1
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Dong J, Yin Z, Kreitler D, Bernstein HJ, Jakoncic J. Bragg Spot Finder (BSF): a new machine-learning-aided approach to deal with spot finding for rapidly filtering diffraction pattern images. J Appl Crystallogr 2024; 57:670-680. [PMID: 38846759 PMCID: PMC11151665 DOI: 10.1107/s1600576724002450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/14/2024] [Indexed: 06/09/2024] Open
Abstract
Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages (Dozor and DIALS), demonstrating that this is an appropriate framework to support future extensions and improvements.
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Affiliation(s)
- Jianxiang Dong
- Department of Computer Science, College of Engineering and Applied Sciences, Stony Brook University, Upton, NY, USA
| | - Zhaozheng Yin
- Department of Computer Science, College of Engineering and Applied Sciences, Stony Brook University, Upton, NY, USA
| | - Dale Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Building 745, Upton, NY, USA
| | - Herbert J. Bernstein
- Ronin Institute for Independent Scholarship, c/o NSLS-II, Brookhaven National Laboratory, Building 745, Upton, NY, USA
| | - Jean Jakoncic
- National Synchrotron Light Source II, Brookhaven National Laboratory, Building 745, Upton, NY, USA
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2
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Aleksich M, Paley DW, Schriber EA, Linthicum W, Oklejas V, Mittan-Moreau DW, Kelly RP, Kotei PA, Ghodsi A, Sierra RG, Aquila A, Poitevin F, Blaschke JP, Vakili M, Milne CJ, Dall'Antonia F, Khakhulin D, Ardana-Lamas F, Lima F, Valerio J, Han H, Gallo T, Yousef H, Turkot O, Bermudez Macias IJ, Kluyver T, Schmidt P, Gelisio L, Round AR, Jiang Y, Vinci D, Uemura Y, Kloos M, Hunter M, Mancuso AP, Huey BD, Parent LR, Sauter NK, Brewster AS, Hohman JN. XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates. J Am Chem Soc 2023; 145:17042-17055. [PMID: 37524069 DOI: 10.1021/jacs.3c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.
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Affiliation(s)
- Mariya Aleksich
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Daniel W Paley
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Elyse A Schriber
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Will Linthicum
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Vanessa Oklejas
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David W Mittan-Moreau
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ryan P Kelly
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Patience A Kotei
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Anita Ghodsi
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Johannes P Blaschke
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | | | | | | | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tamires Gallo
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- MAX IV Laboratory, Lund University, Box 118, SE-22100 Lund, Sweden
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | | | - Luca Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam R Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yifeng Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Doriana Vinci
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yohei Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Mark Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe University, Melbourne 3086, Australia
- Diamond Light Source, Harwell Science & Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Bryan D Huey
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Materials Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lucas R Parent
- Innovation Partnership Building, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - J Nathan Hohman
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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3
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Simbrunner J, Salzmann I, Resel R. Indexing of grazing-incidence X-ray diffraction patterns. CRYSTALLOGR REV 2023. [DOI: 10.1080/0889311x.2023.2187051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Affiliation(s)
- Josef Simbrunner
- Division of Neuroradiology, Vascular and Interventional Radiology, Medical University Graz, Graz, Austria
| | - Ingo Salzmann
- Department of Physics, Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling (CERMM), Centre for NanoScience Research (CeNSR), Concordia University, Montreal, Canada
| | - Roland Resel
- Institute of Solid State Physics, Graz University of Technology, Graz, Austria
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4
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Moynié L, Hoegy F, Milenkovic S, Munier M, Paulen A, Gasser V, Faucon AL, Zill N, Naismith JH, Ceccarelli M, Schalk IJ, Mislin GLA. Hijacking of the Enterobactin Pathway by a Synthetic Catechol Vector Designed for Oxazolidinone Antibiotic Delivery in Pseudomonas aeruginosa. ACS Infect Dis 2022; 8:1894-1904. [PMID: 35881068 DOI: 10.1021/acsinfecdis.2c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Enterobactin (ENT) is a tris-catechol siderophore used to acquire iron by multiple bacterial species. These ENT-dependent iron uptake systems have often been considered as potential gates in the bacterial envelope through which one can shuttle antibiotics (Trojan horse strategy). In practice, siderophore analogues containing catechol moieties have shown promise as vectors to which antibiotics may be attached. Bis- and tris-catechol vectors (BCVs and TCVs, respectively) were shown using structural biology and molecular modeling to mimic ENT binding to the outer membrane transporter PfeA in Pseudomonas aeruginosa. TCV but not BCV appears to cross the outer membrane via PfeA when linked to an antibiotic (linezolid). TCV is therefore a promising vector for Trojan horse strategies against P. aeruginosa, confirming the ENT-dependent iron uptake system as a gate to transport antibiotics into P. aeruginosa cells.
