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Tsimbalyuk S, Donnelly CM, Forwood JK. Structural characterization of human importin alpha 7 in its cargo-free form at 2.5 Å resolution. Sci Rep 2022; 12:315. [PMID: 35013395 PMCID: PMC8748863 DOI: 10.1038/s41598-021-03729-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022] Open
Abstract
Shuttling of macromolecules between nucleus and cytoplasm is a tightly regulated process mediated through specific interactions between cargo and nuclear transport proteins. In the classical nuclear import pathway, importin alpha recognizes cargo exhibiting a nuclear localization signal, and this complex is transported through the nuclear pore complex by importin beta. Humans possess seven importin alpha isoforms that can be grouped into three subfamilies, with many cargoes displaying specificity towards these importin alpha isoforms. The cargo binding sites within importin alpha isoforms are highly conserved in sequence, suggesting that specificity potentially relies on structural differences. Structures of some importin alpha isoforms, both in cargo-bound and free states, have been previously solved. However, there are currently no known structures of cargo free importin alpha isoforms within subfamily 3 (importin alpha 5, 6, 7). Here, we present the first crystal structure of human importin alpha 7 lacking the IBB domain solved at 2.5 Å resolution. The structure reveals a typical importin alpha architecture comprised of ten armadillo repeats and is most structurally conserved with importin alpha 5. Very little difference in structure was observed between the cargo-bound and free states, implying that importin alpha 7 does not undergo conformational change when binding cargo. These structural insights provide a strong platform for further evaluation of structure–function relationships and understanding how isoform specificity within the importin alpha family plays a role in nuclear transport in health and disease.
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Affiliation(s)
- S Tsimbalyuk
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - C M Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - J K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia. .,School of Dentistry and Medical Sciences, Charles Sturt University, Room 2, National Life Sciences Hub, Wagga Wagga, NSW, 2678, Australia.
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2
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Mechanistic and structural insights into histone H2A–H2B chaperone in chromatin regulation. Biochem J 2020; 477:3367-3386. [DOI: 10.1042/bcj20190852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/15/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
Histone chaperones include a wide variety of proteins which associate with histones and regulate chromatin structure. The classic H2A–H2B type of histone chaperones, and the chromatin remodeling complex components possessing H2A–H2B chaperone activity, show a broad range of structures and functions. Rapid progress in the structural and functional study of H2A–H2B chaperones extends our knowledge about the epigenetic regulation of chromatin. In this review, we summarize the most recent advances in the understanding of the structure and function of H2A–H2B chaperones that interact with either canonical or variant H2A–H2B dimers. We discuss the current knowledge of the H2A–H2B chaperones, which present no preference for canonical and variant H2A–H2B dimers, describing how they interact with H2A–H2B to fulfill their functions. We also review recent advances of H2A variant-specific chaperones, demarcating how they achieve specific recognition for histone variant H2A.Z and how these interactions regulate chromatin structure by nucleosome editing. We highlight the universal mechanism underlying H2A–H2B dimers recognition by a large variety of histone chaperones. These findings will shed insight into the biological impacts of histone chaperone, chromatin remodeling complex, and histone variants in chromatin regulation.
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López DJ, Rodríguez JA, Bañuelos S. Nucleophosmin, a multifunctional nucleolar organizer with a role in DNA repair. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140532. [PMID: 32853771 DOI: 10.1016/j.bbapap.2020.140532] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022]
Abstract
Nucleophosmin (NPM1) is a mostly nucleolar protein with crucial functions in cell growth and homeostasis, including regulation of ribosome biogenesis and stress response. Such multiple activities rely on its ability to interact with nucleic acids and with hundreds of proteins, as well as on a dynamic subcellular distribution. NPM1 is thus regulated by a complex interplay between localization and interactions, further modulated by post-translational modifications. NPM1 is a homopentamer, with globular domains connected by long, intrinsically disordered linkers. This configuration allows NPM1 to engage in liquid-liquid phase separation phenomena, which could underlie a key role in nucleolar organization. Here, we will discuss NPM1 conformational and functional versatility, emphasizing its emerging, and still largely unexplored, role in DNA damage repair. Since NPM1 is altered in a subtype of acute myeloid leukaemia (AML), we will also present ongoing research on the molecular mechanisms underlying its pathogenic role and potential NPM1-targeting therapeutic strategies.
