51
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Structural basis for the nuclear export activity of Importin13. EMBO J 2013; 32:899-913. [PMID: 23435562 DOI: 10.1038/emboj.2013.29] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/28/2013] [Indexed: 02/05/2023] Open
Abstract
Importin13 (Imp13) is a bidirectional karyopherin that can mediate both import and export of cargoes. Imp13 recognizes several import cargoes, which include the exon junction complex components Mago-Y14 and the E2 SUMO-conjugating enzyme Ubc9, and one known export cargo, the translation initiation factor 1A (eIF1A). To understand how Imp13 can perform double duty, we determined the 3.6-Å crystal structure of Imp13 in complex with RanGTP and with eIF1A. eIF1A binds at the inner surface of the Imp13 C-terminal arch adjacent and concomitantly to RanGTP illustrating how eIF1A can be exported by Imp13. Moreover, the 3.0-Å structure of Imp13 in its unbound state reveals the existence of an open conformation in the cytoplasm that explains export cargo release and completes the export branch of the Imp13 pathway. Finally, we demonstrate that Imp13 is able to bind and export eIF1A in vivo and that its function is essential.
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52
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Saito N, Matsuura Y. A 2.1-Å-resolution crystal structure of unliganded CRM1 reveals the mechanism of autoinhibition. J Mol Biol 2013; 425:350-64. [PMID: 23164569 DOI: 10.1016/j.jmb.2012.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 11/02/2012] [Accepted: 11/07/2012] [Indexed: 11/27/2022]
Abstract
CRM1 mediates nuclear export of numerous proteins and ribonucleoproteins containing a leucine-rich nuclear export signal (NES). Binding of RanGTP to CRM1 in the nucleus stabilizes cargo association with CRM1, and vice versa, but the mechanism underlying the positive cooperativity in RanGTP and NES binding to CRM1 remains incompletely understood. Herein we report a 2.1-Å-resolution crystal structure of unliganded Saccharomyces cerevisiae CRM1 (Xpo1p) that demonstrates that an internal loop of CRM1 (referred to as HEAT9 loop) is primarily responsible for maintaining the NES-binding cleft in a closed conformation, rendering CRM1 incapable of NES binding in the absence of RanGTP. The structure also shows that the C-terminal tail of CRM1 stabilizes the autoinhibitory conformation of the HEAT9 loop and thereby reinforces autoinhibition. Comparison with the structures of CRM1-NES-RanGTP complexes reveals how binding of RanGTP is associated with a series of allosteric conformational changes in CRM1 that lead to opening of the NES-binding cleft, allowing for stable binding of NES cargoes.
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Affiliation(s)
- Natsumi Saito
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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53
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Sun Q, Carrasco YP, Hu Y, Guo X, Mirzaei H, MacMillan J, Chook YM. Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1. Proc Natl Acad Sci U S A 2013; 110:1303-8. [PMID: 23297231 PMCID: PMC3557022 DOI: 10.1073/pnas.1217203110] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The polyketide natural product Leptomycin B inhibits nuclear export mediated by the karyopherin protein chromosomal region maintenance 1 (CRM1). Here, we present 1.8- to 2.0-Å-resolution crystal structures of CRM1 bound to Leptomycin B and related inhibitors Anguinomycin A and Ratjadone A. Structural and complementary chemical analyses reveal an unexpected mechanism of inhibition involving covalent conjugation and CRM1-mediated hydrolysis of the natural products' lactone rings. Furthermore, mutagenesis reveals the mechanism of hydrolysis by CRM1. The nuclear export signal (NES)-binding groove of CRM1 is able to drive a chemical reaction in addition to binding protein cargoes for transport through the nuclear pore complex.