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Affiliation(s)
- Lucile Moynié
- The Rosalind Franklin Institute, Harwell Campus, Oxfordshire OX11 0QS, U.K
| | - Françoise Hoegy
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - Stefan Milenkovic
- Department of Physics, University of Cagliari, 09042 Monserrato, Italy
| | - Mathilde Munier
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - Aurélie Paulen
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - Véronique Gasser
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - Aline L Faucon
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - Nicolas Zill
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - James H Naismith
- The Rosalind Franklin Institute, Harwell Campus, Oxfordshire OX11 0QS, U.K.,Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford OX3 7BN, U.K
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, 09042 Monserrato, Italy.,IOM/CNR, Sezione di Cagliari, University of Cagliari, 09042 Monserrato, Italy
| | - Isabelle J Schalk
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
| | - Gaëtan L A Mislin
- CNRS, UMR7242 Biotechnologie et Signalisation Cellulaire, 300 Boulevard Sébastien Brant, F-67412 Illkirch, France.,Université de Strasbourg, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), 300 Boulevard Sébastien Brant, F-67412 Illkirch, France
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5
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Wang L, Yun Y, Zhu Z, Niu L. AutoPX: a new software package to process X-ray diffraction data from biomacromolecular crystals. Acta Crystallogr D Struct Biol 2022; 78:890-902. [DOI: 10.1107/s2059798322005745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/27/2022] [Indexed: 11/11/2022] Open
Abstract
A new software package, autoPX, for processing X-ray diffraction data from biomacromolecular crystals is reported. This processing software package is designed on the basis of novel methods such as the location of diffraction spots by an improved Canny operator, indexing by a modified Fourier transform, a novel definition of mosaicity that expresses the dispersion state of reciprocal diffraction spots, and the correction of predicted diffraction spot coordinates by homography transform. New programming of some traditional algorithms necessary for integration and scaling is also included. Several examples of crystal structure determination using data from the SSRF beamlines reduced using autoPX, HKL-2000, DIALS and XDS are also demonstrated, and indicate that autoPX is capable of processing diffraction data from biomacromolecular crystals and providing adequate solutions to problems encountered at the SSRF beamlines.
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6
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Kissel T, Ge C, Hafkenscheid L, Kwekkeboom JC, Slot LM, Cavallari M, He Y, van Schie KA, Vergroesen RD, Kampstra AS, Reijm S, Stoeken-Rijsbergen G, Koeleman C, Voortman LM, Heitman LH, Xu B, Pruijn GJ, Wuhrer M, Rispens T, Huizinga TW, Scherer HU, Reth M, Holmdahl R, Toes RE. Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation. SCIENCE ADVANCES 2022; 8:eabm1759. [PMID: 35138894 PMCID: PMC8827743 DOI: 10.1126/sciadv.abm1759] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/15/2021] [Indexed: 05/05/2023]
Abstract
The hallmark autoantibodies in rheumatoid arthritis are characterized by variable domain glycans (VDGs). Their abundant occurrence results from the selective introduction of N-linked glycosylation sites during somatic hypermutation, and their presence is predictive for disease development. However, the functional consequences of VDGs on autoreactive B cells remain elusive. Combining crystallography, glycobiology, and functional B cell assays allowed us to dissect key characteristics of VDGs on human B cell biology. Crystal structures showed that VDGs are positioned in the vicinity of the antigen-binding pocket, and dynamic modeling combined with binding assays elucidated their impact on binding. We found that VDG-expressing B cell receptors stay longer on the B cell surface and that VDGs enhance B cell activation. These results provide a rationale on how the acquisition of VDGs might contribute to the breach of tolerance of autoreactive B cells in a major human autoimmune disease.