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Affiliation(s)
- David J López
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - José A Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Sonia Bañuelos
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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Díaz-García C, Hornos F, Giudici AM, Cámara-Artigas A, Luque-Ortega JR, Arbe A, Rizzuti B, Alfonso C, Forwood JK, Iovanna JL, Gómez J, Prieto M, Coutinho A, Neira JL. Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution. Biochim Biophys Acta Gen Subj 2020; 1864:129609. [PMID: 32234409 DOI: 10.1016/j.bbagen.2020.129609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. There are several human isoforms of importin α; among them, importin α3 has a particularly high flexibility. METHODS We studied the conformational stability of intact importin α3 (Impα3) and its truncated form, where the 64-residue-long, N-terminal importin-β-binding domain (IBB) has been removed (ΔImpα3), in a wide pH range, with several spectroscopic, biophysical, biochemical methods and with molecular dynamics (MD). RESULTS Both species acquired native-like structure between pH 7 and 10.0, where Impα3 was a dimer (with an apparent self-association constant of ~10 μM) and ΔImpα3 had a higher tendency to self-associate than the intact species. The acquisition of secondary, tertiary and quaternary structure, and the burial of hydrophobic patches, occurred concomitantly. Both proteins unfolded irreversibly at physiological pH, by using either temperature or chemical denaturants, through several partially folded intermediates. The MD simulations support the presence of these intermediates. CONCLUSIONS The thermal stability of Impα3 at physiological pH was very low, but was higher than that of ΔImpα3. Both proteins were stable in a narrow pH range, and they unfolded at physiological pH populating several intermediate species. GENERAL SIGNIFICANCE The low conformational stability explains the flexibility of Impα3, which is needed to carry out its recognition of complex cargo sequences.
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Affiliation(s)
- Clara Díaz-García
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Felipe Hornos
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | | | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain
| | - Juan Román Luque-Ortega
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Materials Physics Center (MPC), 20018 San Sebastián, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Javier Gómez
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Manuel Prieto
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Ana Coutinho
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1649-004 Lisboa, Portugal
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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Dominguez-Berrocal L, Cirri E, Zhang X, Andrini L, Marin GH, Lebel-Binay S, Rebollo A. New Therapeutic Approach for Targeting Hippo Signalling Pathway. Sci Rep 2019; 9:4771. [PMID: 30886324 PMCID: PMC6423280 DOI: 10.1038/s41598-019-41404-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/08/2019] [Indexed: 12/29/2022] Open
Abstract
Nuclear localization signals are short amino acid sequences that target proteins for nuclear import. In this manuscript, we have generated a chimeric tri-functional peptide composed of a cell penetrating peptide (CPP), a nuclear localization sequence and an interfering peptide blocking the interaction between TEAD and YAP, two transcription factors involved in the Hippo signalling pathway, whose deregulation is related to several types of cancer. We have validated the cell penetration and nuclear localization by flow cytometry and fluorescence microscopy and shown that the new generated peptide displays an apoptotic effect in tumor cell lines thanks to the specific nuclear delivery of the cargo, which targets a protein/protein interaction in the nucleus. In addition, the peptide has an anti-tumoral effect in vivo in xenograft models of breast cancer. The chimeric peptide designed in the current study shows encouraging prospects for developing nuclear anti- neoplastic drugs.
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Affiliation(s)
| | - Erica Cirri
- PEP Therapy, 45 rue du Cardinal Lemoine, 75005, Paris, France
| | - Xiguang Zhang
- CIMI Paris, Inserm U1135, 91, bd de l'hôpital, 75013, Paris, France
| | - Laura Andrini
- Facultad de Ciencias Medicas, UNLP-CONICET, 60 and 120, Code, 1900, La Plata, Argentina
| | - Gustavo H Marin
- Facultad de Ciencias Medicas, UNLP-CONICET, 60 and 120, Code, 1900, La Plata, Argentina
| | | | - Angelita Rebollo
- CIMI Paris, Inserm U1135, 91, bd de l'hôpital, 75013, Paris, France.