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MESH Headings
- Acrylates/chemistry
- Acrylates/pharmacology
- Active Transport, Cell Nucleus/drug effects
- Amino Acid Substitution
- Crystallography, X-Ray
- Fatty Acids, Unsaturated/chemistry
- Fatty Acids, Unsaturated/metabolism
- Fatty Acids, Unsaturated/pharmacology
- Humans
- Hydrolysis
- Karyopherins/antagonists & inhibitors
- Karyopherins/chemistry
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Anatomic
- Mutagenesis, Site-Directed
- Nuclear Export Signals/genetics
- Protein Conformation
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Static Electricity
- Triazoles/chemistry
- Triazoles/pharmacology
- Exportin 1 Protein
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Affiliation(s)
| | - Yazmin P. Carrasco
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041
| | - Youcai Hu
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041
| | - Xiaofeng Guo
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041
| | - Hamid Mirzaei
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041
| | - John MacMillan
- Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041
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54
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Monecke T, Haselbach D, Voß B, Russek A, Neumann P, Thomson E, Hurt E, Zachariae U, Stark H, Grubmüller H, Dickmanns A, Ficner R. Structural basis for cooperativity of CRM1 export complex formation. Proc Natl Acad Sci U S A 2013; 110:960-5. [PMID: 23277578 PMCID: PMC3549083 DOI: 10.1073/pnas.1215214110] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-β superfamily termed importins and exportins. The highly versatile exportin chromosome region maintenance 1 (CRM1) is essential for nuclear depletion of numerous structurally and functionally unrelated protein and ribonucleoprotein cargoes. CRM1 has been shown to adopt a toroidal structure in several functional transport complexes and was thought to maintain this conformation throughout the entire nucleocytoplasmic transport cycle. We solved crystal structures of free CRM1 from the thermophilic eukaryote Chaetomium thermophilum. Surprisingly, unbound CRM1 exhibits an overall extended and pitched superhelical conformation. The two regulatory regions, namely the acidic loop and the C-terminal α-helix, are dramatically repositioned in free CRM1 in comparison with the ternary CRM1-Ran-Snurportin1 export complex. Single-particle EM analysis demonstrates that, in a noncrystalline environment, free CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations. Molecular dynamics simulations show that the C-terminal helix plays an important role in regulating the transition from an extended to a compact conformation and reveal how the binding site for nuclear export signals of cargoes is modulated by different CRM1 conformations. Combining these results, we propose a model for the cooperativity of CRM1 export complex assembly involving the long-range allosteric communication between the distant binding sites of GTP-bound Ran and cargo.
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MESH Headings
- Active Transport, Cell Nucleus
- Allosteric Regulation
- Amino Acid Sequence
- Binding Sites
- Chaetomium/chemistry
- Chaetomium/genetics
- Chaetomium/metabolism
- Crystallography, X-Ray
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Fungal Proteins/ultrastructure
- Karyopherins/chemistry
- Karyopherins/genetics
- Karyopherins/metabolism
- Karyopherins/ultrastructure
- Microscopy, Electron
- Models, Biological
- Models, Molecular
- Molecular Dynamics Simulation
- Molecular Sequence Data
- Multiprotein Complexes/chemistry
- Multiprotein Complexes/metabolism
- Protein Conformation
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Cytoplasmic and Nuclear/ultrastructure
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Recombinant Fusion Proteins/ultrastructure
- Sequence Homology, Amino Acid
- Static Electricity
- Exportin 1 Protein
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
| | - David Haselbach
- Dreidimensionale Kryo-Elektronenmikroskopie, Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
| | - Béla Voß
- Abteilung für Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
| | - Andreas Russek
- Abteilung für Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
| | - Piotr Neumann
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
| | - Emma Thomson
- Biochemie-Zentrum der Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Ulrich Zachariae
- Scottish Universities' Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom; and
| | - Holger Stark
- Dreidimensionale Kryo-Elektronenmikroskopie, Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
- Abteilung für Molekulare Kryo-Elektronenmikroskopie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
| | - Helmut Grubmüller
- Abteilung für Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
| | - Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, D-37077 Göttingen, Germany
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55
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Etchin J, Sun Q, Kentsis A, Farmer A, Zhang ZC, Sanda T, Mansour MR, Barcelo C, McCauley D, Kauffman M, Shacham S, Christie AL, Kung AL, Rodig SJ, Chook YM, Look AT. Antileukemic activity of nuclear export inhibitors that spare normal hematopoietic cells. Leukemia 2013; 27:66-74. [PMID: 22847027 PMCID: PMC3542631 DOI: 10.1038/leu.2012.219] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/12/2012] [Accepted: 07/12/2012] [Indexed: 11/29/2022]
