1
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Qin X, Lam A, Zhang X, Sengupta S, Iorgulescu JB, Ni H, Das S, Rager M, Zhou Z, Zuo T, Meara GK, Floru AE, Kemet C, Veerapaneni D, Kashy D, Lin L, Lloyd K, Kwok L, Smith KS, Nagaraju RT, Meijers R, Ceol C, Liu CT, Alexandrescu S, Wu CJ, Keskin DB, George RE, Feng H. CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness. Sci Adv 2024; 10:eadh9547. [PMID: 38489372 PMCID: PMC10942121 DOI: 10.1126/sciadv.adh9547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Solid tumors, especially those with aberrant MYCN activation, often harbor an immunosuppressive microenvironment to fuel malignant growth and trigger treatment resistance. Despite this knowledge, there are no effective strategies to tackle this problem. We found that chemokine-like factor (CKLF) is highly expressed by various solid tumor cells and transcriptionally up-regulated by MYCN. Using the MYCN-driven high-risk neuroblastoma as a model system, we demonstrated that as early as the premalignant stage, tumor cells secrete CKLF to attract CCR4-expressing CD4+ cells, inducing immunosuppression and tumor aggression. Genetic depletion of CD4+ T regulatory cells abolishes the immunorestrictive and protumorigenic effects of CKLF. Our work supports that disrupting CKLF-mediated cross-talk between tumor and CD4+ suppressor cells represents a promising immunotherapeutic approach to battling MYCN-driven tumors.
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Affiliation(s)
- Xiaodan Qin
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Andrew Lam
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Xu Zhang
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Satyaki Sengupta
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - J. Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Molecular Diagnostics Laboratory, Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hongru Ni
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Sanjukta Das
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- School of Biotechnology, KIIT University, Bhubanesw, India
| | - Madison Rager
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Zhenwei Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tao Zuo
- Department of Pathology & Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Grace K. Meara
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Alexander E. Floru
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Chinyere Kemet
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Divya Veerapaneni
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Kashy
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Liang Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Lauren Kwok
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Kaylee S. Smith
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Raghavendar T. Nagaraju
- Faculty of Biology, Medicine and Health, Division of Cancer Sciences, University of Manchester, Manchester, UK
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK
| | - Rob Meijers
- Institute for Protein Innovation, Boston, MA, USA
| | - Craig Ceol
- Department of Molecular, Cell and Cancer Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rani E. George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hui Feng
- Departments of Pharmacology, Physiology & Biophysics and Medicine, Section of Hematology and Medical Oncology, Cancer Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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Priest JM, Nichols EL, Smock RG, Hopkins JB, Mendoza JL, Meijers R, Shen K, Özkan E. Structural insights into the formation of repulsive netrin guidance complexes. Sci Adv 2024; 10:eadj8083. [PMID: 38363837 PMCID: PMC10871540 DOI: 10.1126/sciadv.adj8083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
Abstract
Netrins dictate attractive and repulsive responses during axon growth and cell migration, where the presence of the receptor Uncoordinated-5 (UNC-5) on target cells results in repulsion. Here, we showed that UNC-5 is a heparin-binding protein, determined its structure bound to a heparin fragment, and could modulate UNC-5-heparin affinity using a directed evolution platform or structure-based rational design. We demonstrated that UNC-5 and UNC-6/netrin form a large, stable, and rigid complex in the presence of heparin, and heparin and UNC-5 exclude the attractive UNC-40/DCC receptor from binding to UNC-6/netrin to a large extent. Caenorhabditis elegans with a heparin-binding-deficient UNC-5 fail to establish proper gonad morphology due to abrogated cell migration, which relies on repulsive UNC-5 signaling in response to UNC-6. Combining UNC-5 mutations targeting heparin and UNC-6/netrin contacts results in complete cell migration and axon guidance defects. Our findings establish repulsive netrin responses to be mediated through a glycosaminoglycan-regulated macromolecular complex.
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Affiliation(s)
- Jessica M. Priest
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Institute for Neuroscience, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Ev L. Nichols
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Robert G. Smock
- European Molecular Biology Laboratory (EMBL), Hamburg Site, c/o DESY, 22603 Hamburg, Germany
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Argonne National Laboratory, Illinois Institute of Technology, Chicago, IL 60616, USA
- Department of Physics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Juan L. Mendoza
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Site, c/o DESY, 22603 Hamburg, Germany
- Institute for Protein Innovation (IPI), Boston, MA 02115, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Engin Özkan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Institute for Neuroscience, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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3
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Hao Y, Yan J, Fraser C, Jiang A, Anuganti M, Zhang R, Lloyd K, Jardine J, Coppola J, Meijers R, Li J, Springer TA. Synthetic integrin antibodies discovered by yeast display reveal αV subunit pairing preferences with β subunits. bioRxiv 2024:2024.01.26.577394. [PMID: 38328192 PMCID: PMC10849667 DOI: 10.1101/2024.01.26.577394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Eight of the 24 integrin heterodimers bind to the tripeptide Arg-Gly-Asp (RGD) motif in their extracellular ligands, and play essential roles in cell adhesion, migration, and homeostasis. Despite similarity in recognizing the RGD motif and some redundancy, these integrins can selectively recognize RGD-containing ligands including fibronectin, vitronectin, fibrinogen, nephronectin and the prodomain of the transforming growth factors to fulfill specific functions in cellular processes. Subtype-specific antibodies against RGD-binding integrins are desirable for investigating their specific functions. In this study, we discovered 11 antibodies that exhibit high specificity and affinity towards integrins αVβ3, αVβ5, αVβ6, αVβ8, and α5β1 from a synthetic yeast-displayed Fab library. Of these, 6 are function-blocking antibodies containing an R(G/L/T) D motif in their CDR3 sequences. We report antibody binding specificity, kinetics, and binding affinity for purified integrin ectodomains as well as intact integrins on the cell surface. We further employed these antibodies to reveal binding preferences of the αV subunit for its 5 β-subunit partners: β6=β8>β3>β1=β5.
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4
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Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Pena Murillo GE, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun Biol 2023; 6:1057. [PMID: 37853181 PMCID: PMC10585004 DOI: 10.1038/s42003-023-05416-7] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.
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Affiliation(s)
- Clement E Blanchet
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - E Juncheng
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Christian Löw
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | | | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Rob Meijers
- Institute for Protein Innovation (IPI), 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Gisel Esperanza Pena Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Ekaterina Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tamme Wollweber
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yulong Zhuang
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Dmitri Svergun
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany.
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5
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Guédez G, Loers G, Jeffries CM, Kozak S, Meijers R, Svergun DI, Schachner M, Löw C. X-ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1. FASEB J 2023; 37:e22823. [PMID: 36809668 DOI: 10.1096/fj.202201511r] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/20/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023]
Abstract
The cell adhesion molecule L1 (L1CAM, L1 in short) plays crucial roles during neural development, regeneration after injury, synapse formation, synaptic plasticity and tumor cell migration. L1 belongs to the immunoglobulin superfamily and comprises in its extracellular part six immunoglobulin (Ig)-like domains and five fibronectin type III homologous repeats (FNs). The second Ig-like domain has been validated for self- (so-called homophilic) binding between cells. Antibodies against this domain inhibit neuronal migration in vitro and in vivo. The fibronectin type III homologous repeats FN2 and FN3 bind small molecule agonistic L1 mimetics and contribute to signal transduction. FN3 has a stretch of 25 amino acids that can be triggered with a monoclonal antibody, or the L1 mimetics, to enhance neurite outgrowth and neuronal cell migration in vitro and in vivo. To correlate the structural features of these FNs with function, we determined a high-resolution crystal structure of a FN2FN3 fragment, which is functionally active in cerebellar granule cells and binds several mimetics. The structure illustrates that both domains are connected by a short linker sequence allowing a flexible and largely independent organization of both domains. This becomes further evident by comparing the X-ray crystal structure with models derived from Small-Angle X-ray Scattering (SAXS) data for FN2FN3 in solution. Based on the X-ray crystal structure, we identified five glycosylation sites which we believe are crucial for folding and stability of these domains. Our study signifies an advance in the understanding of structure-functional relationships of L1.