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6
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Zheng W, Wang R, Liu X, Tian S, Yao B, Chen A, Jin S, Li Y. Structural insights into the nuclear import of the histone acetyltransferase males-absent-on-the-first by importin α1. Traffic 2017; 19:19-28. [PMID: 28991411 DOI: 10.1111/tra.12534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 12/21/2022]
Abstract
The histone acetyltransferase males-absent-on-the-first (MOF) acetylates the histone H4, a modification important for many biological processes, including chromatin organization, transcriptional regulation, DNA replication, recombination and repair, as well as autophagy. Depletion of MOF induces serious consequences because of the reduction of histone acetylation, such as nuclear morphological defects and cancer. Despite the critical roles of MOF in the nucleus, the structural or functional mechanisms of the nucleocytoplasmic transport of MOF remain elusive. Here, we identified novel importin α1-specific nuclear localization signals (NLSs) in the N-terminal of human MOF. The crystal structure of MOF NLSs in complex with importin α1 further revealed a unique binding mode of MOF, with two independent NLSs binding to importin α1 major and minor sites, respectively. The second NLS of MOF displays an unexpected α-helical conformation in the C-terminus, with more extensive contacts with importin α1 not limited in the minor site. Mutations of the key residues on MOF and importin α1 lead to the reduction of their interaction as well as the nuclear import of MOF, revealing an essential role of NLS2 of MOF in interacting with importin α1 minor site. Taken together, we provide structural mechanisms underlying the nucleocytoplasmic transport of MOF, which will be of great importance in understanding the functional regulation of MOF in various biological processes.
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Affiliation(s)
- Weili Zheng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xi Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Siyu Tian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Benqiang Yao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Ang Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Shikai Jin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Yong Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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7
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Kapinos LE, Huang B, Rencurel C, Lim RYH. Karyopherins regulate nuclear pore complex barrier and transport function. J Cell Biol 2017; 216:3609-3624. [PMID: 28864541 PMCID: PMC5674887 DOI: 10.1083/jcb.201702092] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/16/2017] [Accepted: 08/08/2017] [Indexed: 01/01/2023] Open
Abstract
Kapinos et al. show that nuclear pore complex permeability and cargo release functionalities are concomitantly regulated by karyopherin occupancy and turnover in a systematic continuum. This highlights increasingly important roles for the soluble nucleocytoplasmic transport machinery that depart from established views of the nuclear pore complex selectivity mechanism. Nucleocytoplasmic transport is sustained by karyopherins (Kaps) and a Ran guanosine triphosphate (RanGTP) gradient that imports nuclear localization signal (NLS)–specific cargoes (NLS-cargoes) into the nucleus. However, how nuclear pore complex (NPC) barrier selectivity, Kap traffic, and NLS-cargo release are systematically linked and simultaneously regulated remains incoherent. In this study, we show that Kapα facilitates Kapβ1 turnover and occupancy at the NPC in a RanGTP-dependent manner that is directly coupled to NLS-cargo release and NPC barrier function. This is underpinned by the binding affinity of Kapβ1 to phenylalanine–glycine nucleoporins (FG Nups), which is comparable with RanGTP·Kapβ1, but stronger for Kapα·Kapβ1. On this basis, RanGTP is ineffective at releasing standalone Kapβ1 from NPCs. Depleting Kapα·Kapβ1 by RanGTP further abrogates NPC barrier function, whereas adding back Kapβ1 rescues it while Kapβ1 turnover softens it. Therefore, the FG Nups are necessary but insufficient for NPC barrier function. We conclude that Kaps constitute integral constituents of the NPC whose barrier, transport, and cargo release functionalities establish a continuum under a mechanism of Kap-centric control.