Abstract
Drugs that target the chief mediator of nuclear export, chromosome region maintenance 1 protein (CRM1) have potential as therapeutics for leukemia, but existing CRM1 inhibitors show variable potencies and a broad range of cytotoxic effects. Here, we report the structural analysis and antileukemic activity of a new generation of small-molecule inhibitors of CRM1. Designated selective inhibitors of nuclear export (SINE), these compounds were developed using molecular modeling to screen a small virtual library of compounds against the nuclear export signal (NES) groove of CRM1. The 2.2-Å crystal structure of the CRM1-Ran-RanBP1 complex bound to KPT-251, a representative molecule of this class of inhibitors, shows that the drug occupies part of the groove in CRM1 that is usually occupied by the NES, but penetrates much deeper into the groove and blocks CRM1-directed protein export. SINE inhibitors exhibit potent antileukemic activity, inducing apoptosis at nanomolar concentrations in a panel of 14 human acute myeloid leukemia (AML) cell lines representing different molecular subtypes of the disease. When administered orally to immunodeficient mice engrafted with human AML cells, KPT-251 had potent antileukemic activity with negligible toxicity to normal hematopoietic cells. Thus, KPT-SINE CRM1 antagonists represent a novel class of drugs that warrant further testing in AML patients.
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MESH Headings
- Active Transport, Cell Nucleus/drug effects
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Apoptosis
- Blotting, Western
- Cell Cycle
- Cell Nucleus/metabolism
- Cell Proliferation
- Cells, Cultured
- Crystallization
- Crystallography, X-Ray
- Female
- Hematopoietic Stem Cells
- Humans
- Interleukin Receptor Common gamma Subunit/physiology
- Karyopherins/chemistry
- Karyopherins/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Nuclear Export Signals
- Nuclear Proteins/chemistry
- Nuclear Proteins/metabolism
- Protein Binding
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Small Molecule Libraries
- Xenograft Model Antitumor Assays
- ran GTP-Binding Protein/chemistry
- ran GTP-Binding Protein/metabolism
- Exportin 1 Protein
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Affiliation(s)
- J Etchin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - Q Sun
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - A Kentsis
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - A Farmer
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Z C Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - T Sanda
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - M R Mansour
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - C Barcelo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - D McCauley
- Karyopharm Therapeutics, Natick, MA, USA
| | - M Kauffman
- Karyopharm Therapeutics, Natick, MA, USA
| | - S Shacham
- Karyopharm Therapeutics, Natick, MA, USA
| | - A L Christie
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - A L Kung
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - S J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Y M Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - A T Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
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56
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Koyama M, Matsuura Y. Mechanistic insights from the recent structures of the CRM1 nuclear export complex and its disassembly intermediate. Biophysics (Nagoya-shi) 2012; 8:145-50. [PMID: 27493531 PMCID: PMC4629651 DOI: 10.2142/biophysics.8.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/16/2012] [Indexed: 01/04/2023] Open
Abstract
CRM1 (also known as exportin 1 or Xpo1) is the most versatile nuclear export receptor (exportin) that carries a broad range of proteins and ribonucleoproteins from the nucleus to the cytoplasm through the nuclear pore complex. The majority of the export substrates of CRM1 contain a short peptide sequence, so-called leucine-rich nuclear export signal (NES), which typically harbor four or five characteristically spaced hydrophobic residues. The transport directionality is determined by the small GTPase Ran and Ran-binding proteins that control the binding and dissociation of cargo. Here we review recent structural studies that advanced understanding of how NES is specifically recognized by CRM1 in the nucleus, and how NES is rapidly dissociated from CRM1 in the cytoplasm.
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Affiliation(s)
- Masako Koyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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57
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Xu D, Farmer A, Collett G, Grishin NV, Chook YM. Sequence and structural analyses of nuclear export signals in the NESdb database. Mol Biol Cell 2012; 23:3677-93. [PMID: 22833565 PMCID: PMC3442415 DOI: 10.1091/mbc.e12-01-0046] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 05/29/2012] [Accepted: 07/16/2012] [Indexed: 12/23/2022] Open
Abstract
We compiled >200 nuclear export signal (NES)-containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the Φ1-X(3)-Φ2-X(2)-Φ3-X-Φ4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt α-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified.