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Affiliation(s)
- Theresa Kissel
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Changrong Ge
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Lise Hafkenscheid
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
- Department of Biotechnology and Biomedicine, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Linda M. Slot
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Marco Cavallari
- Biology III (Department of Molecular Immunology), University of Freiburg, Freiburg, Germany
| | - Yibo He
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Karin A. van Schie
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arieke S.B. Kampstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Sanne Reijm
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Carolien Koeleman
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Lennard M. Voortman
- Department of Cell and Chemical Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Laura H. Heitman
- Oncode Institute and Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Bingze Xu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Ger J.M. Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Theo Rispens
- Department Immunopathology, Sanquin Research, Amsterdam, Netherlands
| | - Tom W.J. Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Hans Ulrich Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Michael Reth
- Biology III (Department of Molecular Immunology), University of Freiburg, Freiburg, Germany
| | - Rikard Holmdahl
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- The Second Affiliated Hospital of Xi’an Jiaotong University (Xibei Hospital), 710004 Xi’an, China
| | - Rene E.M. Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
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7
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Ge C, Tong D, Lönnblom E, Liang B, Cai W, Fahlquist-Hagert C, Li T, Kastbom A, Gjertsson I, Dobritzsch D, Holmdahl R. Antibodies to cartilage oligomeric matrix protein are pathogenic in mice and may be clinically relevant in rheumatoid arthritis. Arthritis Rheumatol 2022; 74:961-971. [PMID: 35080151 PMCID: PMC9320966 DOI: 10.1002/art.42072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/20/2021] [Accepted: 01/18/2022] [Indexed: 11/29/2022]
Abstract
Objective Cartilage oligomeric matrix protein (COMP) is an autoantigen in rheumatoid arthritis (RA) and experimental models of arthritis. This study was undertaken to investigate the structure, function, and relevance of anti‐COMP antibodies. Methods We investigated the pathogenicity of monoclonal anti‐COMP antibodies in mice using passive transfer experiments, and we explored the interaction of anti‐COMP antibodies with cartilage using immunohistochemical staining. The interaction of the monoclonal antibody 15A11 in complex with its specific COMP epitope P6 was determined by x‐ray crystallography. An enzyme‐linked immunosorbent assay and a surface plasma resonance technique were used to study the modulation of calcium ion binding to 15A11. The clinical relevance and value of serum IgG specific to the COMP P6 epitope and its citrullinated variants were evaluated in a large Swedish cohort of RA patients. Results The murine monoclonal anti‐COMP antibody 15A11 induced arthritis in naive mice. The crystal structure of the 15A11–P6 complex explained how the antibody could bind to COMP, which can be modulated by calcium ions. Moreover, serum IgG specific to the COMP P6 peptide and its citrullinated variants was detectable at significantly higher levels in RA patients compared to healthy controls and correlated with a higher disease activity score. Conclusion Our findings provide the structural basis for binding a pathogenic anti‐COMP antibody to cartilage. The recognized epitope can be citrullinated, and levels of antibodies to this epitope are elevated in RA patients and correlate with higher disease activity, implicating a pathogenic role of anti‐COMP antibodies in a subset of RA patients.
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Affiliation(s)
- Changrong Ge
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Dongmei Tong
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Erik Lönnblom
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Bibo Liang
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden.,Center for Medical Immunopharmacology Research, Pharmacology School, Southern Medical University, Guangzhou, China
| | - Weiwei Cai
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Cecilia Fahlquist-Hagert
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden.,Medical Inflammation Research, MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Taotao Li
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden
| | - Alf Kastbom
- Department of Rheumatology in Östergötland, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Inger Gjertsson
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Doreen Dobritzsch
- Section of Biochemistry, Department of Chemistry-BMC, Uppsala University, 171 23, Uppsala, Sweden
| | - Rikard Holmdahl
- Medical Inflammation Research, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 171 77, Stockholm, Sweden.,Center for Medical Immunopharmacology Research, Pharmacology School, Southern Medical University, Guangzhou, China.,Medical Inflammation Research, MediCity Research Laboratory, University of Turku, Turku, Finland
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8
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Griffiths SC, Schwab RA, El Omari K, Bishop B, Iverson EJ, Malinauskas T, Dubey R, Qian M, Covey DF, Gilbert RJC, Rohatgi R, Siebold C. Hedgehog-Interacting Protein is a multimodal antagonist of Hedgehog signalling. Nat Commun 2021; 12:7171. [PMID: 34887403 PMCID: PMC8660895 DOI: 10.1038/s41467-021-27475-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 11/19/2021] [Indexed: 01/20/2023] Open
Abstract
Hedgehog (HH) morphogen signalling, crucial for cell growth and tissue patterning in animals, is initiated by the binding of dually lipidated HH ligands to cell surface receptors. Hedgehog-Interacting Protein (HHIP), the only reported secreted inhibitor of Sonic Hedgehog (SHH) signalling, binds directly to SHH with high nanomolar affinity, sequestering SHH. Here, we report the structure of the HHIP N-terminal domain (HHIP-N) in complex with a glycosaminoglycan (GAG). HHIP-N displays a unique bipartite fold with a GAG-binding domain alongside a Cysteine Rich Domain (CRD). We show that HHIP-N is required to convey full HHIP inhibitory function, likely by interacting with the cholesterol moiety covalently linked to HH ligands, thereby preventing this SHH-attached cholesterol from binding to the HH receptor Patched (PTCH1). We also present the structure of the HHIP C-terminal domain in complex with the GAG heparin. Heparin can bind to both HHIP-N and HHIP-C, thereby inducing clustering at the cell surface and generating a high-avidity platform for SHH sequestration and inhibition. Our data suggest a multimodal mechanism, in which HHIP can bind two specific sites on the SHH morphogen, alongside multiple GAG interactions, to inhibit SHH signalling.