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Affiliation(s)
- Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Binlu Huang
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Chantal Rencurel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
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8
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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9
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Chen C, Wang JCY, Pierson EE, Keifer DZ, Delaleau M, Gallucci L, Cazenave C, Kann M, Jarrold MF, Zlotnick A. Importin β Can Bind Hepatitis B Virus Core Protein and Empty Core-Like Particles and Induce Structural Changes. PLoS Pathog 2016; 12:e1005802. [PMID: 27518410 PMCID: PMC4982637 DOI: 10.1371/journal.ppat.1005802] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/11/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) capsids are found in many forms: immature single-stranded RNA-filled cores, single-stranded DNA-filled replication intermediates, mature cores with relaxed circular double-stranded DNA, and empty capsids. A capsid, the protein shell of the core, is a complex of 240 copies of core protein. Mature cores are transported to the nucleus by a complex that includes both importin α and importin β (Impα and Impβ), which bind to the core protein's C-terminal domains (CTDs). Here we have investigated the interactions of HBV core protein with importins in vitro. Strikingly, empty capsids and free core protein can bind Impβ without Impα. Cryo-EM image reconstructions show that the CTDs, which are located inside the capsid, can extrude through the capsid to be bound by Impβ. Impβ density localized on the capsid exterior near the quasi-sixfold vertices, suggested a maximum of 30 Impβ per capsid. However, examination of complexes using single molecule charge-detection mass spectrometry indicate that some complexes include over 90 Impβ molecules. Cryo-EM of capsids incubated with excess Impβ shows a population of damaged particles and a population of "dark" particles with internal density, suggesting that Impβ is effectively swallowed by the capsids, which implies that the capsids transiently open and close and can be destabilized by Impβ. Though the in vitro complexes with great excess of Impβ are not biological, these results have implications for trafficking of empty capsids and free core protein; activities that affect the basis of chronic HBV infection.
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Affiliation(s)
- Chao Chen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Joseph Che-Yen Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Elizabeth E. Pierson
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - David Z. Keifer
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Mildred Delaleau
- Universite de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Lara Gallucci
- Universite de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Christian Cazenave
- Universite de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Michael Kann
- Universite de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
- CHU de Bordeaux, Bordeaux, France
| | - Martin F. Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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10
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Bending-Twisting Motions and Main Interactions in Nucleoplasmin Nuclear Import. PLoS One 2016; 11:e0157162. [PMID: 27258022 PMCID: PMC4892583 DOI: 10.1371/journal.pone.0157162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
Alpha solenoid proteins play a key role in regulating the classical nuclear import pathway, recognizing a target protein and transporting it into the nucleus. Importin-α (Impα) is the solenoid responsible for cargo protein recognition, and it has been extensively studied by X-ray crystallography to understand the binding specificity. To comprehend the main motions of Impα and to extend the information about the critical interactions during carrier-cargo recognition, we surveyed different conformational states based on molecular dynamics (MD) and normal mode (NM) analyses. Our model of study was a crystallographic structure of Impα complexed with the classical nuclear localization sequence (cNLS) from nucleoplasmin (Npl), which was submitted to multiple 100 ns of MD simulations. Representative conformations were selected for calculating the 87 lowest frequencies NMs of vibration, and a displacement approach was applied along each NM. Based on geometric criteria, using the radius of curvature and inter-repeat angles as the reference metrics, the main motions of Impα were described. Moreover, we determined the salt bridges, hydrogen bonds and hydrophobic interactions in the Impα-NplNLS interface. Our results show the bending and twisting motions participating in the recognition of nuclear proteins, allowing the accommodation and adjustment of a classical bipartite NLS sequence. The essential contacts for the nuclear import were also described and were mostly in agreement with previous studies, suggesting that the residues in the cNLS linker region establish important contacts with Impα adjusting the cNLS backbone. The MD simulations combined with NM analysis can be applied to the Impα-NLS system to help understand interactions between Impα and cNLSs and the analysis of non-classic NLSs.
