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Raudaskoski M. Kinesin Motors in the Filamentous Basidiomycetes in Light of the Schizophyllum commune Genome. J Fungi (Basel) 2022; 8:jof8030294. [PMID: 35330296 PMCID: PMC8950801 DOI: 10.3390/jof8030294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/10/2022] Open
Abstract
Kinesins are essential motor molecules of the microtubule cytoskeleton. All eukaryotic organisms have several genes encoding kinesin proteins, which are necessary for various cell biological functions. During the vegetative growth of filamentous basidiomycetes, the apical cells of long leading hyphae have microtubules extending toward the tip. The reciprocal exchange and migration of nuclei between haploid hyphae at mating is also dependent on cytoskeletal structures, including the microtubules and their motor molecules. In dikaryotic hyphae, resulting from a compatible mating, the nuclear location, synchronous nuclear division, and extensive nuclear separation at telophase are microtubule-dependent processes that involve unidentified molecular motors. The genome of Schizophyllum commune is analyzed as an example of a species belonging to the Basidiomycota subclass, Agaricomycetes. In this subclass, the investigation of cell biology is restricted to a few species. Instead, the whole genome sequences of several species are now available. The analyses of the mating type genes and the genes necessary for fruiting body formation or wood degrading enzymes in several genomes of Agaricomycetes have shown that they are controlled by comparable systems. This supports the idea that the genes regulating the cell biological process in a model fungus, such as the genes encoding kinesin motor molecules, are also functional in other filamentous Agaricomycetes.
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Affiliation(s)
- Marjatta Raudaskoski
- Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
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2
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Solon AL, Tan Z, Schutt KL, Jepsen L, Haynes SE, Nesvizhskii AI, Sept D, Stumpff J, Ohi R, Cianfrocco MA. Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding. SCIENCE ADVANCES 2021; 7:eabj9812. [PMID: 34797717 PMCID: PMC8604404 DOI: 10.1126/sciadv.abj9812] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
Kinesins are regulated in space and time to ensure activation only in the presence of cargo. Kinesin-binding protein (KIFBP), which is mutated in Goldberg-Shprintzen syndrome, binds to and inhibits the catalytic motor heads of 8 of 45 kinesin superfamily members, but the mechanism remains poorly defined. Here, we used cryo–electron microscopy and cross-linking mass spectrometry to determine high-resolution structures of KIFBP alone and in complex with two mitotic kinesins, revealing structural remodeling of kinesin by KIFBP. We find that KIFBP remodels kinesin motors and blocks microtubule binding (i) via allosteric changes to kinesin and (ii) by sterically blocking access to the microtubule. We identified two regions of KIFBP necessary for kinesin binding and cellular regulation during mitosis. Together, this work further elucidates the molecular mechanism of KIFBP-mediated kinesin inhibition and supports a model in which structural rearrangement of kinesin motor domains by KIFBP abrogates motor protein activity.
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Affiliation(s)
- April L. Solon
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhenyu Tan
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Katherine L. Schutt
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Lauren Jepsen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sarah E. Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Michael A. Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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3
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Cook AD, Roberts AJ, Atherton J, Tewari R, Topf M, Moores CA. Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition. J Biol Chem 2021; 297:101063. [PMID: 34375637 PMCID: PMC8526983 DOI: 10.1016/j.jbc.2021.101063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/23/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022] Open
Abstract
Plasmodium parasites cause malaria and are responsible annually for hundreds of thousands of deaths. Kinesins are a superfamily of microtubule-dependent ATPases that play important roles in the parasite replicative machinery, which is a potential target for antiparasite drugs. Kinesin-5, a molecular motor that cross-links microtubules, is an established antimitotic target in other disease contexts, but its mechanism in Plasmodium falciparum is unclear. Here, we characterized P. falciparum kinesin-5 (PfK5) using cryo-EM to determine the motor's nucleotide-dependent microtubule-bound structure and introduced 3D classification of individual motors into our microtubule image processing pipeline to maximize our structural insights. Despite sequence divergence in PfK5, the motor exhibits classical kinesin mechanochemistry, including ATP-induced subdomain rearrangement and cover neck bundle formation, consistent with its plus-ended directed motility. We also observed that an insertion in loop5 of the PfK5 motor domain creates a different environment in the well-characterized human kinesin-5 drug-binding site. Our data reveal the possibility for selective inhibition of PfK5 and can be used to inform future exploration of Plasmodium kinesins as antiparasite targets.