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Affiliation(s)
- Samuel C Griffiths
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Evotec (UK) Ltd., Milton Park, Abingdon, UK
| | - Rebekka A Schwab
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kamel El Omari
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Benjamin Bishop
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ellen J Iverson
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ramin Dubey
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingxing Qian
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MI, USA
| | - Douglas F Covey
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MI, USA
| | - Robert J C Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian Siebold
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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9
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Morawiec A. A remark on ab initio indexing of electron backscatter diffraction patterns. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721009304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
There is a growing interest in ab initio indexing of electron backscatter diffraction (EBSD) patterns. The methods of solving the problem are presented as innovative. The purpose of this note is to point out that ab initio EBSD indexing belongs to the field of indexing single-crystal diffraction data, and it is solved on the same principles as indexing of patterns of other types. It is shown that reasonably accurate EBSD-based data can be indexed by programs designed for X-ray data.
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10
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Kainz MP, Legenstein L, Holzer V, Hofer S, Kaltenegger M, Resel R, Simbrunner J. GIDInd: an automated indexing software for grazing-incidence X-ray diffraction data. J Appl Crystallogr 2021; 54:1256-1267. [PMID: 34429726 PMCID: PMC8366425 DOI: 10.1107/s1600576721006609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022] Open
Abstract
The GIDInd software package is a MATLAB-based application for automated indexing of grazing-incidence X-ray diffraction data. Grazing-incidence X-ray diffraction (GIXD) is a widely used technique for the crystallographic characterization of thin films. The identification of a specific phase or the discovery of an unknown polymorph always requires indexing of the associated diffraction pattern. However, despite the importance of this procedure, only a few approaches have been developed so far. Recently, an advanced mathematical framework for indexing of these specific diffraction patterns has been developed. Here, the successful implementation of this framework in the form of an automated indexing software, named GIDInd, is introduced. GIDInd is based on the assumption of a triclinic unit cell with six lattice constants and a distinct contact plane parallel to the substrate surface. Two approaches are chosen: (i) using only diffraction peaks of the GIXD pattern and (ii) combining the GIXD pattern with a specular diffraction peak. In the first approach the six unknown lattice parameters have to be determined by a single fitting procedure, while in the second approach two successive fitting procedures are used with three unknown parameters each. The output unit cells are reduced cells according to approved crystallographic conventions. Unit-cell solutions are additionally numerically optimized. The computational toolkit is compiled in the form of a MATLAB executable and presented within a user-friendly graphical user interface. The program is demonstrated by application on two independent examples of thin organic films.
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Affiliation(s)
- Manuel Peter Kainz
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Lukas Legenstein
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Valentin Holzer
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Sebastian Hofer
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Martin Kaltenegger
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Roland Resel
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Josef Simbrunner
- Division of Neuroradiology, Vascular and Interventional Radiology, Medical University Graz, Auenbruggerplatz 9, Graz, 8036, Austria
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11
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Peck A, Yao Q, Brewster AS, Zwart PH, Heumann JM, Sauter NK, Jensen GJ. Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation. Acta Crystallogr D Struct Biol 2021; 77:572-586. [PMID: 33950014 PMCID: PMC8098477 DOI: 10.1107/s2059798321002369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/02/2021] [Indexed: 11/11/2022] Open
Abstract
Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.
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Affiliation(s)
- Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Petrus H. Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - John M. Heumann
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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12
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Bortel G, Tegze M, Faigel G. Constrained geometrical analysis of complete K-line patterns for calibrationless auto-indexing. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576720014892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Indexing of Kikuchi and Kossel lines is a crucial step in K-line pattern analysis. Previous approaches mostly rely on the knowledge of unit-cell parameters and experimental geometry. An auto-indexing procedure is introduced that is able to find the unknown lattice, its orientation and the indices of the lines. To achieve this, the unbiased extraction of the precise conical geometrical information from the patterns is combined with existing auto-indexing procedures developed in the field of crystallography. A subsequent lattice-constrained refinement of all lines to the experimental pattern yields reliable lattice and experimental parameters simultaneously. Beyond providing detailed mathematical formulae, the procedure is also demonstrated on an experimental Kossel line pattern.
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13
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Suzuki K, Elegheert J, Song I, Sasakura H, Senkov O, Matsuda K, Kakegawa W, Clayton AJ, Chang VT, Ferrer-Ferrer M, Miura E, Kaushik R, Ikeno M, Morioka Y, Takeuchi Y, Shimada T, Otsuka S, Stoyanov S, Watanabe M, Takeuchi K, Dityatev A, Aricescu AR, Yuzaki M. A synthetic synaptic organizer protein restores glutamatergic neuronal circuits. Science 2020; 369:369/6507/eabb4853. [PMID: 32855309 PMCID: PMC7116145 DOI: 10.1126/science.abb4853] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 12/18/2022]
Abstract
Neuronal synapses undergo structural and functional changes throughout life, which are essential for nervous system physiology. However, these changes may also perturb the excitatory-inhibitory neurotransmission balance and trigger neuropsychiatric and neurological disorders. Molecular tools to restore this balance are highly desirable. Here, we designed and characterized CPTX, a synthetic synaptic organizer combining structural elements from cerebellin-1 and neuronal pentraxin-1. CPTX can interact with presynaptic neurexins and postsynaptic AMPA-type ionotropic glutamate receptors and induced the formation of excitatory synapses both in vitro and in vivo. CPTX restored synaptic functions, motor coordination, spatial and contextual memories, and locomotion in mouse models for cerebellar ataxia, Alzheimer's disease, and spinal cord injury, respectively. Thus, CPTX represents a prototype for structure-guided biologics that can efficiently repair or remodel neuronal circuits.