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11
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Christie M, Chang CW, Róna G, Smith KM, Stewart AG, Takeda AAS, Fontes MRM, Stewart M, Vértessy BG, Forwood JK, Kobe B. Structural Biology and Regulation of Protein Import into the Nucleus. J Mol Biol 2015; 428:2060-90. [PMID: 26523678 DOI: 10.1016/j.jmb.2015.10.023] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/16/2015] [Accepted: 10/24/2015] [Indexed: 11/28/2022]
Abstract
Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g., importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g., importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals, recognized by the adaptor importin-α, and the PY nuclear localization signals, recognized by transportin-1. Post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.
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Affiliation(s)
- Mary Christie
- The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales Faculty of Medicine, Darlinghurst, NSW 2010, Australia
| | - Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gergely Róna
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Kate M Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Alastair G Stewart
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Agnes A S Takeda
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Murray Stewart
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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12
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Arregi I, Falces J, Olazabal-Herrero A, Alonso-Mariño M, Taneva SG, Rodríguez JA, Urbaneja MA, Bañuelos S. Leukemia-Associated Mutations in Nucleophosmin Alter Recognition by CRM1: Molecular Basis of Aberrant Transport. PLoS One 2015; 10:e0130610. [PMID: 26091065 PMCID: PMC4474691 DOI: 10.1371/journal.pone.0130610] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/21/2015] [Indexed: 12/31/2022] Open
Abstract
Nucleophosmin (NPM) is a nucleocytoplasmic shuttling protein, normally enriched in nucleoli, that performs several activities related to cell growth. NPM mutations are characteristic of a subtype of acute myeloid leukemia (AML), where mutant NPM seems to play an oncogenic role. AML-associated NPM mutants exhibit altered subcellular traffic, being aberrantly located in the cytoplasm of leukoblasts. Exacerbated export of AML variants of NPM is mediated by the nuclear export receptor CRM1, and due, in part, to a mutationally acquired novel nuclear export signal (NES). To gain insight on the molecular basis of NPM transport in physiological and pathological conditions, we have evaluated the export efficiency of NPM in cells, and present new data indicating that, in normal conditions, wild type NPM is weakly exported by CRM1. On the other hand, we have found that AML-associated NPM mutants efficiently form complexes with CRM1HA (a mutant CRM1 with higher affinity for NESs), and we have quantitatively analyzed CRM1HA interaction with the NES motifs of these mutants, using fluorescence anisotropy and isothermal titration calorimetry. We have observed that the affinity of CRM1HA for these NESs is similar, which may help to explain the transport properties of the mutants. We also describe NPM recognition by the import machinery. Our combined cellular and biophysical studies shed further light on the determinants of NPM traffic, and how it is dramatically altered by AML-related mutations.
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Affiliation(s)
- Igor Arregi
- Unidad de Biofísica (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Jorge Falces
- Unidad de Biofísica (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Anne Olazabal-Herrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - Marián Alonso-Mariño
- Unidad de Biofísica (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Stefka G. Taneva
- Unidad de Biofísica (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - José A. Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - María A. Urbaneja
- Unidad de Biofísica (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Sonia Bañuelos
- Unidad de Biofísica (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
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13
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Bernardes NE, Takeda AAS, Dreyer TR, Freitas FZ, Bertolini MC, Fontes MRM. Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal. PLoS One 2015; 10:e0128687. [PMID: 26091498 PMCID: PMC4474859 DOI: 10.1371/journal.pone.0128687] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/29/2015] [Indexed: 01/07/2023] Open
Abstract
Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site.
