dynein construct by pyrazolo-pyrimidinone-based compounds. These data, along with functional assays of dynein motility and mutagenesis studies, suggest that the compounds inhibit dynein by engaging the regulatory ATPase sites in the AAA3 and AAA4 domains, and not by interacting with dynein's main catalytic site in the AAA1 domain. A double Walker B mutation of the AAA3 and AAA4 sites substantially reduces enzyme activity, suggesting that targeting these regulatory domains is sufficient to inhibit dynein. Our findings reveal how chemical inhibitors can be designed to disrupt allosteric communication across dynein's AAA domains.
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Affiliation(s)
- Cristina C Santarossa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional PhD program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan B Steinman
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Linas Urnavicius
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nan Chen
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yasuhiro Hirata
- Tri-Institutional Therapeutics Discovery Institute, New York, NY 10065, USA
| | - Yoshiyuki Fukase
- Tri-Institutional Therapeutics Discovery Institute, New York, NY 10065, USA
| | - Nicolas Coudray
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY 10016, USA
| | - Damian C Ekiert
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Gira Bhabha
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA.
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
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Yamamoto R, Hwang J, Ishikawa T, Kon T, Sale WS. Composition and function of ciliary inner-dynein-arm subunits studied in Chlamydomonas reinhardtii. Cytoskeleton (Hoboken) 2021; 78:77-96. [PMID: 33876572 DOI: 10.1002/cm.21662] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/30/2021] [Accepted: 04/15/2021] [Indexed: 11/09/2022]
Abstract
Motile cilia (also interchangeably called "flagella") are conserved organelles extending from the surface of many animal cells and play essential functions in eukaryotes, including cell motility and environmental sensing. Large motor complexes, the ciliary dyneins, are present on ciliary outer-doublet microtubules and drive movement of cilia. Ciliary dyneins are classified into two general types: the outer dynein arms (ODAs) and the inner dynein arms (IDAs). While ODAs are important for generation of force and regulation of ciliary beat frequency, IDAs are essential for control of the size and shape of the bend, features collectively referred to as waveform. Also, recent studies have revealed unexpected links between IDA components and human diseases. In spite of their importance, studies on IDAs have been difficult since they are very complex and composed for several types of IDA motors, each unique in composition and location in the axoneme. Thanks in part to genetic, biochemical, and structural analysis of Chlamydomonas reinhardtii, we are beginning to understand the organization and function of the ciliary IDAs. In this review, we summarize the composition of Chlamydomonas IDAs particularly focusing on each subunit, and discuss the assembly, conservation, and functional role(s) of these IDA subunits. Furthermore, we raise several additional questions/challenges regarding IDAs, and discuss future perspectives of IDA studies.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Juyeon Hwang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Takashi Ishikawa
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Winfield S Sale
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
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Kopf A, Kiermaier E. Dynamic Microtubule Arrays in Leukocytes and Their Role in Cell Migration and Immune Synapse Formation. Front Cell Dev Biol 2021; 9:635511. [PMID: 33634136 PMCID: PMC7900162 DOI: 10.3389/fcell.2021.635511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
The organization of microtubule arrays in immune cells is critically important for a properly operating immune system. Leukocytes are white blood cells of hematopoietic origin, which exert effector functions of innate and adaptive immune responses. During these processes the microtubule cytoskeleton plays a crucial role for establishing cell polarization and directed migration, targeted secretion of vesicles for T cell activation and cellular cytotoxicity as well as the maintenance of cell integrity. Considering this large spectrum of distinct effector functions, leukocytes require flexible microtubule arrays, which timely and spatially reorganize allowing the cells to accommodate their specific tasks. In contrast to other specialized cell types, which typically nucleate microtubule filaments from non-centrosomal microtubule organizing centers (MTOCs), leukocytes mainly utilize centrosomes for sites of microtubule nucleation. Yet, MTOC localization as well as microtubule organization and dynamics are highly plastic in leukocytes thus allowing the cells to adapt to different environmental constraints. Here we summarize our current knowledge on microtubule organization and dynamics during immune processes and how these microtubule arrays affect immune cell effector functions. We particularly highlight emerging concepts of microtubule involvement during maintenance of cell shape and physical coherence.