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Affiliation(s)
- Kunimichi Suzuki
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Jonathan Elegheert
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
| | - Inseon Song
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany
| | - Hiroyuki Sasakura
- Department of Medical Cell Biology, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Oleg Senkov
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany
| | - Keiko Matsuda
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Wataru Kakegawa
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Amber J Clayton
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
| | - Veronica T Chang
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Maura Ferrer-Ferrer
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany
| | - Eriko Miura
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Rahul Kaushik
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany
| | - Masashi Ikeno
- Department of Medical Cell Biology, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Yuki Morioka
- Department of Medical Cell Biology, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Yuka Takeuchi
- Department of Medical Cell Biology, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Tatsuya Shimada
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shintaro Otsuka
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Stoyan Stoyanov
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Kosei Takeuchi
- Department of Medical Cell Biology, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Alexander Dityatev
- Molecular Neuroplasticity, German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany.
- Center for Behavioral Brain Sciences (CBBS), 39106 Magdeburg, Germany
- Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - A Radu Aricescu
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK.
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michisuke Yuzaki
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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14
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EM-detwin: A Program for Resolving Indexing Ambiguity in Serial Crystallography Using the Expectation-Maximization Algorithm. CRYSTALS 2020. [DOI: 10.3390/cryst10070588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Serial crystallography (SX), first used as an application of X-ray free-electron lasers (XFELs), is becoming a useful method to determine atomic-resolution structures of proteins from micrometer-sized crystals with bright X-ray sources. Because of unknown orientations of crystals in SX, indexing ambiguity issue arises when the symmetry of Bravais lattice is higher than the space group symmetry, making some diffraction signals wrongly merged to the total intensity in twinned orientations. In this research, we developed a program within the CrystFEL framework, the EM-detwin, to resolve this indexing ambiguity problem based on the expectation-maximization algorithm. Testing results on the performance of the EM-detwin have demonstrated its usefulness in correctly indexing diffraction data as a valuable tool for SX data analysis.
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15
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Simbrunner J, Schrode B, Domke J, Fritz T, Salzmann I, Resel R. An efficient method for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2020; 76:345-357. [PMID: 32356785 PMCID: PMC7233012 DOI: 10.1107/s2053273320001266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 11/10/2022]
Abstract
Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacenequinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.
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Affiliation(s)
- Josef Simbrunner
- Department of Neuroradiology, Vascular and Interventional Radiology, Medical University Graz, Auenbruggerplatz 9, Graz, 8036, Austria
| | - Benedikt Schrode
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
| | - Jari Domke
- Institute of Solid State Physics, Friedrich Schiller University Jena, Helmholtzweg 5, Jena, 07743, Germany
| | - Torsten Fritz
- Institute of Solid State Physics, Friedrich Schiller University Jena, Helmholtzweg 5, Jena, 07743, Germany
| | - Ingo Salzmann
- Department of Physics, Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling (CERMM), Centre for NanoScience Research (CeNSR), Concordia University, 7141 Sherbrooke Street W., SP 265-20, Montreal, Québec H4B 1R6, Canada
| | - Roland Resel
- Institute of Solid State Physics, Graz University of Technology, Petersgasse 16, Graz, 8010, Austria
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16
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Bernstein HJ, Andrews LC, Diaz JA, Jakoncic J, Nguyen T, Sauter NK, Soares AS, Wei JY, Wlodek MR, Xerri MA. Best practices for high data-rate macromolecular crystallography (HDRMX). STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014302. [PMID: 31934601 PMCID: PMC6952294 DOI: 10.1063/1.5128498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/11/2019] [Indexed: 05/13/2023]
Abstract
In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format.