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Affiliation(s)
- Natalia E. Bernardes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Botucatu, SP, Brazil
| | - Agnes A. S. Takeda
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Botucatu, SP, Brazil
| | - Thiago R. Dreyer
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Botucatu, SP, Brazil
| | - Fernanda Z. Freitas
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, Universidade Estadual Paulista, UNESP, Araraquara, SP, Brazil
| | - Maria Célia Bertolini
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, Universidade Estadual Paulista, UNESP, Araraquara, SP, Brazil
| | - Marcos R. M. Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Botucatu, SP, Brazil
- * E-mail:
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14
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Konarev PV, Svergun DI. A posteriori determination of the useful data range for small-angle scattering experiments on dilute monodisperse systems. IUCRJ 2015; 2:352-360. [PMID: 25995844 PMCID: PMC4420545 DOI: 10.1107/s2052252515005163] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/13/2015] [Indexed: 05/29/2023]
Abstract
Small-angle X-ray and neutron scattering (SAXS and SANS) experiments on solutions provide rapidly decaying scattering curves, often with a poor signal-to-noise ratio, especially at higher angles. On modern instruments, the noise is partially compensated for by oversampling, thanks to the fact that the angular increment in the data is small compared with that needed to describe adequately the local behaviour and features of the scattering curve. Given a (noisy) experimental data set, an important question arises as to which part of the data still contains useful information and should be taken into account for the interpretation and model building. Here, it is demonstrated that, for monodisperse systems, the useful experimental data range is defined by the number of meaningful Shannon channels that can be determined from the data set. An algorithm to determine this number and thus the data range is developed, and it is tested on a number of simulated data sets with various noise levels and with different degrees of oversampling, corresponding to typical SAXS/SANS experiments. The method is implemented in a computer program and examples of its application to analyse the experimental data recorded under various conditions are presented. The program can be employed to discard experimental data containing no useful information in automated pipelines, in modelling procedures, and for data deposition or publication. The software is freely accessible to academic users.
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Affiliation(s)
- Petr V. Konarev
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
- Laboratory of Reflectometry and Small-angle Scattering, Institute of Crystallography of the Russian Academy of Sciences, Leninsky prospekt 59, Moscow 119333, Russian Federation
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
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15
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Róna G, Pálinkás HL, Borsos M, Horváth A, Scheer I, Benedek A, Nagy GN, Zagyva I, Vértessy BG. NLS copy-number variation governs efficiency of nuclear import - case study on dUTPases. FEBS J 2014; 281:5463-78. [DOI: 10.1111/febs.13086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 09/10/2014] [Accepted: 09/29/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Gergely Róna
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - Hajnalka L. Pálinkás
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Doctoral School of Multidisciplinary Medical Science; University of Szeged; Hungary
| | - Máté Borsos
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - András Horváth
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Ildikó Scheer
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - András Benedek
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - Gergely N. Nagy
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - Imre Zagyva
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
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16
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Bernardes NE, Takeda AAS, Freitas FZ, Bertolini MC, Fontes MRM. Crystallization and preliminary X-ray crystallographic analysis of importin-α from Neurospora crassa. Acta Crystallogr F Struct Biol Commun 2014; 70:501-4. [PMID: 24699749 PMCID: PMC3976073 DOI: 10.1107/s2053230x14005068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/05/2014] [Indexed: 01/18/2023] Open
Abstract
Importin-α recognizes cargo proteins that contain classical nuclear localization sequences (NLS) and, in complex with importin-β, is able to translocate nuclear proteins through the nuclear pore complex. The filamentous fungus Neurospora crassa is a well studied organism that has been widely used as a model organism for fundamental aspects of eukaryotic biology, and is important for understanding the specific mechanisms of protein transport to the cell nucleus. In this work, the crystallization and preliminary X-ray diffraction analysis of importin-α from N. crassa (IMPα-Nc) complexed with a classical NLS peptide (SV40 NLS) are reported. IMPα-Nc-SV40 NLS crystals diffracted X-rays to 2.0 Å resolution and the structure was solved by molecular-replacement techniques, leading to a monomeric structure. The observation of the electron-density map indicated the presence of SV40 NLSs interacting at both the minor and major NLS-binding sites of the protein.