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Affiliation(s)
- Alexander D Cook
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Joseph Atherton
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Rita Tewari
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom.
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021; 60:13331-13342. [PMID: 33951246 PMCID: PMC8251789 DOI: 10.1002/anie.202100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Tubulin plays essential roles in vital cellular activities and is the target of a wide range of proteins and ligands. Here, using a combined computational and crystallographic fragment screening approach, we addressed the question of how many binding sites exist in tubulin. We identified 27 distinct sites, of which 11 have not been described previously, and analyzed their relationship to known tubulin-protein and tubulin-ligand interactions. We further observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. Our results offer a unique structural basis for the development of novel small molecules for use as tubulin modulators in basic research applications or as drugs. Furthermore, our method lays down a framework that may help to discover new pockets in other pharmaceutically important targets and characterize them in terms of chemical tractability and allosteric modulation.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Dario Gioia
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
| | - Andrea E. Prota
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - May E. Sharpe
- Swiss Light SourcePaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea Cavalli
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
- Department of Pharmacy and BiotechnologyAlma Mater StudiorumUniversity of Bolognavia Belmeloro 640126BolognaItaly
| | - Michel O. Steinmetz
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
- University of BaselBiozentrum4056BaselSwitzerland
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5
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Dario Gioia
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
| | - Andrea E. Prota
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - May E. Sharpe
- Swiss Light Source Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
- Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna via Belmeloro 6 40126 Bologna Italy
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
- University of Basel Biozentrum 4056 Basel Switzerland
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Budaitis BG, Jariwala S, Rao L, Yue Y, Sept D, Verhey KJ, Gennerich A. Pathogenic mutations in the kinesin-3 motor KIF1A diminish force generation and movement through allosteric mechanisms. J Cell Biol 2021; 220:211720. [PMID: 33496723 PMCID: PMC7844421 DOI: 10.1083/jcb.202004227] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/27/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
The kinesin-3 motor KIF1A functions in neurons, where its fast and superprocessive motility facilitates long-distance transport, but little is known about its force-generating properties. Using optical tweezers, we demonstrate that KIF1A stalls at an opposing load of ~3 pN but more frequently detaches at lower forces. KIF1A rapidly reattaches to the microtubule to resume motion due to its class-specific K-loop, resulting in a unique clustering of force generation events. To test the importance of neck linker docking in KIF1A force generation, we introduced mutations linked to human neurodevelopmental disorders. Molecular dynamics simulations predict that V8M and Y89D mutations impair neck linker docking. Indeed, both mutations dramatically reduce the force generation of KIF1A but not the motor’s ability to rapidly reattach to the microtubule. Although both mutations relieve autoinhibition of the full-length motor, the mutant motors display decreased velocities, run lengths, and landing rates and delayed cargo transport in cells. These results advance our understanding of how mutations in KIF1A can manifest in disease.
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Affiliation(s)
- Breane G Budaitis
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Kristen J Verhey
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
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7
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Garcia-Saez I, Skoufias DA. Eg5 targeting agents: From new anti-mitotic based inhibitor discovery to cancer therapy and resistance. Biochem Pharmacol 2020; 184:114364. [PMID: 33310050 DOI: 10.1016/j.bcp.2020.114364] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Eg5, the product of Kif11 gene, also known as kinesin spindle protein, is a motor protein involved in the proper establishment of a bipolar mitotic spindle. Eg5 is one of the 45 different kinesins coded in the human genome of the kinesin motor protein superfamily. Over the last three decades Eg5 has attracted great interest as a promising new mitotic target. The identification of monastrol as specific inhibitor of the ATPase activity of the motor domain of Eg5 inhibiting the Eg5 microtubule motility in vitro and in cellulo sparked an intense interest in academia and industry to pursue the identification of novel small molecules that target Eg5 in order to be used in cancer chemotherapy based on the anti-mitotic strategy. Several Eg5 inhibitors entered clinical trials. Currently the field is faced with the problem that most of the inhibitors tested exhibited only limited efficacy. However, one Eg5 inhibitor, Arry-520 (clinical name filanesib), has demonstrated clinical efficacy in patients with multiple myeloma and is scheduled to enter phase III clinical trials. At the same time, new trends in Eg5 inhibitor research are emerging, including an increased interest in novel inhibitor binding sites and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of Eg5-inhibitor complexes, traces the possible development of resistance to Eg5 inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this active field in drug discovery.