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Affiliation(s)
- Aglaja Kopf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Eva Kiermaier
- Life and Medical Sciences Institute, Immune and Tumor Biology, University of Bonn, Bonn, Germany
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Jessop M, Felix J, Gutsche I. AAA+ ATPases: structural insertions under the magnifying glass. Curr Opin Struct Biol 2021; 66:119-128. [PMID: 33246198 PMCID: PMC7973254 DOI: 10.1016/j.sbi.2020.10.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
AAA+ ATPases are a diverse protein superfamily which power a vast number of cellular processes, from protein degradation to genome replication and ribosome biogenesis. The latest advances in cryo-EM have resulted in a spectacular increase in the number and quality of AAA+ ATPase structures. This abundance of new information enables closer examination of different types of structural insertions into the conserved core, revealing discrepancies in the current classification of AAA+ modules into clades. Additionally, combined with biochemical data, it has allowed rapid progress in our understanding of structure-functional relationships and provided arguments both in favour and against the existence of a unifying molecular mechanism for the ATPase activity and action on substrates, stimulating further intensive research.
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Affiliation(s)
- Matthew Jessop
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
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40
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Rao Q, Han L, Wang Y, Chai P, Kuo YW, Yang R, Hu F, Yang Y, Howard J, Zhang K. Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Nat Struct Mol Biol 2021; 28:799-810. [PMID: 34556869 PMCID: PMC8500839 DOI: 10.1038/s41594-021-00656-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022]
Abstract
Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of Tetrahymena thermophila OAD arrays bound to MTDs in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide the MTDs. ATP hydrolysis in turn relaxes the TTH interfaces to effect free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins.
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Affiliation(s)
- Qinhui Rao
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Long Han
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Yue Wang
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Pengxin Chai
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Yin-wei Kuo
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Renbin Yang
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Fangheng Hu
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Yuchen Yang
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Jonathon Howard
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
| | - Kai Zhang
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT USA
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41
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Liu X, Rao L, Gennerich A. The regulatory function of the AAA4 ATPase domain of cytoplasmic dynein. Nat Commun 2020; 11:5952. [PMID: 33230227 PMCID: PMC7683685 DOI: 10.1038/s41467-020-19477-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Cytoplasmic dynein is the primary motor for microtubule minus-end-directed transport and is indispensable to eukaryotic cells. Although each motor domain of dynein contains three active AAA+ ATPases (AAA1, 3, and 4), only the functions of AAA1 and 3 are known. Here, we use single-molecule fluorescence and optical tweezers studies to elucidate the role of AAA4 in dynein's mechanochemical cycle. We demonstrate that AAA4 controls the priming stroke of the motion-generating linker, which connects the dimerizing tail of the motor to the AAA+ ring. Before ATP binds to AAA4, dynein remains incapable of generating motion. However, when AAA4 is bound to ATP, the gating of AAA1 by AAA3 prevails and dynein motion can occur. Thus, AAA1, 3, and 4 work together to regulate dynein function. Our work elucidates an essential role for AAA4 in dynein's stepping cycle and underscores the complexity and crosstalk among the motor's multiple AAA+ domains.
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Affiliation(s)
- Xinglei Liu
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Linke H, Höcker B, Furuta K, Forde NR, Curmi PMG. Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers. Biophys Rev 2020; 12:1041-1054. [PMID: 32651904 PMCID: PMC7429643 DOI: 10.1007/s12551-020-00717-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. However, from the study of highly evolved, biological motors, it remains difficult to discern detailed mechanisms, for example, about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the "holy grail" of designing and building a functional synthetic protein motor has not been realized. Here, we review the progress made to date, and we put forward a roadmap for achieving the aim of constructing the first artificial, autonomously running protein motor. Specifically, we propose to break down the task into (i) enzymatic control of track binding, (ii) the engineering of asymmetry and (iii) the engineering of allosteric control for internal communication. We also propose specific approaches for solving each of these challenges.