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Affiliation(s)
- Gabriela Guédez
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Sandra Kozak
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Institute for Protein Innovation, Boston, Massachusetts, USA
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
| | - Melitta Schachner
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.,European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
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6
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Gura T, Acker-Palmer A, Kolodkin A, Meijers R, Mizuno N, Seiradake E, Tessier-Lavigne M. Molecular neuroscience community shares perspectives. Neuron 2022; 110:3656-3660. [PMID: 36356578 DOI: 10.1016/j.neuron.2022.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In May, an interdisciplinary group gathered in Crete for the Molecular Neurobiology Workshop. Scientists shared data acquired by vastly diverse techniques to understand how the nervous system, with only a limited number of components, is assembled to respond to infinite stimuli. Ideas of molecular cues, timing, switching, and context emerged.
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Affiliation(s)
- Trisha Gura
- Institute for Protein Innovation, Boston, MA, USA.
| | - Amparo Acker-Palmer
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt and Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Alex Kolodkin
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rob Meijers
- Institute for Protein Innovation, Boston, MA, USA
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute and National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elena Seiradake
- Department of Biochemistry, University of Oxford and Kavli Institute for Nanoscience Discovery, Oxford, UK
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7
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Kozak S, Bloch Y, De Munck S, Mikula A, Bento I, Savvides SN, Meijers R. Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis. Acta Crystallogr D Struct Biol 2020; 76:1244-1255. [PMID: 33263330 PMCID: PMC7709199 DOI: 10.1107/s2059798320013753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022] Open
Abstract
Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy.
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Affiliation(s)
- Sandra Kozak
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Steven De Munck
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Aleksandra Mikula
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Isabel Bento
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Savvas N. Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Unit for Structural Biology, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
- Institute for Protein Innovation, 4 Blackfan Circle, Boston, MA 02115, USA
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8
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Garde S, Calzada J, Sánchez C, Gaya P, Narbad A, Meijers R, Mayer MJ, Ávila M. Erratum to “Effect of Lactococcus lactis expressing phage endolysin on the late blowing defect of cheese caused by Clostridium tyrobutyricum” [Int. J. Food Microbiol. 329 (2020) 108686]. Int J Food Microbiol 2020; 331:108794. [DOI: 10.1016/j.ijfoodmicro.2020.108794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Moritz A, Anjanappa R, Wagner C, Bunk S, Hofmann M, Pszolla G, Saikia A, Garcia-Alai M, Meijers R, Rammensee HG, Springer S, Maurer D. High-throughput peptide-MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules. Sci Immunol 2020; 4:4/37/eaav0860. [PMID: 31324691 DOI: 10.1126/sciimmunol.aav0860] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/21/2019] [Indexed: 12/26/2022]
Abstract
Major histocompatibility complex (MHC) class I molecules present short peptide ligands on the cell surface for interrogation by cytotoxic CD8+ T cells. MHC class I complexes presenting tumor-associated peptides such as neoantigens represent key targets of cancer immunotherapy approaches currently in development, making them important for efficacy and safety screenings. Without peptide ligand, MHC class I complexes are unstable and decay quickly, making the production of soluble monomers for analytical purposes labor intensive. We have developed a disulfide-stabilized HLA-A*02:01 molecule that is stable without peptide but can form peptide-MHC complexes (pMHCs) with ligands of choice in a one-step loading procedure. We illustrate the similarity between the engineered mutant and the wild-type molecule with respect to affinity of wild-type or affinity-matured T cell receptors (TCRs) and present a crystal structure corroborating the binding kinetics measurements. In addition, we demonstrate a high-throughput binding kinetics measurement platform to analyze the binding characteristics of bispecific TCR (bsTCR) molecules against diverse pMHC libraries produced with the disulfide-stabilized HLA-A*02:01 molecule. We show that bsTCR affinities for pMHCs are indicative of in vitro function and generate a bsTCR binding motif to identify potential off-target interactions in the human proteome. These findings showcase the potential of the platform and the engineered HLA-A*02:01 molecule in the emerging field of pMHC-targeting biologics.
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Affiliation(s)
- Andreas Moritz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany. .,Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | | | | | - Ankur Saikia
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
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10
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Tamhane T, Saini SK, Anjanappa R, Saikia A, Ramskov S, Donia M, Swane IM, Jakobsen SN, Zacharia M, Meijers R, Springer S, Hadrup S. Empty-loadable MHC class I tetramers for efficient detection of antigen-specific T cells. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.86.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The peptide-dependent stability of MHC class I molecules poses a substantial challenge for their use for peptide-MHC multimer-based approaches to comprehensively analyze T cell immunity. We demonstrate here the generation, analysis, and use of empty-loadable (peptide-free) MHC class I tetramers made from disulfide-stabilized MHC molecules.
A disulfide bond links the α1 and α2 helices of MHC class I molecule at the extreme end of the F pocket. It allows in vitro folding of recombinant A2 with a dipeptide and subsequent removal of the dipeptide to yield stable peptide-receptive MHC monomers. Empty-loadable tetramers prepared using disulfide-stabilized MHC monomers can be loaded with peptides within minutes. These tetramers efficiently detects antigen-specific T cells. Furthermore, peptide-MHC tetramers prepared using disulfide-stabilized MHC molecules provide a better staining index for antigen-specific T cell detection compared to multimers prepared with wild-type MHC class I molecules. We demonstrate the value of empty-loadable tetramers that are converted to antigen-specific tetramers by a single-step peptide addition, for the identification of T cells specific to several neo- and cancer-associated antigens in melanoma. Disulfide stabilization has been achieved with several MHC class I allotypes-HLA-A* 02:01, HLA-A*01:01, HLA-A*03:01, HLA-A*11:01, HLA-A*24:02, HLA-B*07:02, and H-2Kb.
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Affiliation(s)
- Tripti Tamhane
- 1Department of Health Technology, Technical University of Denmark, Denmark
| | - Sunil Kumar Saini
- 1Department of Health Technology, Technical University of Denmark, Denmark
| | | | | | - Sofie Ramskov
- 1Department of Health Technology, Technical University of Denmark, Denmark
| | - Marco Donia
- 3Center for Cancer Immune Therapy, Herlev Hospital, Denmark
| | | | | | | | - Rob Meijers
- 5Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | | | - Sine Hadrup
- 1Department of Health Technology, Technical University of Denmark, Denmark
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11
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Heidemann J, Kölbel K, Konijnenberg A, Van Dyck J, Garcia-Alai M, Meijers R, Sobott F, Uetrecht C. Further insights from structural mass spectrometry into endocytosis adaptor protein assemblies. Int J Mass Spectrom 2020; 447:116240. [PMID: 33244295 PMCID: PMC7116418 DOI: 10.1016/j.ijms.2019.116240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
As a fundament in many biologically relevant processes, endocytosis in its different guises has been arousing interest for decades and still does so. This is true for the actual transport and its initiation alike. In clathrin-mediated endocytosis, a comparatively well understood endocytic pathway, a set of adaptor proteins bind specific lipids in the plasma membrane, subsequently assemble and thus form a crucial bridge from clathrin to actin for the ongoing process. These adaptor proteins are highly interesting themselves and the subject of this manuscript. Using many of the instruments that are available now in the mass spectrometry toolbox, we added some facets to the picture of how these minimal assemblies may look, how they form, and what influences the structure. Especially, lipids in the adaptor protein complexes result in reduced charging of a normal sized complex due to their specific binding position. The results further support our structural model of a double ring structure with interfacial lipids.
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Affiliation(s)
- Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Knut Kölbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Albert Konijnenberg
- University of Antwerp, Biomolecular & Analytical Mass Spectrometry, Chemistry Dept. Campus Groenenborger V4, Groenenborgerlaan, 171 2020, Antwerp, Belgium
| | - Jeroen Van Dyck
- University of Antwerp, Biomolecular & Analytical Mass Spectrometry, Chemistry Dept. Campus Groenenborger V4, Groenenborgerlaan, 171 2020, Antwerp, Belgium
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Frank Sobott
- University of Antwerp, Biomolecular & Analytical Mass Spectrometry, Chemistry Dept. Campus Groenenborger V4, Groenenborgerlaan, 171 2020, Antwerp, Belgium
- Astbury Centre for Structural Molecular and Cellular Biology, School of Molecular and Cellular Biology, University of Leeds, LS3 9JT, United Kingdom
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Corresponding author. Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany.