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Affiliation(s)
- Herbert J Bernstein
- Ronin Institute for Independent Scholarship, c/o NSLS-II Bldg 745, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Lawrence C Andrews
- Ronin Institute for Independent Scholarship, 9515 NE 137th St., Kirkland, Washington 98034, USA
| | - Jorge A Diaz
- Ronin Institute for Independent Scholarship, c/o NSLS-II Bldg 745, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Jean Jakoncic
- Brookhaven National Laboratory, NSLS-II Bldg 745, Upton, New York 11973, USA
| | - Thu Nguyen
- Stony Brook University, Stony Brook, New York 11794, USA
| | - Nicholas K Sauter
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA
| | - Alexei S Soares
- Brookhaven National Laboratory, NSLS-II Bldg 745, Upton, New York 11973, USA
| | - Justin Y Wei
- Mount Sinai High School, 110 N Country Rd., Mt Sinai, New York 11766, USA
| | | | - Mario A Xerri
- Mount Sinai High School, 110 N Country Rd., Mt Sinai, New York 11766, USA
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17
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Moynié L, Milenkovic S, Mislin GLA, Gasser V, Malloci G, Baco E, McCaughan RP, Page MGP, Schalk IJ, Ceccarelli M, Naismith JH. The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model. Nat Commun 2019; 10:3673. [PMID: 31413254 PMCID: PMC6694100 DOI: 10.1038/s41467-019-11508-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/16/2019] [Indexed: 11/17/2022] Open
Abstract
Bacteria use small molecules called siderophores to scavenge iron. Siderophore-Fe3+ complexes are recognised by outer-membrane transporters and imported into the periplasm in a process dependent on the inner-membrane protein TonB. The siderophore enterobactin is secreted by members of the family Enterobacteriaceae, but many other bacteria including Pseudomonas species can use it. Here, we show that the Pseudomonas transporter PfeA recognises enterobactin using extracellular loops distant from the pore. The relevance of this site is supported by in vivo and in vitro analyses. We suggest there is a second binding site deeper inside the structure and propose that correlated changes in hydrogen bonds link binding-induced structural re-arrangements to the structural adjustment of the periplasmic TonB-binding motif.
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Affiliation(s)
- Lucile Moynié
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, UK
- The Research Complex at Harwell, Harwell Campus, Oxfordshire, OX11 0FA, UK
- The Rosalind Franklin Institute, Didcot, OX11 0FA, UK
| | - Stefan Milenkovic
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP Monserrato-Sestu Km 0.700, Monserrato, 09042, Italy
| | - Gaëtan L A Mislin
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France
| | - Véronique Gasser
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP Monserrato-Sestu Km 0.700, Monserrato, 09042, Italy
| | - Etienne Baco
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France
- CNRS, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France
| | | | - Malcolm G P Page
- Department of Life Sciences & Chemistry, Campus Ring 1, Bremen, 28759, Germany
| | - Isabelle J Schalk
- Université de Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, Illkirch, F-67413, Strasbourg, France.
- Istituto Officina dei Materiali-CNR, Cittadella Universitaria, Monserrato, 09042, Italy.
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP Monserrato-Sestu Km 0.700, Monserrato, 09042, Italy.
- Istituto Officina dei Materiali-CNR, Cittadella Universitaria, Monserrato, 09042, Italy.
| | - James H Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, 7 Roosevelt Drive, Oxford, OX3 7BN, UK.
- The Research Complex at Harwell, Harwell Campus, Oxfordshire, OX11 0FA, UK.
- The Rosalind Franklin Institute, Didcot, OX11 0FA, UK.
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18
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Powell HR. From then till now: changing data collection methods in single crystal X-ray crystallography since 1912. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1615483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Simbrunner J, Hofer S, Schrode B, Garmshausen Y, Hecht S, Resel R, Salzmann I. Indexing grazing-incidence X-ray diffraction patterns of thin films: lattices of higher symmetry. J Appl Crystallogr 2019; 52:428-439. [PMID: 30996719 PMCID: PMC6448685 DOI: 10.1107/s1600576719003029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/27/2019] [Indexed: 11/24/2022] Open
Abstract
A general indexing procedure for grazing-incidence X-ray diffraction patterns recorded from fibre-textured films is introduced for lattices of monoclinic and higher-symmetry systems. The analytical mathematical expressions are given and their use is demonstrated in detail for two cases (monoclinic and orthorhombic). Grazing-incidence X-ray diffraction studies on organic thin films are often performed on systems showing fibre-textured growth. However, indexing their experimental diffraction patterns is generally challenging, especially if low-symmetry lattices are involved. Recently, analytical mathematical expressions for indexing experimental diffraction patterns of triclinic lattices were provided. In the present work, the corresponding formalism for crystal lattices of higher symmetry is given and procedures for applying these equations for indexing experimental data are described. Two examples are presented to demonstrate the feasibility of the indexing method. For layered crystals of the prototypical organic semiconductors diindenoperylene and (ortho-difluoro)sexiphenyl, as grown on highly oriented pyrolytic graphite, their yet unknown unit-cell parameters are determined and their crystallographic lattices are identified as monoclinic and orthorhombic, respectively.