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Affiliation(s)
- Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, SE 22100, Lund, Sweden
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia.
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Amabile S, Jeffries L, McGrath JM, Ji W, Spencer-Manzon M, Zhang H, Lakhani SA. DYNC1H1-related disorders: A description of four new unrelated patients and a comprehensive review of previously reported variants. Am J Med Genet A 2020; 182:2049-2057. [PMID: 32656949 DOI: 10.1002/ajmg.a.61729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 11/05/2022]
Abstract
Heterozygous variants in the DYNC1H1 gene have been associated chiefly with intellectual disability (ID), malformations in cortical development (MCD), spinal muscular atrophy (SMA), and Charcot-Marie-Tooth axonal type 20 (CMT), with fewer reports describing other intersecting phenotypes. To better characterize the variable syndromes associated with DYNC1H1, we undertook a detailed analysis of reported patients in the medical literature through June 30, 2019. In sum we identified 200 patients from 143 families harboring 103 different DYNC1H1 variants, and added reports for four unrelated patients identified at our center, three with novel variants. The most common features associated with DYNC1H1 were neuromuscular (NM) disease (largely associated with variants in the stem domain), ID with MCD (largely associated with variants in the motor domain), or a combination of these phenotypes. Despite these trends, exceptions are noted throughout. Overall, DYNC1H1 is associated with variable neurodevelopmental and/or neuromuscular phenotypes that overlap. To avoid confusion DYNC1H1 disorders may be best categorized at this time by more general descriptions rather than phenotype-specific nomenclature such as SMA or CMT. We therefore propose the terms: DYNC1H1-related NM disorder, DYNC1H1-related CNS disorder, and DYNC1H1-related combined disorder. Our single center's experience may be evidence that disease-causing variants in this gene are more prevalent than currently recognized.
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Affiliation(s)
- Sonia Amabile
- Department of Pediatrics, Pediatric Genomics Discovery Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Jeffries
- Department of Pediatrics, Pediatric Genomics Discovery Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James M McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Department of Pediatrics, Pediatric Genomics Discovery Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Saquib A Lakhani
- Department of Pediatrics, Pediatric Genomics Discovery Program, Yale University School of Medicine, New Haven, Connecticut, USA
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44
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Canty JT, Yildiz A. Activation and Regulation of Cytoplasmic Dynein. Trends Biochem Sci 2020; 45:440-453. [PMID: 32311337 PMCID: PMC7179903 DOI: 10.1016/j.tibs.2020.02.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 12/30/2022]
Abstract
Cytoplasmic dynein is an AAA+ motor that drives the transport of many intracellular cargoes towards the minus end of microtubules (MTs). Previous in vitro studies characterized isolated dynein as an exceptionally weak motor that moves slowly and diffuses on an MT. Recent studies altered this view by demonstrating that dynein remains in an autoinhibited conformation on its own, and processive motility is activated when it forms a ternary complex with dynactin and a cargo adaptor. This complex assembles more efficiently in the presence of Lis1, providing an explanation for why Lis1 is a required cofactor for most cytoplasmic dynein-driven processes in cells. This review describes how dynein motility is activated and regulated by cargo adaptors and accessory proteins.
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Affiliation(s)
- John T Canty
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Physics Department, University of California at Berkeley, Berkeley, CA 94720, USA.