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Affiliation(s)
- Natalia E. Bernardes
- Departamento de Física e Biofísica, Instituto de Biociências, UNESP – Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Agnes A. S. Takeda
- Departamento de Física e Biofísica, Instituto de Biociências, UNESP – Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Fernanda Z. Freitas
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP – Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Maria Célia Bertolini
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP – Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Marcos R. M. Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, UNESP – Universidade Estadual Paulista, Botucatu, SP, Brazil
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17
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Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
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18
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Kim J, Izadyar A, Shen M, Ishimatsu R, Amemiya S. Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy. Anal Chem 2014; 86:2090-8. [PMID: 24460147 PMCID: PMC3955255 DOI: 10.1021/ac403607s] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/25/2014] [Indexed: 12/20/2022]
Abstract
Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.
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Affiliation(s)
| | | | | | | | - Shigeru Amemiya
- Department of Chemistry, University
of Pittsburgh, 219 Parkman
Avenue, Pittsburgh, Pennsylvania 15260, United States
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19
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Róna G, Marfori M, Borsos M, Scheer I, Takács E, Tóth J, Babos F, Magyar A, Erdei A, Bozóky Z, Buday L, Kobe B, Vértessy BG. Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2495-505. [PMID: 24311590 DOI: 10.1107/s0907444913023354] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/19/2013] [Indexed: 01/12/2024]
Abstract
Phosphorylation adjacent to nuclear localization signals (NLSs) is involved in the regulation of nucleocytoplasmic transport. The nuclear isoform of human dUTPase, an enzyme that is essential for genomic integrity, has been shown to be phosphorylated on a serine residue (Ser11) in the vicinity of its nuclear localization signal; however, the effect of this phosphorylation is not yet known. To investigate this issue, an integrated set of structural, molecular and cell biological methods were employed. It is shown that NLS-adjacent phosphorylation of dUTPase occurs during the M phase of the cell cycle. Comparison of the cellular distribution of wild-type dUTPase with those of hyperphosphorylation- and hypophosphorylation-mimicking mutants suggests that phosphorylation at Ser11 leads to the exclusion of dUTPase from the nucleus. Isothermal titration microcalorimetry and additional independent biophysical techniques show that the interaction between dUTPase and importin-α, the karyopherin molecule responsible for `classical' NLS binding, is weakened significantly in the case of the S11E hyperphosphorylation-mimicking mutant. The structures of the importin-α-wild-type and the importin-α-hyperphosphorylation-mimicking dUTPase NLS complexes provide structural insights into the molecular details of this regulation. The data indicate that the post-translational modification of dUTPase during the cell cycle may modulate the nuclear availability of this enzyme.
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Affiliation(s)
- Gergely Róna
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 1113 Budapest, Hungary
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20
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Kim J, Izadyar A, Nioradze N, Amemiya S. Nanoscale mechanism of molecular transport through the nuclear pore complex as studied by scanning electrochemical microscopy. J Am Chem Soc 2013; 135:2321-9. [PMID: 23320434 PMCID: PMC3572272 DOI: 10.1021/ja311080j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates molecular transport across the nuclear envelope between the nucleus and cytoplasm of a eukaryotic cell. Small molecules (<40 kDa) diffuse through the large pore of this multiprotein complex. A passively impermeable macromolecule tagged with a signal peptide is chaperoned through the nanopore by nuclear transport receptors (e.g., importins) owing to their interactions with barrier-forming proteins. Presently, this bimodal transport mechanism is not well understood and is described by controversial models. Herein, we report on a dynamic and spatially resolved mechanism for NPC-mediated molecular transport through nanoscale central and peripheral routes with distinct permeabilities. Specifically, we develop a nanogap-based approach of scanning electrochemical microscopy to precisely measure the extremely high permeability of the nuclear envelope to a small probe molecule, (ferrocenylmethyl)trimethylammonium. Effective medium theories indicate that the passive permeability of 5.9 × 10(-2) cm/s corresponds to the free diffusion of the probe molecule through ~22 nanopores with a radius of 24 nm and a length of 35 nm. Peripheral routes are blocked by wheat germ agglutinin to yield 2-fold lower permeability for 17 nm-radius central routes. This lectin is also used in fluorescence assays to find that importins facilitate the transport of signal-tagged albumin mainly through the 7 nm-thick peripheral route rather than through the sufficiently large central route. We propose that this spatial selectivity is regulated by the conformational changes in barrier-forming proteins that transiently and locally expand the impermeably thin peripheral route while blocking the central route.