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Affiliation(s)
- Darui Xu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Alicia Farmer
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Garen Collett
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Nick V. Grishin
- Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
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58
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Xu D, Grishin NV, Chook YM. NESdb: a database of NES-containing CRM1 cargoes. Mol Biol Cell 2012; 23:3673-6. [PMID: 22833564 PMCID: PMC3442414 DOI: 10.1091/mbc.e12-01-0045] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 05/16/2012] [Accepted: 07/16/2012] [Indexed: 12/27/2022] Open
Abstract
The leucine-rich nuclear export signal (NES) is the only known class of targeting signal that directs macromolecules out of the cell nucleus. NESs are short stretches of 8-15 amino acids with regularly spaced hydrophobic residues that bind the export karyopherin CRM1. NES-containing proteins are involved in numerous cellular and disease processes. We compiled a database named NESdb that contains 221 NES-containing CRM1 cargoes that were manually curated from the published literature. Each NESdb entry is annotated with information about sequence and structure of both the NES and the cargo protein, as well as information about experimental evidence of NES-mapping and CRM1-mediated nuclear export. NESdb will be updated regularly and will serve as an important resource for nuclear export signals. NESdb is freely available to nonprofit organizations at http://prodata.swmed.edu/LRNes.
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Affiliation(s)
- Darui Xu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Nick V. Grishin
- Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390
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59
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60
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Turner JG, Dawson J, Sullivan DM. Nuclear export of proteins and drug resistance in cancer. Biochem Pharmacol 2012; 83:1021-32. [PMID: 22209898 PMCID: PMC4521586 DOI: 10.1016/j.bcp.2011.12.016] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/09/2011] [Accepted: 12/12/2011] [Indexed: 12/14/2022]
Abstract
The intracellular location of a protein is crucial to its normal functioning in a cell. Cancer cells utilize the normal processes of nuclear-cytoplasmic transport through the nuclear pore complex of a cell to effectively evade anti-neoplastic mechanisms. CRM1-mediated export is increased in various cancers. Proteins that are exported in cancer include tumor-suppressive proteins such as retinoblastoma, APC, p53, BRAC1, FOXO proteins, INI1/hSNF5, galectin-3, Bok, nucleophosmin, RASSF2, Merlin, p21(CIP), p27(KIP1), N-WASP/FAK, estradiol receptor and Tob, drug targets topoisomerase I and IIα and BCR-ABL, and the molecular chaperone protein Hsp90. Here, we review in detail the current processes and known structures involved in the export of a protein through the nuclear pore complex. We also discuss the export receptor molecule CRM1 and its binding to the leucine-rich nuclear export signal of the cargo protein and the formation of a nuclear export trimer with RanGTP. The therapeutic potential of various CRM1 inhibitors will be addressed, including leptomycin B, ratjadone, KOS-2464, and specific small molecule inhibitors of CRM1, N-azolylacrylate analogs, FOXO export inhibitors, valtrate, acetoxychavicol acetate, CBS9106, and SINE inhibitors. We will also discuss examples of how drug resistance may be reversed by targeting the exported proteins topoisomerase IIα, BCR-ABL, and galectin-3. As effective and less toxic CRM1 export inhibitors become available, they may be used as both single agents and in combination with current chemotherapeutic drugs. We believe that the future development of low-toxicity, small-molecule CRM1 inhibitors may provide a new approach to treating cancer.