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Lis1 activates dynein motility by modulating its pairing with dynactin. Nat Cell Biol 2020; 22:570-578. [PMID: 32341547 PMCID: PMC7212015 DOI: 10.1038/s41556-020-0501-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Lissencephaly-1 (Lis1) is a key cofactor for dynein-mediated intracellular transport towards the minus-ends of microtubules. It remains unclear whether Lis1 serves as an inhibitor or an activator of mammalian dynein motility. Here we use single-molecule imaging and optical trapping to show that Lis1 does not directly alter the stepping and force production of individual dynein motors assembled with dynactin and a cargo adaptor. Instead, Lis1 promotes the formation of an active complex with dynactin. Lis1 also favours the recruitment of two dyneins to dynactin, resulting in increased velocity, higher force production and more effective competition against kinesin in a tug-of-war. Lis1 dissociates from motile complexes, indicating that its primary role is to orchestrate the assembly of the transport machinery. We propose that Lis1 binding releases dynein from its autoinhibited state, which provides a mechanistic explanation for why Lis1 is required for efficient transport of many dynein-associated cargos in cells.
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Force-Generating Mechanism of Axonemal Dynein in Solo and Ensemble. Int J Mol Sci 2020; 21:ijms21082843. [PMID: 32325779 PMCID: PMC7215579 DOI: 10.3390/ijms21082843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/12/2020] [Accepted: 04/15/2020] [Indexed: 11/17/2022] Open
Abstract
In eukaryotic cilia and flagella, various types of axonemal dyneins orchestrate their distinct functions to generate oscillatory bending of axonemes. The force-generating mechanism of dyneins has recently been well elucidated, mainly in cytoplasmic dyneins, thanks to progress in single-molecule measurements, X-ray crystallography, and advanced electron microscopy. These techniques have shed light on several important questions concerning what conformational changes accompany ATP hydrolysis and whether multiple motor domains are coordinated in the movements of dynein. However, due to the lack of a proper expression system for axonemal dyneins, no atomic coordinates of the entire motor domain of axonemal dynein have been reported. Therefore, a substantial amount of knowledge on the molecular architecture of axonemal dynein has been derived from electron microscopic observations on dynein arms in axonemes or on isolated axonemal dynein molecules. This review describes our current knowledge and perspectives of the force-generating mechanism of axonemal dyneins in solo and in ensemble.
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Kubo S, Shima T, Takada S. How Cytoplasmic Dynein Couples ATP Hydrolysis Cycle to Diverse Stepping Motions: Kinetic Modeling. Biophys J 2020; 118:1930-1945. [PMID: 32272056 DOI: 10.1016/j.bpj.2020.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/07/2020] [Accepted: 03/17/2020] [Indexed: 01/20/2023] Open
Abstract
Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of a microtubule by ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein exhibits various bipedal stepping motions: inchworm and hand-over-hand motions, as well as nonalternating steps of one head. However, the molecular basis to achieve such diverse stepping manners remains unclear because of the lack of an experimental method to observe stepping and the ATPase reaction of dynein simultaneously. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and perform Gillespie Monte Carlo simulations that qualitatively reproduce most experimental data obtained to date. The model represents the status of each motor domain as five states according to conformation and nucleotide- and microtubule-binding conditions of the domain. In addition, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, similarly to experimental data. The model reproduced key experimental motility-related properties, including velocity and run length, as functions of the ATP concentration and external force, therefore providing a plausible explanation of how dynein achieves various stepping manners with explicit characterization of nucleotide states. Our model highlights the uniqueness of dynein in the coupling of ATPase with its movement during both inchworm and hand-over-hand stepping.
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Affiliation(s)
- Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.