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12
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Meijers R, Smock RG, Zhang Y, Wang JH. Netrin Synergizes Signaling and Adhesion through DCC. Trends Biochem Sci 2019; 45:6-12. [PMID: 31704057 DOI: 10.1016/j.tibs.2019.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Netrin is a prototypical axon guidance cue. Structural studies have revealed how netrin interacts with the deleted in colorectal cancer (DCC) receptor, other receptors, and co-factors for signaling. Recently, genetic studies suggested that netrin is involved in neuronal haptotaxis, which requires a reversible adhesion process. Structural data indicate that netrin can also mediate trans-adhesion between apposing cells decorated with its receptors on the condition that the auxiliary guidance cue draxin is present. Here, we propose that netrin is involved in conditional adhesion, a reversible and localized process that can contribute to cell adhesion and migration. We suggest that netrin-mediated adhesion and signaling are linked, and that local environmental factors in the ventricular zone, the floor plate, or other tissues coordinate its function.
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Affiliation(s)
- Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany.
| | - Robert G Smock
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871 China
| | - Jia-Huai Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871 China; Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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13
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Saini SK, Tamhane T, Anjanappa R, Saikia A, Ramskov S, Donia M, Svane IM, Jakobsen SN, Garcia-Alai M, Zacharias M, Meijers R, Springer S, Hadrup SR. Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells. Sci Immunol 2019; 4:4/37/eaau9039. [DOI: 10.1126/sciimmunol.aau9039] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/20/2019] [Indexed: 12/17/2022]
Abstract
The peptide-dependent stability of MHC class I molecules poses a substantial challenge for their use in peptide-MHC multimer–based approaches to comprehensively analyze T cell immunity. To overcome this challenge, we demonstrate the use of functionally empty MHC class I molecules stabilized by a disulfide bond to link the α1and α2helices close to the F pocket. Peptide-loaded disulfide-stabilized HLA-A*02:01 shows complete structural overlap with wild-type HLA-A*02:01. Peptide-MHC multimers prepared using disulfide-stabilized HLA-A*02:01, HLA-A*24:02, and H-2Kbcan be used to identify antigen-specific T cells, and they provide a better staining index for antigen-specific T cell detection compared with multimers prepared with wild-type MHC class I molecules. Disulfide-stabilized MHC class I molecules can be loaded with peptide in the multimerized form without affecting their capacity to stain T cells. We demonstrate the value of empty-loadable tetramers that are converted to antigen-specific tetramers by a single-step peptide addition through their use to identify T cells specific for mutation-derived neoantigens and other cancer-associated antigens in human melanoma.
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14
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Tamhane T, Saini SK, Anjanappa R, Saikia A, Ramskov S, Donia M, Svane IMS, Jakobsen SN, Garcia-Alai M, Zacharias M, Meijers R, Springer S, Hadrup SR. Abstract B049: Empty MHC class I molecules for improved detection of antigen-specific T-cells. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-b049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Major histocompatibility complex (MHC) class I multimers have been widely used to identify antigen specific T-cells for immune monitoring, epitope discovery, and T-cell isolation. A bottleneck to many peptide-MHC driven applications for T-cell interrogation is the peptide ligand dependent stability of the MHC class I proteins, which thus compels high-affinity peptide dependent in-vitro folding of each MHC protein and the use of a peptide-exchange technology to investigate antigens of interest. To overcome this challenge, we demonstrate the use of empty peptide-receptive MHC class I molecule for detection of antigen specific T-cells. This strategy is based on an HLA-A*02:01 variant which is stabilized by a disulfide bond to link the alpha-1 and alpha-2 helices close to the F pocket. Determined by the crystal structure, peptide-loaded disulfide-stabilized HLA-A*02:01 show complete structural overlap to wild-type HLA-A*02:01. Following peptide loading, we used such disulfide-stabilized HLA-A*02:01 molecules to form fluorescence labeled tetramers and applied them for detections of T-cell responses against common viruses in healthy donor peripheral blood mononuclear cells. In all tested samples, disulfide-stabilized HLA-A*02:01 tetramers detected T-cell with same specificity as wild-type MHC tetramers and they consistently provide a better staining index for antigen-specific T-cell detection. Importantly, disulfide-stabilized MHC class I molecules can be loaded with peptide in the multimerized form without impacting the T-cell staining capacity. We demonstrate the value of empty loadable tetramers, converted to antigen-specific tetramers by a single-step peptide addition, for identification of T-cells specific to several neo- and cancer-associated antigens among tumor-infiltrating lymphocytes in melanoma.To evaluate if the disulfide linkage has an impact on TCR recognition of peptide-MHC complexes, we determined and compared TCR fingerprints of T-cell clones specific to a given peptide-MHC complex using both the wild-type and the disulfide-stabilized HLA-A*02:01 multimers. No differences were observed in the TCR interaction profile between the disulfide optimized and the wild-type MHC class I. In conclusion, disulfide-stabilized empty HLA class I proteins are a potentially powerful tool for interrogating T-cell recognition—offering a fast and flexible transformation from an empty peptide receptive state to a set of personalized reagents generated to match individual tumor characteristics for T-cell monitoring or selection.
Citation Format: Tripti Tamhane, Sunil Kumar Saini, Raghavendra Anjanappa, Ankur Saikia, Sofie Ramskov, Marco Donia, Inge Marie Stenfoft Svane, Søren Nyboe Jakobsen, Maria Garcia-Alai, Martin Zacharias, Rob Meijers, Sebastian Springer, Sine Reker Hadrup. Empty MHC class I molecules for improved detection of antigen-specific T-cells [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B049.
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Affiliation(s)
- Tripti Tamhane
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Sunil Kumar Saini
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Raghavendra Anjanappa
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Ankur Saikia
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Sofie Ramskov
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Marco Donia
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Inge Marie Stenfoft Svane
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Søren Nyboe Jakobsen
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Maria Garcia-Alai
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Rob Meijers
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Sebastian Springer
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
| | - Sine Reker Hadrup
- Technical University of Denmark, Kongens Lyngby, Denmark; Jacobs University Bremen, Bremen, Germany; Jacobs University Bremen, Bremen, Germany; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; European Molecular Biology Laboratory, Hamburg, Germany; Technical University of Munich, Garching, Germany
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15
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Abstract
Glycosaminoglycans (GAGs) play a widespread role in embryonic development, as deletion of enzymes that contribute to GAG synthesis lead to deficiencies in cell migration and tissue modelling. Despite the biochemical and structural characterization of individual protein/GAG interactions, there is no concept available that links the molecular mechanisms of GAG/protein engagements to tissue development. Here, we focus on the role of GAG polymers in mediating interactions between cell surface receptors and their ligands. We categorize several switches that lead to ligand activation, inhibition, selection and addition, based on recent structural studies of select receptor/ligand complexes. Based on these principles, we propose that individual GAG polymers may affect several receptor pathways in parallel, orchestrating a cellular response to an environmental cue. We believe that it is worthwhile to study the role of GAGs as molecular switches, as this may lead to novel drug candidates to target processes such as angiogenesis, neuroregeneration and tumour metastasis.
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Affiliation(s)
- Robert G Smock
- European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
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16
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Gómez‐Torres N, Dunne M, Garde S, Meijers R, Narbad A, Ávila M, Mayer MJ. Development of a specific fluorescent phage endolysin for in situ detection of Clostridium species associated with cheese spoilage. Microb Biotechnol 2018; 11:332-345. [PMID: 29160025 PMCID: PMC5812242 DOI: 10.1111/1751-7915.12883] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 02/28/2017] [Revised: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022] Open
Abstract
Late blowing defect (LBD) is a major cause of spoilage in cheeses, caused by the growth of Clostridium spp. in the cheese matrix. We investigated the application of CTP1L, a bacteriophage endolysin active against Clostridium tyrobutyricum, and its enzymatically active and cell wall-binding domains (EAD and CBD) attached to green fluorescent protein (GFP) to detect dairy-related Clostridium species by fluorescence microscopy. GFP-CTP1L and GFP-CBD demonstrated specificity for Clostridium spp. by labelling 15 and 17 of 20 Clostridium strains, respectively, but neither bound to other members of the cheese microbiota. However, GFP-EAD did not label any Clostridium strain tested. Unexpectedly, GFP-CTP1L and GFP-CBD were also able to bind to clostridial spores. In addition, GFP-CBD allowed us to visualize the vegetative cells of C. tyrobutyricum directly in the matrix of a LBD cheese. Site-directed mutants of GFP-CTP1L and GFP-CBD were made to examine the amino acids involved in binding and oligomer formation. Oligomerization was not essential for binding, but specific mutations in the CBD which affected oligomer formation also affected binding and lytic activity. We conclude that GFP-CTP1L and GFP-CBD could be good biomarkers for rapid detection of Clostridium spores in milk, so measures can be taken for the prevention of LBD in cheese, and also provide effective tools to study the development of Clostridium populations during cheese ripening.