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Affiliation(s)
- Josef Simbrunner
- Department of Neuroradiology, Vascular and Interventional Radiology, Medical University Graz, Auenbruggerplatz 9, Graz, 8036, Austria
| | - Sebastian Hofer
- Institute of Solid State Physics, Technical University Graz, Petersgasse 16, Graz, 8010, Austria
| | - Benedikt Schrode
- Institute of Solid State Physics, Technical University Graz, Petersgasse 16, Graz, 8010, Austria
| | - Yves Garmshausen
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, Berlin, 12489, Germany
| | - Stefan Hecht
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, Berlin, 12489, Germany
| | - Roland Resel
- Institute of Solid State Physics, Technical University Graz, Petersgasse 16, Graz, 8010, Austria
| | - Ingo Salzmann
- Department of Physics, Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling (CERMM), Centre for Nanoscience Research (CeNSR), Concordia University, 7141 Sherbrooke Street W., SP 265-20, Montreal, Quebec, Canada H4B 1R6
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20
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Ross JF, Wildsmith GC, Johnson M, Hurdiss DL, Hollingsworth K, Thompson RF, Mosayebi M, Trinh CH, Paci E, Pearson AR, Webb ME, Turnbull WB. Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages. J Am Chem Soc 2019; 141:5211-5219. [PMID: 30856321 PMCID: PMC6449800 DOI: 10.1021/jacs.8b11480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The self-assembly
of proteins into higher order structures is ubiquitous
in living systems. It is also an essential process for the bottom-up
creation of novel molecular architectures and devices for synthetic
biology. However, the complexity of protein–protein interaction
surfaces makes it challenging to mimic natural assembly processes
in artificial systems. Indeed, many successful computationally designed
protein assemblies are prescreened for “designability”,
limiting the choice of components. Here, we report a simple and pragmatic
strategy to assemble chosen multisubunit proteins into more complex
structures. A coiled-coil domain appended to one face of the pentameric
cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular
supra-molecular complexes. Analysis of a tubular structure determined
by X-ray crystallography has revealed a hierarchical assembly process
that displays features reminiscent of the polymorphic assembly of
polyomavirus proteins. The approach provides a simple and straightforward
method to direct the assembly of protein building blocks which present
either termini on a single face of an oligomer. This scaffolding approach
can be used to generate bespoke supramolecular assemblies of functional
proteins. Additionally, structural resolution of the scaffolded assemblies
highlight “native-state” forced protein–protein
interfaces, which may prove useful as starting conformations for future
computational design.
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Affiliation(s)
- James F Ross
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Gemma C Wildsmith
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Michael Johnson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Daniel L Hurdiss
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Kristian Hollingsworth
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Majid Mosayebi
- School of Mathematics , University of Bristol , Bristol BS8 1TW , United Kingdom.,BrisSynBio, Life Sciences Building , University of Bristol , Bristol BS8 1TQ , United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics , Universität Hamburg , Hamburg D-22761 , Germany
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - W Bruce Turnbull
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
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21
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Ge C, Xu B, Liang B, Lönnblom E, Lundström SL, Zubarev RA, Ayoglu B, Nilsson P, Skogh T, Kastbom A, Malmström V, Klareskog L, Toes REM, Rispens T, Dobritzsch D, Holmdahl R. Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies. Arthritis Rheumatol 2019; 71:210-221. [PMID: 30152126 DOI: 10.1002/art.40698] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/23/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Anti-citrullinated protein antibodies (ACPAs) develop many years before the clinical onset of rheumatoid arthritis (RA). This study was undertaken to address the molecular basis of the specificity and cross-reactivity of ACPAs from patients with RA. METHODS Antibodies isolated from RA patients were expressed as monoclonal chimeric antibodies with mouse Fc. These antibodies were characterized for glycosylation using mass spectrometry, and their cross-reactivity was assessed using Biacore and Luminex immunoassays. The crystal structures of the antigen-binding fragment (Fab) of the monoclonal ACPA E4 in complex with 3 different citrullinated peptides were determined using x-ray crystallography. The prevalence of autoantibodies reactive against 3 of the citrullinated peptides that also interacted with E4 was investigated by Luminex immunoassay in 2 Swedish cohorts of RA patients. RESULTS Analysis of the crystal structures of a monoclonal ACPA from human RA serum in complex with citrullinated peptides revealed key residues of several complementarity-determining regions that recognized the citrulline as well as the neighboring peptide backbone, but with limited contact with the side chains of the peptides. The same citrullinated peptides were recognized by high titers of serum autoantibodies in 2 large cohorts of RA patients. CONCLUSION These data show, for the first time, how ACPAs derived from human RA serum recognize citrulline. The specific citrulline recognition and backbone-mediated interactions provide a structural explanation for the promiscuous recognition of citrullinated peptides by RA-specific ACPAs.