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Affiliation(s)
- Joel G. Turner
- Blood and Marrow Transplant Department and Experimental Therapeutics Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Jana Dawson
- Blood and Marrow Transplant Department and Experimental Therapeutics Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Daniel M. Sullivan
- Blood and Marrow Transplant Department and Experimental Therapeutics Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
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61
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Zhang ZC, Satterly N, Fontoura BMA, Chook YM. Evolutionary development of redundant nuclear localization signals in the mRNA export factor NXF1. Mol Biol Cell 2011; 22:4657-68. [PMID: 21965294 PMCID: PMC3226482 DOI: 10.1091/mbc.e11-03-0222] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unexpected redundancy in the nuclear import pathways used by the essential mRNA export factor NXF1 increases progressively from fungi to nematodes and insects to chordates, potentially paralleling the increasing complexity in mRNA export regulation and the evolution of new nuclear functions for NXF1. In human cells, the mRNA export factor NXF1 resides in the nucleoplasm and at nuclear pore complexes. Karyopherin β2 or transportin recognizes a proline–tyrosine nuclear localization signal (PY-NLS) in the N-terminal tail of NXF1 and imports it into the nucleus. Here biochemical and cellular studies to understand the energetic organization of the NXF1 PY-NLS reveal unexpected redundancy in the nuclear import pathways used by NXF1. Human NXF1 can be imported via importin β, karyopherin β2, importin 4, importin 11, and importin α. Two NLS epitopes within the N-terminal tail, an N-terminal basic segment and a C-terminal R-X2-5-P-Y motif, provide the majority of binding energy for all five karyopherins. Mutation of both NLS epitopes abolishes binding to the karyopherins, mislocalized NXF1 to the cytoplasm, and significantly compromised its mRNA export function. The understanding of how different karyopherins recognize human NXF1, the examination of NXF1 sequences from divergent eukaryotes, and the interactions of NXF1 homologues with various karyopherins reveals the evolutionary development of redundant NLSs in NXF1 of higher eukaryotes. Redundancy of nuclear import pathways for NXF1 increases progressively from fungi to nematodes and insects to chordates, potentially paralleling the increasing complexity in mRNA export regulation and the evolution of new nuclear functions for NXF1.
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Affiliation(s)
- Zi Chao Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
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62
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Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E. Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell 2011; 146:277-89. [PMID: 21784248 DOI: 10.1016/j.cell.2011.06.039] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 04/15/2011] [Accepted: 06/24/2011] [Indexed: 01/25/2023]
Abstract
Despite decades of research, the structure and assembly of the nuclear pore complex (NPC), which is composed of ∼30 nucleoporins (Nups), remain elusive. Here, we report the genome of the thermophilic fungus Chaetomium thermophilum (ct) and identify the complete repertoire of Nups therein. The thermophilic proteins show improved properties for structural and biochemical studies compared to their mesophilic counterparts, and purified ctNups enabled the reconstitution of the inner pore ring module that spans the width of the NPC from the anchoring membrane to the central transport channel. This module is composed of two large Nups, Nup192 and Nup170, which are flexibly bridged by short linear motifs made up of linker Nups, Nic96 and Nup53. This assembly illustrates how Nup interactions can generate structural plasticity within the NPC scaffold. Our findings therefore demonstrate the utility of the genome of a thermophilic eukaryote for studying complex molecular machines.
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Affiliation(s)
- Stefan Amlacher
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany
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63
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Fox AM, Ciziene D, McLaughlin SH, Stewart M. Electrostatic interactions involving the extreme C terminus of nuclear export factor CRM1 modulate its affinity for cargo. J Biol Chem 2011; 286:29325-29335. [PMID: 21708948 PMCID: PMC3190738 DOI: 10.1074/jbc.m111.245092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 06/17/2011] [Indexed: 12/11/2022] Open
Abstract
The toroid-shaped nuclear protein export factor CRM1 is constructed from 21 tandem HEAT repeats, each of which contains an inner (B) and outer (A) α-helix joined by loops. Proteins targeted for export have a nuclear export signal (NES) that binds between the A-helices of HEAT repeats 11 and 12 on the outer surface of CRM1. RanGTP binding increases the affinity of CRM1 for NESs. In the absence of RanGTP, the CRM1 C-terminal helix, together with the HEAT repeat 9 loop, modulates its affinity for NESs. Here we show that there is an electrostatic interaction between acidic residues at the extreme distal tip of the C-terminal helix and basic residues on the HEAT repeat 12 B-helix that lies on the inner surface of CRM1 beneath the NES binding site. Small angle x-ray scattering indicates that the increased affinity for NESs generated by mutations in the C-terminal helix is not associated with large scale changes in CRM1 conformation, consistent with the modulation of NES affinity being mediated by a local change in CRM1 near the NES binding site. These data also suggest that in the absence of RanGTP, the C-terminal helix lies across the CRM1 toroid in a position similar to that seen in the CRM1-Snurportin crystal structure. By creating local changes that stabilize the NES binding site in its closed conformation and thereby reducing the affinity of CRM1 for NESs, the C-terminal helix and HEAT 9 loop facilitate release of NES-containing cargo in the cytoplasm and also inhibit their return to the nucleus.