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Affiliation(s)
- Natalia Gómez‐Torres
- Departamento de Tecnología de AlimentosInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Carretera de La Coruña km 728040MadridSpain
| | - Matthew Dunne
- European Molecular Biology Laboratory (EMBL) Hamburg OutstationNotkestrasse 8522607HamburgGermany
- Present address:
Institute of Food, Nutrition and HealthETH ZurichLFV B36, Schmelzbergstr. 78092ZurichSwitzerland
| | - Sonia Garde
- Departamento de Tecnología de AlimentosInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Carretera de La Coruña km 728040MadridSpain
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL) Hamburg OutstationNotkestrasse 8522607HamburgGermany
| | - Arjan Narbad
- Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceColneyNorwichNR4 7UAUK
| | - Marta Ávila
- Departamento de Tecnología de AlimentosInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Carretera de La Coruña km 728040MadridSpain
| | - Melinda J. Mayer
- Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceColneyNorwichNR4 7UAUK
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17
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Liu Y, Bhowmick T, Liu Y, Gao X, Mertens HDT, Svergun DI, Xiao J, Zhang Y, Wang JH, Meijers R. Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC. Neuron 2018; 97:1261-1267.e4. [PMID: 29503192 PMCID: PMC5871715 DOI: 10.1016/j.neuron.2018.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/19/2017] [Accepted: 02/05/2018] [Indexed: 11/25/2022]
Abstract
Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding. Video Abstract
Crystal structure of cysteine knot domain of Draxin in complex with DCC Crystal structure of Netrin-1 in complex with a Draxin fragment Netrin-1 contains a competing binding site for DCC and Draxin on the EGF-3 domain Draxin tethers Netrin-1 and DCC together to promote fasciculation
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Tuhin Bhowmick
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Yiqiong Liu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871 Beijing, China
| | - Xuefan Gao
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Science and Peking-Tsinghua Centre for Life Sciences, Peking University, 100871 Beijing, China.
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871 Beijing, China.
| | - Jia-Huai Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany.
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18
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Falke S, Dierks K, Blanchet C, Graewert M, Cipriani F, Meijers R, Svergun D, Betzel C. Multi-channel in situ dynamic light scattering instrumentation enhancing biological small-angle X-ray scattering experiments at the PETRA III beamline P12. J Synchrotron Radiat 2018; 25:361-372. [PMID: 29488914 DOI: 10.1107/s1600577517017568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/07/2017] [Indexed: 06/08/2023]
Abstract
Small-angle X-ray scattering (SAXS) analysis of biomolecules is increasingly common with a constantly high demand for comprehensive and efficient sample quality control prior to SAXS experiments. As monodisperse sample suspensions are desirable for SAXS experiments, latest dynamic light scattering (DLS) techniques are most suited to obtain non-invasive and rapid information about the particle size distribution of molecules in solution. A multi-receiver four-channel DLS system was designed and adapted at the BioSAXS endstation of the EMBL beamline P12 at PETRA III (DESY, Hamburg, Germany). The system allows the collection of DLS data within round-shaped sample capillaries used at beamline P12. Data obtained provide information about the hydrodynamic radius of biological particles in solution and dispersity of the solution. DLS data can be collected directly prior to and during an X-ray exposure. To match the short X-ray exposure times of around 1 s for 20 exposures at P12, the DLS data collection periods that have been used up to now of 20 s or commonly more were substantially reduced, using a novel multi-channel approach collecting DLS data sets in the SAXS sample capillary at four different neighbouring sample volume positions in parallel. The setup allows online scoring of sample solutions applied for SAXS experiments, supports SAXS data evaluation and for example indicates local inhomogeneities in a sample solution in a time-efficient manner. Biological macromolecules with different molecular weights were applied to test the system and obtain information about the performance. All measured hydrodynamic radii are in good agreement with DLS results obtained by employing a standard cuvette instrument. Moreover, applying the new multi-channel DLS setup, a reliable radius determination of sample solutions in flow, at flow rates normally used for size-exclusion chromatography-SAXS experiments, and at higher flow rates, was verified as well. This study also shows and confirms that the newly designed sample compartment with attached DLS instrumentation does not disturb SAXS measurements.
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Affiliation(s)
- Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, University Hamburg, c/o DESY, Building 22a, Notkestrasse 85, Hamburg 22603, Germany
| | - Karsten Dierks
- Xtal Concepts GmbH, Marlowring 19, Hamburg 22525, Germany
| | - Clement Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o Notkestrasse 85, Hamburg 22607, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o Notkestrasse 85, Hamburg 22607, Germany
| | - Florent Cipriani
- European Molecular Biology Laboratory (EMBL), 71 Avenue des Martyrs, Grenoble 38042, France
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o Notkestrasse 85, Hamburg 22607, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o Notkestrasse 85, Hamburg 22607, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University Hamburg, c/o DESY, Building 22a, Notkestrasse 85, Hamburg 22603, Germany
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19
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Garcia-Alai MM, Heidemann J, Skruzny M, Gieras A, Mertens HDT, Svergun DI, Kaksonen M, Uetrecht C, Meijers R. Epsin and Sla2 form assemblies through phospholipid interfaces. Nat Commun 2018; 9:328. [PMID: 29362354 PMCID: PMC5780493 DOI: 10.1038/s41467-017-02443-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 05/08/2017] [Accepted: 11/30/2017] [Indexed: 01/22/2023] Open
Abstract
In clathrin-mediated endocytosis, adapter proteins assemble together with clathrin through interactions with specific lipids on the plasma membrane. However, the precise mechanism of adapter protein assembly at the cell membrane is still unknown. Here, we show that the membrane–proximal domains ENTH of epsin and ANTH of Sla2 form complexes through phosphatidylinositol 4,5-bisphosphate (PIP2) lipid interfaces. Native mass spectrometry reveals how ENTH and ANTH domains form assemblies by sharing PIP2 molecules. Furthermore, crystal structures of epsin Ent2 ENTH domain from S. cerevisiae in complex with PIP2 and Sla2 ANTH domain from C. thermophilum illustrate how allosteric phospholipid binding occurs. A comparison with human ENTH and ANTH domains reveal only the human ENTH domain can form a stable hexameric core in presence of PIP2, which could explain functional differences between fungal and human epsins. We propose a general phospholipid-driven multifaceted assembly mechanism tolerating different adapter protein compositions to induce endocytosis. Adapter proteins assist clathrin coated pit assembly. Here, the authors combine native mass spectrometry, crystallography and SAXS measurements and show that the membrane–proximal domains of the adaptor proteins epsin and Sla2 form complexes mediated through phosphatidylinositol 4,5-bisphosphate interfaces leading to assembly formation.
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Affiliation(s)
- Maria M Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Michal Skruzny
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Anna Gieras
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.,University Medical Center Hamburg - Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marko Kaksonen
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany. .,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.