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Affiliation(s)
- Isabel Garcia-Saez
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Dimitrios A Skoufias
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
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8
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Hunter B, Allingham JS. These motors were made for walking. Protein Sci 2020; 29:1707-1723. [PMID: 32472639 DOI: 10.1002/pro.3895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
Kinesins are a diverse group of adenosine triphosphate (ATP)-dependent motor proteins that transport cargos along microtubules (MTs) and change the organization of MT networks. Shared among all kinesins is a ~40 kDa motor domain that has evolved an impressive assortment of motility and MT remodeling mechanisms as a result of subtle tweaks and edits within its sequence. Several elegant studies of different kinesin isoforms have exposed the purpose of structural changes in the motor domain as it engages and leaves the MT. However, few studies have compared the sequences and MT contacts of these kinesins systematically. Along with clever strategies to trap kinesin-tubulin complexes for X-ray crystallography, new advancements in cryo-electron microscopy have produced a burst of high-resolution structures that show kinesin-MT interfaces more precisely than ever. This review considers the MT interactions of kinesin subfamilies that exhibit significant differences in speed, processivity, and MT remodeling activity. We show how their sequence variations relate to their tubulin footprint and, in turn, how this explains the molecular activities of previously characterized mutants. As more high-resolution structures become available, this type of assessment will quicken the pace toward establishing each kinesin's design-function relationship.
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Affiliation(s)
- Byron Hunter
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - John S Allingham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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9
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Bodrug T, Wilson-Kubalek EM, Nithianantham S, Thompson AF, Alfieri A, Gaska I, Major J, Debs G, Inagaki S, Gutierrez P, Gheber L, McKenney RJ, Sindelar CV, Milligan R, Stumpff J, Rosenfeld SS, Forth ST, Al-Bassam J. The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. eLife 2020; 9:e51131. [PMID: 31958056 PMCID: PMC7015671 DOI: 10.7554/elife.51131] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022] Open
Abstract
Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a regulatory mechanism involving direct binding between tail and motor domains and its fundamental role in microtubule sliding. Kinesin-5 tails decrease microtubule-stimulated ATP-hydrolysis by specifically engaging motor domains in the nucleotide-free or ADP states. Cryo-EM reveals that tail binding stabilizes an open motor domain ATP-active site. Full-length motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering. The tail is critical for motors to zipper together two microtubules by generating substantial sliding forces. The tail is essential for mitotic spindle localization, which becomes severely reduced in tail-deleted motors. Our studies suggest a revised microtubule-sliding model, in which kinesin-5 tails stabilize motor domains in the microtubule-bound state by slowing ATP-binding, resulting in high-force production at both homotetramer ends.
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Affiliation(s)
- Tatyana Bodrug
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Elizabeth M Wilson-Kubalek
- Department of Integrative Structural and Computational BiologyScripps Research InstituteLa JollaUnited States
| | - Stanley Nithianantham
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Alex F Thompson
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - April Alfieri
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Ignas Gaska
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Jennifer Major
- Department of Cancer BiologyLerner Research Institute, Cleveland ClinicLorainUnited States
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Garrett Debs
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | - Sayaka Inagaki
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Pedro Gutierrez
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Larisa Gheber
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and TechnologyBen-Gurion University of the NegevNegevIsrael
| | - Richard J McKenney
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | | | - Ronald Milligan
- Department of Integrative Structural and Computational BiologyScripps Research InstituteLa JollaUnited States
| | - Jason Stumpff
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Steven S Rosenfeld
- Department of Cancer BiologyLerner Research Institute, Cleveland ClinicLorainUnited States
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Scott T Forth
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Jawdat Al-Bassam
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
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