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Affiliation(s)
- Abigail M Fox
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Danguole Ciziene
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Stephen H McLaughlin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.
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Ellyard JI, Benk AS, Taylor B, Rada C, Neuberger MS. The dependence of Ig class-switching on the nuclear export sequence of AID likely reflects interaction with factors additional to Crm1 exportin. Eur J Immunol 2011; 41:485-90. [PMID: 21268017 PMCID: PMC3437479 DOI: 10.1002/eji.201041011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 10/21/2010] [Accepted: 11/09/2010] [Indexed: 01/31/2023]
Abstract
Activation-induced deaminase (AID) is a B lymphocyte-specific DNA deaminase that triggers Ig class-switch recombination (CSR) and somatic hypermutation. It shuttles between cytoplasm and nucleus, containing a nuclear export sequence (NES) at its carboxyterminus. Intriguingly, the precise nature of this NES is critical to AID's function in CSR, though not in somatic hypermutation. Many alterations to the NES, while preserving its nuclear export function, destroy CSR ability. We have previously speculated that AID's ability to potentiate CSR may critically depend on the affinity of interaction between its NES and Crm1 exportin. Here, however, by comparing multiple AID NES mutants, we find that - beyond a requirement for threshold Crm1 binding - there is little correlation between CSR and Crm1 binding affinity. The results suggest that CSR, as well as the stabilisation of AID, depend on an interaction between the AID C-terminal decapeptide and factor(s) additional to Crm1.
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Affiliation(s)
- Julia I Ellyard
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, UK
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65
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Han H, Cui ZQ, Wang W, Zhang ZP, Wei HP, Zhou YF, Zhang XE. New regulatory mechanisms for the intracellular localization and trafficking of influenza A virus NS1 protein revealed by comparative analysis of A/PR/8/34 and A/Sydney/5/97. J Gen Virol 2010; 91:2907-17. [PMID: 20826615 DOI: 10.1099/vir.0.024943-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During influenza A virus infection, the NS1 protein is engaged in different functions in different intracellular compartments. In this study, we showed that the NS1 of A/PR/8/34 localized in different positions from that of A/Sydney/5/97 when transiently expressed in Madin-Darby canine kidney cells. Residue 221 of NS1 was identified to be a new key residue involved in the C-terminal nuclear localization signal (NLS) and nucleolar localization signal (NoLS) of NS1 from A/Sydney/5/97. Analysis of chimeric NS1 and further mutants showed that residues responsible for the binding between NS1 and the cleavage and polyadenylation specificity factor (CPSF) are correlated with the intracellular localization of transiently expressed NS1 proteins. Fluorescence loss in photobleaching imaging revealed that the NS1 protein with both functional NLSs and nuclear export signal (NES) was able to shuttle between the nucleus and cytoplasm. Drug inhibition experiments and fluorescence resonance energy transfer analysis suggested that NS1 was exported out of the cell nuclei via a Crm1-independent pathway. Moreover, it is likely that another cytoplasmic localization-related sequence exists in the NS1 protein other than the leucine-rich NES. These findings provide new insights into the mechanism of intracellular localization and trafficking of influenza A virus NS1 protein, which is important for understanding its function.
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Affiliation(s)
- Han Han
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan 430071, PR China
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66
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Xu D, Farmer A, Chook YM. Recognition of nuclear targeting signals by Karyopherin-β proteins. Curr Opin Struct Biol 2010; 20:782-90. [PMID: 20951026 DOI: 10.1016/j.sbi.2010.09.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/10/2010] [Accepted: 09/15/2010] [Indexed: 12/22/2022]
Abstract
The Karyopherin-β family of nuclear transport factors mediates the majority of nucleocytoplasmic transport. Although each of the 19 Karyopherin-βs transports unique sets of cargos, only three classes of nuclear localization and export signals, or NLSs and NESs, have been characterized. The short basic classical-NLS was first discovered in the 1980s and their karyopherin-bound structures were first reported more than 10 years ago. More recently, structural and biophysical studies of Karyopherin-β2-cargo complexes led to definition of the complex and diverse PY-NLS. Structural knowledge of the leucine-rich NES is finally available more than 10 years after the discovery of its recognition by the exportin CRM1. We review recent findings relating to how these three classes of nuclear targeting signals are recognized by their Karyopherin-β nuclear transport factors.