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20
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Affiliation(s)
- Lorenzo I Finci
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jie Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.,The Francis Crick Institute, London, NW1 2BE, UK
| | - Xiaqin Sun
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Robert G Smock
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
| | - Yan Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China. .,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jia-Huai Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China. .,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
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21
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Schneider TR, Bourenkov G, Martinez-Molledo M, Karpics I, Quistgaard EM, Hoffmann G, Cipriani F, Marquez J, Meijers R, Loew C. Structure determination of a membrane protein with data collected from micro-crystals in lipidic cubic phase at room temperature in low-background CrystalDirect crystallization plates. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Meijers R, Perrakis A. Editorial overview: New constructs and expression of proteins. Curr Opin Struct Biol 2016; 38:v-vi. [DOI: 10.1016/j.sbi.2016.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Kozak S, Lercher L, Karanth MN, Meijers R, Carlomagno T, Boivin S. Optimization of protein samples for NMR using thermal shift assays. J Biomol NMR 2016; 64:281-9. [PMID: 26984476 PMCID: PMC4869703 DOI: 10.1007/s10858-016-0027-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/08/2016] [Indexed: 05/09/2023]
Abstract
Maintaining a stable fold for recombinant proteins is challenging, especially when working with highly purified and concentrated samples at temperatures >20 °C. Therefore, it is worthwhile to screen for different buffer components that can stabilize protein samples. Thermal shift assays or ThermoFluor(®) provide a high-throughput screening method to assess the thermal stability of a sample under several conditions simultaneously. Here, we describe a thermal shift assay that is designed to optimize conditions for nuclear magnetic resonance studies, which typically require stable samples at high concentration and ambient (or higher) temperature. We demonstrate that for two challenging proteins, the multicomponent screen helped to identify ingredients that increased protein stability, leading to clear improvements in the quality of the spectra. Thermal shift assays provide an economic and time-efficient method to find optimal conditions for NMR structural studies.
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Affiliation(s)
- Sandra Kozak
- SPC Facility, European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Lukas Lercher
- SCB Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Megha N Karanth
- SCB Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Rob Meijers
- SPC Facility, European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Teresa Carlomagno
- SCB Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.
- Research Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Brunswick, Germany.
| | - Stephane Boivin
- SPC Facility, European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.
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24
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Dunne M, Leicht S, Krichel B, Mertens HDT, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R. Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product. J Biol Chem 2016; 291:4882-93. [PMID: 26683375 PMCID: PMC4777826 DOI: 10.1074/jbc.m115.671172] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/16/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages produce endolysins, which lyse the bacterial host cell to release newly produced virions. The timing of lysis is regulated and is thought to involve the activation of a molecular switch. We present a crystal structure of the activated endolysin CTP1L that targets Clostridium tyrobutyricum, consisting of a complex between the full-length protein and an N-terminally truncated C-terminal cell wall binding domain (CBD). The truncated CBD is produced through an internal translation start site within the endolysin gene. Mutants affecting the internal translation site change the oligomeric state of the endolysin and reduce lytic activity. The activity can be modulated by reconstitution of the full-length endolysin-CBD complex with free CBD. The same oligomerization mechanism applies to the CD27L endolysin that targets Clostridium difficile and the CS74L endolysin that targets Clostridium sporogenes. When the CTP1L endolysin gene is introduced into the commensal bacterium Lactococcus lactis, the truncated CBD is also produced, showing that the alternative start codon can be used in other bacterial species. The identification of a translational switch affecting oligomerization presented here has implications for the design of effective endolysins for the treatment of bacterial infections.
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Affiliation(s)
- Matthew Dunne
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Leicht
- the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Boris Krichel
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Haydyn D T Mertens
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Thompson
- the Synchrotron Soleil, L'Orme des Merisiers, BP 48, Saint Aubin, 91192 Gif sur Yvette, France
| | - Jeroen Krijgsveld
- the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Dmitri I Svergun
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Natalia Gómez-Torres
- the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Departamento de Tecnología de Alimentos, Carretera de La Coruña km 7, 28040 Madrid, Spain
| | - Sonia Garde
- the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Departamento de Tecnología de Alimentos, Carretera de La Coruña km 7, 28040 Madrid, Spain
| | - Charlotte Uetrecht
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany, the European XFEL GmbH, Notkestrasse 85, 22607 Hamburg, Germany, and
| | - Arjan Narbad
- the Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - Melinda J Mayer
- the Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - Rob Meijers
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany,
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25
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Shepard W, Duran D, Couster SL, Blache F, Delmotte A, Fourme R, Fox G, Meijers R, Moreno T, Pierre-Joseph S, Savko M. Recent results and developments on PROXIMA 2A. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s205327331509717x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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26
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Boivin S, Kozak S, Rasmussen G, Nemtanu IM, Vieira V, Meijers R. An integrated pipeline for sample preparation and characterization at the EMBL@PETRA3 synchrotron facilities. Methods 2015; 95:70-7. [PMID: 26255961 DOI: 10.1016/j.ymeth.2015.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 11/26/2022] Open
Abstract
The characterization of macromolecular samples at synchrotrons has traditionally been restricted to direct exposure to X-rays, but beamline automation and diversification of the user community has led to the establishment of complementary characterization facilities off-line. The Sample Preparation and Characterization (SPC) facility at the EMBL@PETRA3 synchrotron provides synchrotron users access to a range of biophysical techniques for preliminary or parallel sample characterization, to optimize sample usage at the beamlines. Here we describe a sample pipeline from bench to beamline, to assist successful structural characterization using small angle X-ray scattering (SAXS) or macromolecular X-ray crystallography (MX). The SPC has developed a range of quality control protocols to assess incoming samples and to suggest optimization protocols. A high-throughput crystallization platform has been adapted to reach a broader user community, to include chemists and biologists that are not experts in structural biology. The SPC in combination with the beamline and computational facilities at EMBL Hamburg provide a full package of integrated facilities for structural biology and can serve as model for implementation of such resources for other infrastructures.
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Affiliation(s)
- Stephane Boivin
- Sample Preparation and Characterization Facility, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, Hamburg 22607, Germany
| | - Sandra Kozak
- Sample Preparation and Characterization Facility, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, Hamburg 22607, Germany
| | - Gry Rasmussen
- Sample Preparation and Characterization Facility, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, Hamburg 22607, Germany
| | - Ioana Maria Nemtanu
- Sample Preparation and Characterization Facility, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, Hamburg 22607, Germany
| | - Vanessa Vieira
- Sample Preparation and Characterization Facility, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, Hamburg 22607, Germany
| | - Rob Meijers
- Sample Preparation and Characterization Facility, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, Hamburg 22607, Germany.
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27
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Kaljunen H, Schiefelbein SHH, Stummer D, Kozak S, Meijers R, Christiansen G, Rentmeister A. Structural Elucidation of the Bispecificity of A Domains as a Basis for Activating Non-natural Amino Acids. Angew Chem Int Ed Engl 2015; 54:8833-6. [DOI: 10.1002/anie.201503275] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 01/01/2023]
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28
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Kaljunen H, Schiefelbein SHH, Stummer D, Kozak S, Meijers R, Christiansen G, Rentmeister A. Strukturelle Aufklärung der Bispezifität von A-Domänen als Basis für die Aktivierung nicht-natürlicher Aminosäuren. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503275] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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29
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Schürmann M, Meijers R, Schneider TR, Steinbüchel A, Cianci M. 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7(T): crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Acta Crystallogr D Biol Crystallogr 2015; 71:1360-72. [PMID: 26057676 PMCID: PMC4461206 DOI: 10.1107/s1399004715006616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/01/2015] [Indexed: 01/19/2023]
Abstract
3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase (AcdDPN7; EC 3.13.1.4) was identified during investigation of the 3,3'-dithiodipropionic acid (DTDP) catabolic pathway in the betaproteobacterium Advenella mimigardefordensis strain DPN7(T). DTDP is an organic disulfide and a precursor for the synthesis of polythioesters (PTEs) in bacteria, and is of interest for biotechnological PTE production. AcdDPN7 catalyzes sulfur abstraction from 3SP-CoA, a key step during the catabolism of DTDP. Here, the crystal structures of apo AcdDPN7 at 1.89 Å resolution and of its complex with the CoA moiety from the substrate analogue succinyl-CoA at 2.30 Å resolution are presented. The apo structure shows that AcdDPN7 belongs to the acyl-CoA dehydrogenase superfamily fold and that it is a tetramer, with each subunit containing one flavin adenine dinucleotide (FAD) molecule. The enzyme does not show any dehydrogenase activity. Dehydrogenase activity would require a catalytic base (Glu or Asp residue) at either position 246 or position 366, where a glutamine and a glycine are instead found, respectively, in this desulfinase. The positioning of CoA in the crystal complex enabled the modelling of a substrate complex containing 3SP-CoA. This indicates that Arg84 is a key residue in the desulfination reaction. An Arg84Lys mutant showed a complete loss of enzymatic activity, suggesting that the guanidinium group of the arginine is essential for desulfination. AcdDPN7 is the first desulfinase with an acyl-CoA dehydrogenase fold to be reported, which underlines the versatility of this enzyme scaffold.