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Affiliation(s)
- Jiyeon Kim
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania, 15260
| | | | - Nikoloz Nioradze
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania, 15260
| | - Shigeru Amemiya
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania, 15260
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21
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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22
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Keck KM, Pemberton LF. Histone chaperones link histone nuclear import and chromatin assembly. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:277-89. [PMID: 22015777 PMCID: PMC3272145 DOI: 10.1016/j.bbagrm.2011.09.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/08/2011] [Accepted: 09/12/2011] [Indexed: 12/12/2022]
Abstract
Histone chaperones are proteins that shield histones from nonspecific interactions until they are assembled into chromatin. After their synthesis in the cytoplasm, histones are bound by different histone chaperones, subjected to a series of posttranslational modifications and imported into the nucleus. These evolutionarily conserved modifications, including acetylation and methylation, can occur in the cytoplasm, but their role in regulating import is not well understood. As part of histone import complexes, histone chaperones may serve to protect the histones during transport, or they may be using histones to promote their own nuclear localization. In addition, there is evidence that histone chaperones can play an active role in the import of histones. Histone chaperones have also been shown to regulate the localization of important chromatin modifying enzymes. This review is focused on the role histone chaperones play in the early biogenesis of histones, the distinct cytoplasmic subcomplexes in which histone chaperones have been found in both yeast and mammalian cells and the importins/karyopherins and nuclear localization signals that mediate the nuclear import of histones. We also address the role that histone chaperone localization plays in human disease. This article is part of a Special Issue entitled: Histone chaperones and chromatin assembly.
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Affiliation(s)
- Kristin M. Keck
- Center for Cell Signaling, Department of Microbiology, Immunology and Cancer Biology University of Virginia, Charlottesville, VA 22908, USA
| | - Lucy F. Pemberton
- Center for Cell Signaling, Department of Microbiology, Immunology and Cancer Biology University of Virginia, Charlottesville, VA 22908, USA
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23
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Marfori M, Lonhienne TG, Forwood JK, Kobe B. Structural Basis of High-Affinity Nuclear Localization Signal Interactions with Importin-α. Traffic 2012; 13:532-48. [DOI: 10.1111/j.1600-0854.2012.01329.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 01/13/2012] [Accepted: 01/16/2012] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Jade K. Forwood
- School of Biomedical Sciences; Charles Sturt University; Wagga Wagga; NSW; 2650; Australia
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24
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Arregi I, Falces J, Bañuelos S, Urbaneja MA, Taneva SG. The Nuclear Transport Machinery Recognizes Nucleoplasmin–Histone Complexes. Biochemistry 2011; 50:7104-10. [DOI: 10.1021/bi2008867] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Igor Arregi
- Unidad de Biofı́sica (CSIC/UPV-EHU),
Departamento de Bioquı́mica y Biologı́a Molecular, Universidad del Paı́s Vasco, POB 644, 48080 Bilbao,
Spain
| | - Jorge Falces
- Unidad de Biofı́sica (CSIC/UPV-EHU),
Departamento de Bioquı́mica y Biologı́a Molecular, Universidad del Paı́s Vasco, POB 644, 48080 Bilbao,
Spain
| | - Sonia Bañuelos
- Unidad de Biofı́sica (CSIC/UPV-EHU),
Departamento de Bioquı́mica y Biologı́a Molecular, Universidad del Paı́s Vasco, POB 644, 48080 Bilbao,
Spain
| | - Marı́a A. Urbaneja
- Unidad de Biofı́sica (CSIC/UPV-EHU),
Departamento de Bioquı́mica y Biologı́a Molecular, Universidad del Paı́s Vasco, POB 644, 48080 Bilbao,
Spain
| | - Stefka G. Taneva
- Unidad de Biofı́sica (CSIC/UPV-EHU),
Departamento de Bioquı́mica y Biologı́a Molecular, Universidad del Paı́s Vasco, POB 644, 48080 Bilbao,
Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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