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Affiliation(s)
- Darui Xu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
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67
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Forwood JK, Lange A, Zachariae U, Marfori M, Preast C, Grubmüller H, Stewart M, Corbett AH, Kobe B. Quantitative Structural Analysis of Importin-β Flexibility: Paradigm for Solenoid Protein Structures. Structure 2010; 18:1171-83. [DOI: 10.1016/j.str.2010.06.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 05/04/2010] [Accepted: 06/01/2010] [Indexed: 12/24/2022]
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68
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Koyama M, Matsuura Y. An allosteric mechanism to displace nuclear export cargo from CRM1 and RanGTP by RanBP1. EMBO J 2010; 29:2002-13. [PMID: 20485264 PMCID: PMC2892370 DOI: 10.1038/emboj.2010.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/16/2010] [Indexed: 11/09/2022] Open
Abstract
The karyopherin CRM1 mediates nuclear export of proteins and ribonucleoproteins bearing a leucine-rich nuclear export signal (NES). To elucidate the precise mechanism by which NES-cargos are dissociated from CRM1 in the cytoplasm, which is important for transport directionality, we determined a 2.0-A resolution crystal structure of yeast CRM1:RanBP1:RanGTP complex, an intermediate in the disassembly of the CRM1 nuclear export complex. The structure shows that on association of Ran-binding domain (RanBD) of RanBP1 with CRM1:NES-cargo:RanGTP complex, RanBD and the C-terminal acidic tail of Ran induce a large movement of the intra-HEAT9 loop of CRM1. The loop moves to the CRM1 inner surface immediately behind the NES-binding site and causes conformational rearrangements in HEAT repeats 11 and 12 so that the hydrophobic NES-binding cleft on the CRM1 outer surface closes, squeezing out the NES-cargo. This allosteric mechanism accelerates dissociation of NES by over two orders of magnitude. Structure-based mutagenesis indicated that the HEAT9 loop also functions as an allosteric autoinhibitor to stabilize CRM1 in a conformation that is unable to bind NES-cargo in the absence of RanGTP.
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Affiliation(s)
- Masako Koyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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69
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Structures of the tRNA export factor in the nuclear and cytosolic states. Nature 2009; 461:60-5. [PMID: 19680239 DOI: 10.1038/nature08394] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 08/06/2009] [Indexed: 11/08/2022]
Abstract
Transfer RNAs are among the most ubiquitous molecules in cells, central to decoding information from messenger RNAs on translating ribosomes. In eukaryotic cells, tRNAs are actively transported from their site of synthesis in the nucleus to their site of function in the cytosol. This is mediated by a dedicated nucleo-cytoplasmic transport factor of the karyopherin-beta family (Xpot, also known as Los1 in Saccharomyces cerevisiae). Here we report the 3.2 A resolution structure of Schizosaccharomyces pombe Xpot in complex with tRNA and RanGTP, and the 3.1 A structure of unbound Xpot, revealing both nuclear and cytosolic snapshots of this transport factor. Xpot undergoes a large conformational change on binding cargo, wrapping around the tRNA and, in particular, binding to the tRNA 5' and 3' ends. The binding mode explains how Xpot can recognize all mature tRNAs in the cell and yet distinguish them from those that have not been properly processed, thus coupling tRNA export to quality control.
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Dong X, Biswas A, Süel KE, Jackson LK, Martinez R, Gu H, Chook YM. Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 2009; 458:1136-41. [PMID: 19339969 PMCID: PMC3437623 DOI: 10.1038/nature07975] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 03/06/2009] [Indexed: 01/17/2023]
Abstract
CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 A structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.
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Affiliation(s)
- Xiuhua Dong
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, Texas 75390-9041, USA
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