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Affiliation(s)
- Marc Schürmann
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas R. Schneider
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Michele Cianci
- European Molecular Biology Laboratory Hamburg Unit, EMBL, Notkestrasse 85, 22603 Hamburg, Germany
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30
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Graewert MA, Franke D, Jeffries CM, Blanchet CE, Ruskule D, Kuhle K, Flieger A, Schäfer B, Tartsch B, Meijers R, Svergun DI. Automated pipeline for purification, biophysical and x-ray analysis of biomacromolecular solutions. Sci Rep 2015; 5:10734. [PMID: 26030009 PMCID: PMC5377070 DOI: 10.1038/srep10734] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/22/2015] [Indexed: 01/16/2023] Open
Abstract
Small angle X-ray scattering (SAXS), an increasingly popular method for structural analysis of biological macromolecules in solution, is often hampered by inherent sample polydispersity. We developed an all-in-one system combining in-line sample component separation with parallel biophysical and SAXS characterization of the separated components. The system coupled to an automated data analysis pipeline provides a novel tool to study difficult samples at the P12 synchrotron beamline (PETRA-3, EMBL/DESY, Hamburg).
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Affiliation(s)
- Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Clement E. Blanchet
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Darja Ruskule
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Katja Kuhle
- Robert Koch-Institut, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Antje Flieger
- Robert Koch-Institut, Division of Enteropathogenic Bacteria and Legionella (FG11), Burgstr. 37, 38855 Wernigerode, Germany
| | - Bernd Schäfer
- Malvern Instruments GmbH, Rigipsstr. 19, 71083 Herrenberg, Germany
| | - Bernd Tartsch
- Malvern Instruments GmbH, Rigipsstr. 19, 71083 Herrenberg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, 22607 Hamburg, Germany
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31
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Skruzny M, Desfosses A, Prinz S, Dodonova S, Gieras A, Uetrecht C, Jakobi A, Abella M, Hagen W, Schulz J, Meijers R, Rybin V, Briggs J, Sachse C, Kaksonen M. An Organized Co-assembly of Clathrin Adaptors Is Essential for Endocytosis. Dev Cell 2015; 33:150-62. [DOI: 10.1016/j.devcel.2015.02.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/29/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
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32
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Choo JAL, Thong SY, Yap J, van Esch WJE, Raida M, Meijers R, Lescar J, Verhelst SHL, Grotenbreg GM. Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Choo JAL, Thong SY, Yap J, van Esch WJE, Raida M, Meijers R, Lescar J, Verhelst SHL, Grotenbreg GM. Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides. Angew Chem Int Ed Engl 2014; 53:13390-4. [DOI: 10.1002/anie.201406295] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/20/2014] [Indexed: 12/19/2022]
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34
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Finci LI, Krüger N, Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HDT, Svergun DI, Zhang Y, Wang JH, Meijers R. The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue. Neuron 2014; 83:839-849. [PMID: 25123307 DOI: 10.1016/j.neuron.2014.07.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2014] [Indexed: 01/01/2023]
Abstract
Netrin-1 is a guidance cue that can trigger either attraction or repulsion effects on migrating axons of neurons, depending on the repertoire of receptors available on the growth cone. How a single chemotropic molecule can act in such contradictory ways has long been a puzzle at the molecular level. Here we present the crystal structure of netrin-1 in complex with the Deleted in Colorectal Cancer (DCC) receptor. We show that one netrin-1 molecule can simultaneously bind to two DCC molecules through a DCC-specific site and through a unique generic receptor binding site, where sulfate ions staple together positively charged patches on both DCC and netrin-1. Furthermore, we demonstrate that UNC5A can replace DCC on the generic receptor binding site to switch the response from attraction to repulsion. We propose that the modularity of binding allows for the association of other netrin receptors at the generic binding site, eliciting alternative turning responses.
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Affiliation(s)
- Lorenzo I Finci
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA. 02215, USA
| | - Nina Krüger
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Xiaqin Sun
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jie Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Magda Chegkazi
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Yu Wu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Gundolf Schenk
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Yan Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China
| | - Jia-Huai Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, China.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA. 02215, USA
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
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Boivin S, Kozak S, Vieira V, Rasmussen G, Meijers R. Optimizing buffer conditions to improve crystallizability and SAXS measurement. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314088573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Sample Preparation and Characterization (SPC) facility at EMBL Hamburg is situated next to the PETRA3 beamlines for protein crystallography and small angle scattering (SAXS) that are operated by EMBL. The facility is equipped with molecular biology and biophysical instrumentation to carry out purification and characterization of macromolecular samples. It serves a mixed community of local EMBL scientists, beamline visitors and scientists from the European Union research area. Most incoming samples are destined for high-throughput crystallization at the facility or characterization by SAXS. The facility offers standardized quality control reports on each incoming sample, including characterization by mass spectrometry and Thermofluor. Based on this report, local staff can suggest and perform optimization protocols that increase the stability of the sample. For instance, Thermofluor screens(1) were developed that probe the effect of buffers and additives that are commonly used in sample preparation. These systematic screens provide a high-throughput method to identify stabilizing conditions for sample purification, storage and structural characterization. This technique has been also a valuable asset providing a high-throughput method for assessing the crystallizability of proteins by screening for conditions which contribute to the protein sample homogeneity, stability and solubility. The home-made screens have been tested on more than 200 different protein constructs at SPC facility. The aim of the SPC facility is to integrate off-line biophysical techniques with synchrotron beamlines, to offer the European user community a full package for sample characterization. The facility is especially geared towards cell biologists with little experience in structure determination. Expert staff is available to help to plan, perform and interpret biophysical experiments. It is possible for users to book SPC equipment together with their synchrotron beamtime, for protein purification, circular dichroism and isothermal calorimetry. Funded access to the facility is currently provided by the European Community's Seventh Framework Programme Biostruct-X. For further information, please contact spc@embl-hamburg.de.
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Duran D, Le Couster S, Fox G, Fourme R, Meijers R, Samama JP, Savko M, Shepard W. PROXIMA 2A: A New Micro-focus Beamline for Macromolecular Crystallography. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314083272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
PROXIMA 2A is a new micro-focus and energy tunable beamline dedicated to biological macromolecular crystallography at Synchrotron SOLEIL. The beamline officially opened in March 2013, and its first year of user operation has yielded excellent results. The X-ray source is a powerful in-vacuum U24 undulator coupled to a cryo-cooled Si[111] channel-cut monochromator and a pair of focussing bimorph mirrors in Kirpatrick-Baez configuration. This combination delivers a photon flux of over 10**12 ph/s into a focal spot of 10 μm × 5 μm (H×V FWHM), which is tunable over 6 – 15 keV. The supports of the optical elements have been designed to minimise the effects of vibrations and thermal dilations on the X-ray beam position, which is stable to within 5 microns over a day. The experimental station consists of a high performance micro-diffractometer, a cryostream, an area detector (ADSC Q315r), and an X-ray fluorescence detector. The X-ray energies for MAD experiments are directly calibrated on the sample. A robot equipped with a large 9 uni-puck dewar (CATS Irelec) is available to users for the automated transfer and screening of cryo-cooled samples. The users launch their experiments via an MXCuBE interface [1], which permits the centering of the sample, collecting of diffraction images, recording of X-ray spectra and the transfer of samples. The X-ray diffraction data are of an excellent quality, and the users readily exploit the micro-focused X-rays to select the best zones of their crystals. The first year of results from users has yielded a variety of success stories including novel protein structures resolved from crystals as small as 5 microns, as well as those solved by SAD & MAD methods. The future perspectives include automated helical and grid scans, in situ plate screening and multi-crystal merging techniques.