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48
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Toda A, Nishikawa Y, Tanaka H, Yagi T, Kurisu G. The complex of outer-arm dynein light chain-1 and the microtubule-binding domain of the γ heavy chain shows how axonemal dynein tunes ciliary beating. J Biol Chem 2020; 295:3982-3989. [PMID: 32014992 PMCID: PMC7086020 DOI: 10.1074/jbc.ra119.011541] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/29/2020] [Indexed: 01/07/2023] Open
Abstract
Axonemal dynein is a microtubule-based molecular motor that drives ciliary/flagellar beating in eukaryotes. In axonemal dynein, the outer-arm dynein (OAD) complex, which comprises three heavy chains (α, β, and γ), produces the main driving force for ciliary/flagellar motility. It has recently been shown that axonemal dynein light chain-1 (LC1) binds to the microtubule-binding domain (MTBD) of OADγ, leading to a decrease in its microtubule-binding affinity. However, it remains unclear how LC1 interacts with the MTBD and controls the microtubule-binding affinity of OADγ. Here, we have used X-ray crystallography and pulldown assays to examine the interaction between LC1 and the MTBD, identifying two important sites of interaction in the MTBD. Solving the LC1-MTBD complex from Chlamydomonas reinhardtii at 1.7 Å resolution, we observed that one site is located in the H5 helix and that the other is located in the flap region that is unique to some axonemal dynein MTBDs. Mutational analysis of key residues in these sites indicated that the H5 helix is the main LC1-binding site. We modeled the ternary structure of the LC1-MTBD complex bound to microtubules based on the known dynein-microtubule complex. This enabled us to propose a structural basis for both formations of the ternary LC1-MTBD-microtubule complex and LC1-mediated tuning of MTBD binding to the microtubule, suggesting a molecular model for how axonemal dynein senses the curvature of the axoneme and tunes ciliary/flagellar beating.
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Affiliation(s)
- Akiyuki Toda
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yosuke Nishikawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Toshiki Yagi
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima 727-0023, Japan
| | - Genji Kurisu
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan, To whom correspondence should be addressed. E-mail:
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49
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Nishida N, Komori Y, Takarada O, Watanabe A, Tamura S, Kubo S, Shimada I, Kikkawa M. Structural basis for two-way communication between dynein and microtubules. Nat Commun 2020; 11:1038. [PMID: 32098965 PMCID: PMC7042235 DOI: 10.1038/s41467-020-14842-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
The movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain via a coiled-coil stalk, but the structural basis of this communication remains elusive. Here, we regulate MTBD either in high-affinity or low-affinity states by introducing a disulfide bond to the stalk and analyze the resulting structures by NMR and cryo-EM. In the MT-unbound state, the affinity changes of MTBD are achieved by sliding of the stalk α-helix by a half-turn, which suggests that structural changes propagate from the ATPase-domain to MTBD. In addition, MT binding induces further sliding of the stalk α-helix even without the disulfide bond, suggesting how the MT-induced conformational changes propagate toward the ATPase domain. Based on differences in the MT-binding surface between the high- and low-affinity states, we propose a potential mechanism for the directional bias of dynein movement on MT tracks.
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Affiliation(s)
- Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Yuta Komori
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Osamu Takarada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Atsushi Watanabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoko Tamura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoshi Kubo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Torisawa T, Kimura A. The Generation of Dynein Networks by Multi-Layered Regulation and Their Implication in Cell Division. Front Cell Dev Biol 2020; 8:22. [PMID: 32083077 PMCID: PMC7004958 DOI: 10.3389/fcell.2020.00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic dynein-1 (hereafter referred to as dynein) is a major microtubule-based motor critical for cell division. Dynein is essential for the formation and positioning of the mitotic spindle as well as the transport of various cargos in the cell. A striking feature of dynein is that, despite having a wide variety of functions, the catalytic subunit is coded in a single gene. To perform various cellular activities, there seem to be different types of dynein that share a common catalytic subunit. In this review, we will refer to the different kinds of dynein as “dyneins.” This review attempts to classify the mechanisms underlying the emergence of multiple dyneins into four layers. Inside a cell, multiple dyneins generated through the multi-layered regulations interact with each other to form a network of dyneins. These dynein networks may be responsible for the accurate regulation of cellular activities, including cell division. How these networks function inside a cell, with a focus on the early embryogenesis of Caenorhabditis elegans embryos, is discussed, as well as future directions for the integration of our understanding of molecular layering to understand the totality of dynein’s function in living cells.
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Affiliation(s)
- Takayuki Torisawa
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
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