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Ibáñez de Opakua A, Geraets JA, Frieg B, Dienemann C, Savastano A, Rankovic M, Cima-Omori MS, Schröder GF, Zweckstetter M. Molecular interactions of FG nucleoporin repeats at high resolution. Nat Chem 2022; 14:1278-1285. [PMID: 36138110 PMCID: PMC9630130 DOI: 10.1038/s41557-022-01035-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022]
Abstract
Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG–FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities. ![]()
Proteins rich in phenylalanine-glycine (FG) repeats can phase separate through FG–FG interactions. The molecular interactions of an important FG-repeat protein, nucleoporin 98, have now been studied in liquid-like transient and amyloid-like cohesive states. These interactions underlie the behaviour of FG-repeat proteins and their function in physiological and pathological cell activities.
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Affiliation(s)
| | - James A Geraets
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Benedikt Frieg
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | | | - Marija Rankovic
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany
| | | | - Gunnar F Schröder
- Institute of Biological Information Processing (Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases, Göttingen, Germany. .,Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Göttingen, Germany.
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Pothula KR, Geraets JA, Ferber II, Schröder GF. Clustering polymorphs of tau and IAPP fibrils with the CHEP algorithm. Prog Biophys Mol Biol 2021; 160:16-25. [PMID: 33556421 DOI: 10.1016/j.pbiomolbio.2020.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
Recent steps towards automation have improved the quality and efficiency of the entire cryo-electron microscopy workflow, from sample preparation to image processing. Most of the image processing steps are now quite automated, but there are still a few steps which need the specific intervention of researchers. One such step is the identification and separation of helical protein polymorphs at early stages of image processing. Here, we tested and evaluated our recent clustering approach on three datasets containing amyloid fibrils, demonstrating that the proposed unsupervised clustering method automatically and effectively identifies the polymorphs from cryo-EM images. As an automated polymorph separation method, it has the potential to complement automated helical picking, which typically cannot easily distinguish between polymorphs with subtle differences in morphology, and is therefore a useful tool for the image processing and structure determination of helical proteins.
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Affiliation(s)
- Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - James A Geraets
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Inda I Ferber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
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Geraets JA, Pothula KR, Schröder GF. Integrating cryo-EM and NMR data. Curr Opin Struct Biol 2020; 61:173-181. [PMID: 32028106 DOI: 10.1016/j.sbi.2020.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/06/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) is increasingly used as a technique to determine the atomic structure of challenging biological systems. Recent advances in microscope engineering, electron detection, and image processing have allowed the structural determination of bigger and more flexible targets than possible with the complementary techniques X-ray crystallography and NMR spectroscopy. However, there exist many biological targets for which atomic resolution cannot be currently achieved with cryo-EM, making unambiguous determination of the protein structure impossible. Although determining the structure of large biological systems using solely NMR is often difficult, highly complementary experimental atomic-level data for each molecule can be derived from the spectra, and used in combination with cryo-EM data. We review here strategies with which both techniques can be synergistically combined, in order to reach detail and understanding unattainable by each technique acting alone; and the types of biological systems for which such an approach would be desirable.
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Affiliation(s)
- James A Geraets
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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Abdelnabi R, Geraets JA, Ma Y, Mirabelli C, Flatt JW, Domanska A, Delang L, Jochmans D, Kumar TA, Jayaprakash V, Sinha BN, Leyssen P, Butcher SJ, Neyts J. A novel druggable interprotomer pocket in the capsid of rhino- and enteroviruses. PLoS Biol 2019; 17:e3000281. [PMID: 31185007 PMCID: PMC6559632 DOI: 10.1371/journal.pbio.3000281] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/08/2019] [Indexed: 12/22/2022] Open
Abstract
Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are "capsid binders" that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhibitors and by means of cryo-electron microscopy (EM), followed by resistance selection and reverse genetics, we discovered a hitherto unknown druggable pocket that is formed by viral proteins VP1 and VP3 and that is conserved across entero-/rhinovirus species. We propose that these inhibitors stabilize a key region of the virion, thereby preventing the conformational expansion needed for viral RNA release. A medicinal chemistry effort resulted in the identification of analogues targeting this pocket with broad-spectrum activity against Coxsackieviruses B (CVBs) and compounds with activity against enteroviruses (EV) of groups C and D, and even rhinoviruses (RV). Our findings provide novel insights in the biology of the entry of entero-/rhinoviruses and open new avenues for the design of broad-spectrum antivirals against these pathogens.
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Affiliation(s)
- Rana Abdelnabi
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - James A. Geraets
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Yipeng Ma
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Justin W. Flatt
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Aušra Domanska
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leen Delang
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Dirk Jochmans
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Timiri Ajay Kumar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Pieter Leyssen
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Sarah J. Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail: (JN); (SJB)
| | - Johan Neyts
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
- * E-mail: (JN); (SJB)
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Geraets JA, Baldwin JPC, Twarock R, Hancock Y. A proposed simulation method for directed self-assembly of nanographene. J Phys Condens Matter 2017; 29:355901. [PMID: 28653962 PMCID: PMC5802380 DOI: 10.1088/1361-648x/aa7c0b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
A methodology for predictive kinetic self-assembly modeling of bottom-up chemical synthesis of nanographene is proposed. The method maintains physical transparency in using a novel array format to efficiently store molecule information and by using array operations to determine reaction possibilities. Within a minimal model approach, the parameter space for the bond activation energies (i.e. molecule functionalization) at fixed reaction temperature and initial molecule concentrations is explored. Directed self-assembly of nanographene from functionalized tetrabenzanthracene and benzene is studied with regions in the activation energy phase-space showing length-to-width ratio tunability. The degree of defects and reaction reproducibility in the simulations is also determined, with the rate of functionalized benzene addition providing additional control of the dimension and quality of the nanographene. Comparison of the reaction energetics to available density functional theory data suggests the synthesis may be experimentally tenable using aryl-halide cross-coupling and noble metal surface-assisted catalysis. With full access to the intermediate reaction network and with dynamic coupling to density functional theory-informed tight-binding simulation, the method is proposed as a computationally efficient means towards detailed simulation-driven design of new nanographene systems.
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Affiliation(s)
- J A Geraets
- Department of Physics, University of York, Heslington, York YO10 5DD,
United Kingdom
- Department of Biology, University of York, Heslington, York YO10 5DD,
United Kingdom
- York Centre for Complex Systems Analysis,
University of York, Heslington,
York YO10 5GE, United Kingdom
| | - J P C Baldwin
- Department of Physics, University of York, Heslington, York YO10 5DD,
United Kingdom
| | - R Twarock
- Department of Biology, University of York, Heslington, York YO10 5DD,
United Kingdom
- York Centre for Complex Systems Analysis,
University of York, Heslington,
York YO10 5GE, United Kingdom
- Department of Mathematics, University of York, Heslington, York YO10 5DD,
United Kingdom
| | - Y Hancock
- Department of Physics, University of York, Heslington, York YO10 5DD,
United Kingdom
- York Centre for Complex Systems Analysis,
University of York, Heslington,
York YO10 5GE, United Kingdom
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Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R. Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data. PLoS Comput Biol 2015; 11:e1004146. [PMID: 25793998 PMCID: PMC4368512 DOI: 10.1371/journal.pcbi.1004146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design.
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Affiliation(s)
- James A Geraets
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
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