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Dunne M, Mertens HDT, Garefalaki V, Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A, Meijers R. The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLoS Pathog 2014; 10:e1004228. [PMID: 25058163 PMCID: PMC4110038 DOI: 10.1371/journal.ppat.1004228] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [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: 10/31/2013] [Accepted: 05/19/2014] [Indexed: 02/04/2023] Open
Abstract
The bacteriophage ΦCD27 is capable of lysing Clostridium difficile, a pathogenic bacterium that is a major cause for nosocomial infection. A recombinant CD27L endolysin lyses C. difficile in vitro, and represents a promising alternative as a bactericide. To better understand the lysis mechanism, we have determined the crystal structure of an autoproteolytic fragment of the CD27L endolysin. The structure covers the C-terminal domain of the endolysin, and represents a novel fold that is identified in a number of lysins that target Clostridia bacteria. The structure indicates endolysin cleavage occurs at the stem of the linker connecting the catalytic domain with the C-terminal domain. We also solved the crystal structure of the C-terminal domain of a slow cleaving mutant of the CTP1L endolysin that targets C. tyrobutyricum. Two distinct dimerization modes are observed in the crystal structures for both endolysins, despite a sequence identity of only 22% between the domains. The dimers are validated to be present for the full length protein in solution by right angle light scattering, small angle X-ray scattering and cross-linking experiments using the cross-linking amino acid p-benzoyl-L-phenylalanine (pBpa). Mutagenesis on residues contributing to the dimer interfaces indicates that there is a link between the dimerization modes and the autocleavage mechanism. We show that for the CTP1L endolysin, there is a reduction in lysis efficiency that is proportional to the cleavage efficiency. We propose a model for endolysin triggering, where the extended dimer presents the inactive state, and a switch to the side-by-side dimer triggers the cleavage of the C-terminal domain. This leads to the release of the catalytic portion of the endolysin, enabling the efficient digestion of the bacterial cell wall. Clostridium difficile infection is a common cause of hospital-acquired diarrhea, following broad-spectrum antibiotic treatment particularly in elderly patients. Bacteriophage therapy could provide an alternative treatment, but a better understanding of the viral components that lyse the bacterial cell is necessary. Here, we report on the activation of two endolysins from bacteriophages that lyse Clostridia. The structures of autoproteolytic fragments of two endolysins were determined by X-ray crystallography. Based on the structures, we introduced mutations that affect the autolytic cleavage of the enzymatic portion of the endolysins, and we show that two oligomeric states have an effect on the cleavage mechanism. Moreover, the lysis activity is affected when autocleavage is inhibited for one endolysin. We propose that the cleavage and oligomerization are linked, and they provide the endolysin with a trigger and release mechanism that leads to activation. The identification of a trigger and release factor may not only be relevant to Clostridia endolysins, but could be an important factor in the triggering of many bacteriophage endolysins. A fuller understanding of this activation mechanism will help in the design of recombinant endolysins or bacteriophages with a more efficient therapeutic potential.
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Affiliation(s)
- Matthew Dunne
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | | | | | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Andrew Thompson
- Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin, Gif sur Yvette, France
| | - Edward A. Lemke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Melinda J. Mayer
- Institute of Food Research, Colney, Norwich, United Kingdom
- * E-mail: (MJM); (RM)
| | - Arjan Narbad
- Institute of Food Research, Colney, Norwich, United Kingdom
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
- * E-mail: (MJM); (RM)
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Boivin S, Kozak S, Meijers R. Optimization of protein purification and characterization using Thermofluor screens. Protein Expr Purif 2013; 91:192-206. [DOI: 10.1016/j.pep.2013.08.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/29/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
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39
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Duran D, Couster SL, Desjardins K, Delmotte A, Fox G, Meijers R, Moreno T, Savko M, Shepard W. PROXIMA 2A – A New Fully Tunable Micro-focus Beamline for Macromolecular Crystallography. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/425/1/012005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Richter T, Lüth H, Schäpers T, Meijers R, Jeganathan K, Estévez Hernández S, Calarco R, Marso M. Electrical transport properties of single undoped and n-type doped InN nanowires. Nanotechnology 2009; 20:405206. [PMID: 19738304 DOI: 10.1088/0957-4484/20/40/405206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Electrical transport properties of undoped and n-type doped InN nanowires grown by molecular beam epitaxy were studied by current-voltage and back-gate field-effect transistor measurements. The current-voltage characteristics show ohmic behavior in the temperature range between 4 and 300 K. Down to about 120 K a linear decrease in resistance with temperature is observed. The investigation of a large number of nanowires revealed for undoped as well as doped wires an approximately linear relation between the normalized conductance and diameter for wires with a diameter below 100 nm. This shows that the main conduction takes place in the tubular surface accumulation layer of the wires. In contrast, for doped wires with a diameter larger than 100 nm a quadratic dependence of conduction on the diameter was found, which is attributed to bulk conductance as the main contribution. The successful doping of the wires is confirmed by an enhanced conduction and by the results of the back-gate field-effect transistor measurements.
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Affiliation(s)
- T Richter
- Institute of Bio- and Nanosystems (IBN-1) and JARA Jülich Aachen Research Alliance, Research Centre Jülich GmbH, D-52425 Jülich, Germany
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41
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Meijers R, Cedergren-Zeppezauer E. A variety of electrostatic interactions and adducts can activate NAD(P) cofactors for hydride transfer. Chem Biol Interact 2008; 178:24-8. [PMID: 19028476 DOI: 10.1016/j.cbi.2008.10.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 10/14/2008] [Accepted: 10/15/2008] [Indexed: 11/17/2022]
Abstract
In NAD(P)-dependent enzymes the coenzyme gives or takes a hydride ion, but how the nicotinamide ring is activated to form the transition state for hydride transfer is not clear. On the basis of ultra-high resolution X-ray crystal structures of liver alcohol dehydrogenase (LADH) in complex with NADH and a number of substrate analogues we proposed that the activation of NADH is an integral part of the enzyme mechanism of aldehyde reduction [R. Meijers, R.J. Morris, H.W. Adolph, A. Merli, V.S. Lamzin, E.S. Cedergren-Zeppezauer, On the enzymatic activation of NADH, The Journal of Biological Chemistry 276(12) (2001) 9316-9321, %U http://www.ncbi.nlm.nih.gov/pubmed/11134046; R. Meijers, H.-W. Adolph, Z. Dauter, K.S. Wilson, V.S. Lamzin, E.S. Cedergren-Zeppezauer, Structural evidence for a ligand coordination switch in liver alcohol dehydrogenase, Biochemistry 46(18) (2007) 5446-5454, %U http://www.ncbi.nlm.nih.gov/pubmed/17429946]. We observed a nicotinamide with a severely distorted pyridine ring and a water molecule in close proximity to the ring. Quantum chemical calculations indicated that (de)protonation of the water molecule can be directly coupled to activation of NADH for hydride transfer. A systematic search of the Protein Data Bank (PDB) for atoms that come within van der Waals distance of the pyridine ring of the nicotinamide reveals that a large number of NAD(P)-containing protein complexes are involved in electrostatic interactions with the enzymatic environment. Using the deposited diffraction data to analyze the cofactor and its surroundings, we observe several adducts between protein atoms and the pyridine ring that were not previously reported. This further indicates that the enzymatic activation of NAD(P) induced by electrostatic interactions is an essential part of the hydride transfer mechanism.
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Affiliation(s)
- Rob Meijers
- Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin, France.
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42
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Wang JH, Chen Q, Meijers R, Schmucker D, Liu J, Zhang H. Decoding homophilic recognition specificity of Dscam, a neuronal receptor with thousands isoforms. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308097134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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43
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Abstract
We present acoustic charge transport in GaN nanowires (GaN NWs). The GaN NWs were grown by molecular beam epitaxy (MBE) on silicon(111) substrates. The nanowires were removed from the silicon substrate, aligned using surface acoustic waves (SAWs) on the piezoelectric substrate LiNbO(3) and finally contacted by electron beam lithography. Then, a SAW was used to create an acoustoelectric current in the GaN NWs which was detected as a function of radio-frequency (RF) wave frequency and its power. The presented method and our experimental findings open up a route towards new acoustic charge transport nanostructure devices in a wide bandgap material such as GaN.
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Affiliation(s)
- J Ebbecke
- Experimentalphysik I, Institut für Physik der Universität Augsburg, Universitätsstraße 1, 86135 Augsburg, Germany. School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh,EH14 4AS, UK
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44
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Grotenbreg GM, Roan NR, Guillen E, Meijers R, Wang JH, Bell GW, Starnbach MN, Ploegh HL. Discovery of CD8+ T cell epitopes in Chlamydia trachomatis infection through use of caged class I MHC tetramers. Proc Natl Acad Sci U S A 2008; 105:3831-6. [PMID: 18245382 PMCID: PMC2268777 DOI: 10.1073/pnas.0711504105] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Indexed: 11/18/2022] Open
Abstract
Class I MHC tetramers allow direct phenotypic identification of CD8(+) T cell populations, but their production remains laborious. A peptide exchange strategy that employs class I MHC products loaded with conditional ligands (caged MHC molecules) provides a fast and straightforward method to obtain diverse arrays of class I MHC tetramers and facilitates CD8(+) T cell epitope discovery. Here, we describe the development of photocleavable analogs of the FAPGNYPAL (SV9) epitope that bind H-2K(b) and H-2D(b) with full retention of their structural and functional integrity. We ranked all possible H-2K(b) octameric and H-2D(b) nonameric epitopes that span the genome of Chlamydia trachomatis and prepared MHC tetramers from approximately 2,000 of the highest scoring peptides by replacement of the SV9 analog with the peptide of choice. The resulting 2,000-member class I MHC tetramer array allowed the discovery of two variants of an epitope derived from polymorphic membrane protein I (PmpI) and an assessment of the kinetics of emergence and the effector function of the corresponding CD8(+) T cells.
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Affiliation(s)
| | | | - Eduardo Guillen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139
| | - Rob Meijers
- Medicine
- Laboratory of Immunology, Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA 02115
| | - Jia-huai Wang
- Pediatrics, and
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; and
- Laboratory of Immunology, Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA 02115
| | - George W. Bell
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139
| | | | - Hidde L. Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139
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45
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Polenta L, Rossi M, Cavallini A, Calarco R, Marso M, Meijers R, Richter T, Stoica T, Lüth H. Investigation on localized states in GaN nanowires. ACS Nano 2008; 2:287-292. [PMID: 19206629 DOI: 10.1021/nn700386w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
GaN nanowires with diameters ranging between 50 and 500 nm were investigated by electrical and photoinduced current techniques to determine the influence of their size on the opto-electronic behavior of nanodevices. The conductivity, photoconductivity, and persistent photoconductivity behavior of GaN nanowires are observed to strongly depend on the wire diameter. In particular, by spectral photoconductivity measurements, three main sub-band-gap optoelectronic transitions were detected, ascribed to the localized states giving rise to the characteristic blue, green, and yellow bands of GaN. Photoconductivity with below-band-gap excitation varies orders of magnitude with the wire diameter, similarly to that observed for near-band-edge excitation. Moreover, yellow-band-related signal shows a superlinear behavior with respect to the band-edge signal, offering new information for the modeling of the carrier recombination mechanism along the nanowires. The photoconductivity results agree well with a model which takes into account a uniform distribution of the localized states inside the wire and their direct recombination with the electrons in the conduction band.
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Affiliation(s)
- L Polenta
- CNISM and Physics Department, University of Bologna, V.le Berti-Pichat 6/2, 40127 Bologna, Italy.
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46
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Meijers R, Puettmann-Holgado R, Skiniotis G, Liu JH, Walz T, Wang JH, Schmucker D. Structural basis of Dscam isoform specificity. Nature 2007; 449:487-91. [PMID: 17721508 DOI: 10.1038/nature06147] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2007] [Accepted: 08/07/2007] [Indexed: 01/22/2023]
Abstract
The Dscam gene gives rise to thousands of diverse cell surface receptors thought to provide homophilic and heterophilic recognition specificity for neuronal wiring and immune responses. Mutually exclusive splicing allows for the generation of sequence variability in three immunoglobulin ecto-domains, D2, D3 and D7. We report X-ray structures of the amino-terminal four immunoglobulin domains (D1-D4) of two distinct Dscam isoforms. The structures reveal a horseshoe configuration, with variable residues of D2 and D3 constituting two independent surface epitopes on either side of the receptor. Both isoforms engage in homo-dimerization coupling variable domain D2 with D2, and D3 with D3. These interactions involve symmetric, antiparallel pairing of identical peptide segments from epitope I that are unique to each isoform. Structure-guided mutagenesis and swapping of peptide segments confirm that epitope I, but not epitope II, confers homophilic binding specificity of full-length Dscam receptors. Phylogenetic analysis shows strong selection of matching peptide sequences only for epitope I. We propose that peptide complementarity of variable residues in epitope I of Dscam is essential for homophilic binding specificity.
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Affiliation(s)
- Rob Meijers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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47
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Meijers R, Adolph HW, Dauter Z, Wilson KS, Lamzin VS, Cedergren-Zeppezauer ES. Structural evidence for a ligand coordination switch in liver alcohol dehydrogenase. Biochemistry 2007; 46:5446-54. [PMID: 17429946 DOI: 10.1021/bi6023594] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of substrate analogues as inhibitors provides a way to understand and manipulate enzyme function. Here we report two 1 A resolution crystal structures of liver alcohol dehydrogenase in complex with NADH and two inhibitors: dimethyl sulfoxide and isobutyramide. Both structures present a dynamic state of inhibition. In the dimethyl sulfoxide complex structure, the inhibitor is caught in transition on its way to the active site using a flash-freezing protocol and a cadmium-substituted enzyme. One inhibitor molecule is partly located in the first and partly in the second coordination sphere of the active site metal. A hydroxide ion bound to the active site metal lies close to the pyridine ring of NADH, which is puckered in a twisted boat conformation. The cadmium ion is coordinated by both the hydroxide ion and the inhibitor molecule, providing structural evidence of a coordination switch at the active site metal ion. The structure of the isobutyramide complex reveals the partial formation of an adduct between the isobutyramide inhibitor and NADH. It provides evidence of the contribution of a shift from the keto to the enol tautomer during aldehyde reduction. The different positions of the inhibitors further refine the knowledge of the dynamics of the enzyme mechanism and explain how the crowded active site can facilitate the presence of a substrate and a metal-bound hydroxide ion.
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Affiliation(s)
- Rob Meijers
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Federal Republic of Germany.
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48
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Meijers R, Puettmann Holgado R, Skiniotis Y, Liu JH, Walz T, Schmucker D, Wang JH. Structural basis of Dscam isoform specificity. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306099442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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49
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Milekhin AG, Meijers R, Richter T, Calarco R, Lüth H, Paez Sierra BA, Zahn DRT. Surface enhanced Raman scattering by GaN nanocolumns. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/pssc.200565148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Meijers R, Lai CC, Yang Y, Liu JH, Zhong W, Wang JH, Reinherz EL. Crystal structures of murine MHC Class I H-2 D(b) and K(b) molecules in complex with CTL epitopes from influenza A virus: implications for TCR repertoire selection and immunodominance. J Mol Biol 2004; 345:1099-110. [PMID: 15644207 DOI: 10.1016/j.jmb.2004.11.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 11/08/2004] [Accepted: 11/09/2004] [Indexed: 11/16/2022]
Abstract
Cytotoxic T lymphocyte (CTL) responses against influenza A virus in C57BL/6 mice are dominated by a small number of viral peptides among many that are capable of binding to major histocompatibility complex (MHC) class I molecules. The basis of this limited immune recognition is unknown. Here, we present X-ray structures of MHC class I molecules in complex with two immunodominant epitopes (PA(224-233)/D(b) and PB1(703-711)/K(b)) and one non-immunogenic epitope (HA(468-477)/D(b)) of the influenza A virus. The immunodominant peptides are each characterized by a bulge at the C terminus, lifting P6 and P7 residues out of the MHC groove, presenting featured structural elements to T-cell receptors (TCRs). Immune recognition of PA(224-233)/D(b) will focus largely on the exposed P7 arginine residue. In contrast, the non-immunogenic HA(468-477) peptide lacks prominent features in this C-terminal bulge. In the K(b)-bound PB1(703-711) epitope, the bulge results from a non-canonical binding motif, such that the mode of presentation of this peptide strongly resembles that of D(b)-bound peptides. Given that PA(224-233)/D(b), PB1(703-711)/K(b) and the previously defined NP(366-374)/D(b) epitopes dominate the primary response to influenza A virus in C57BL/6 mice, our findings indicate that residues of the C-terminal bulge are important in selection of the immunodominant CTL repertoire.
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Affiliation(s)
- Rob Meijers
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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