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Affiliation(s)
| | - Bingze Xu
- Karolinska Institutet, Stockholm, Sweden
| | - Bibo Liang
- Karolinska Institutet, Stockholm, Sweden, and Southern Medical University, Guangzhou, China
| | | | | | | | - Burcu Ayoglu
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- KTH Royal Institute of Technology, Stockholm, Sweden
| | | | | | - Vivianne Malmström
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lars Klareskog
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - René E M Toes
- Leiden University Medical Center, Leiden, The Netherlands
| | - Theo Rispens
- University of Amsterdam, Amsterdam, The Netherlands
| | | | - Rikard Holmdahl
- Karolinska Institutet, Stockholm, Sweden, and Southern Medical University, Guangzhou, China
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22
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Li C, Li X, Kirian R, Spence JCH, Liu H, Zatsepin NA. SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCRJ 2019; 6:72-84. [PMID: 30713705 PMCID: PMC6327178 DOI: 10.1107/s2052252518014951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008 ▸), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012 ▸), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
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Affiliation(s)
- Chufeng Li
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, People’s Republic of China
- Department of Engineering Physics, Tsinghua University, Beijing, 100086, People’s Republic of China
| | - Richard Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, People’s Republic of China
| | - Nadia A. Zatsepin
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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23
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Moynié L, Serra I, Scorciapino MA, Oueis E, Page MG, Ceccarelli M, Naismith JH. Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogen Acinetobacter baumannii. eLife 2018; 7:42270. [PMID: 30558715 PMCID: PMC6300358 DOI: 10.7554/elife.42270] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/02/2018] [Indexed: 01/05/2023] Open
Abstract
New strategies are urgently required to develop antibiotics. The siderophore uptake system has attracted considerable attention, but rational design of siderophore antibiotic conjugates requires knowledge of recognition by the cognate outer-membrane transporter. Acinetobacter baumannii is a serious pathogen, which utilizes (pre)acinetobactin to scavenge iron from the host. We report the structure of the (pre)acinetobactin transporter BauA bound to the siderophore, identifying the structural determinants of recognition. Detailed biophysical analysis confirms that BauA recognises preacinetobactin. We show that acinetobactin is not recognised by the protein, thus preacinetobactin is essential for iron uptake. The structure shows and NMR confirms that under physiological conditions, a molecule of acinetobactin will bind to two free coordination sites on the iron preacinetobactin complex. The ability to recognise a heterotrimeric iron-preacinetobactin-acinetobactin complex may rationalize contradictory reports in the literature. These results open new avenues for the design of novel antibiotic conjugates (trojan horse) antibiotics.
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Affiliation(s)
- Lucile Moynié
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, England.,Research Complex at Harwell, Rutherford Laboratory, Didcot, England
| | - Ilaria Serra
- Department of Physics, University of Cagliari, Cagliari, Italy.,Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Italy
| | - Mariano A Scorciapino
- Department of Physics, University of Cagliari, Cagliari, Italy.,Department of Chemical and Geological Sciences, University of Cagliari, Cagliari, Italy
| | - Emilia Oueis
- Biomedical Sciences Research Complex, The University of St Andrews, Scotland, United Kingdom
| | - Malcolm Gp Page
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | | | - James H Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, England.,Research Complex at Harwell, Rutherford Laboratory, Didcot, England.,The Rosalind Franklin Institute, Didcot, England
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24
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Dix SR, Owen HJ, Sun R, Ahmad A, Shastri S, Spiewak HL, Mosby DJ, Harris MJ, Batters SL, Brooker TA, Tzokov SB, Sedelnikova SE, Baker PJ, Bullough PA, Rice DW, Thomas MS. Structural insights into the function of type VI secretion system TssA subunits. Nat Commun 2018; 9:4765. [PMID: 30420757 PMCID: PMC6232143 DOI: 10.1038/s41467-018-07247-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/23/2018] [Indexed: 11/22/2022] Open
Abstract
The type VI secretion system (T6SS) is a multi-protein complex that injects bacterial effector proteins into target cells. It is composed of a cell membrane complex anchored to a contractile bacteriophage tail-like apparatus consisting of a sharpened tube that is ejected by the contraction of a sheath against a baseplate. We present structural and biochemical studies on TssA subunits from two different T6SSs that reveal radically different quaternary structures in comparison to the dodecameric E. coli TssA that arise from differences in their C-terminal sequences. Despite this, the different TssAs retain equivalent interactions with other components of the complex and position their highly conserved N-terminal ImpA_N domain at the same radius from the centre of the sheath as a result of their distinct domain architectures, which includes additional spacer domains and highly mobile interdomain linkers. Together, these variations allow these distinct TssAs to perform a similar function in the complex. TssA is an important component of the bacterial type VI secretion system (T6SS). Here, Dix et al. integrate structural, phylogenetic and functional analysis of the TssA subunits, providing new insights into their role in T6SS assembly and function.
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Affiliation(s)
- Samuel R Dix
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hayley J Owen
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Ruyue Sun
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Asma Ahmad
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Sravanthi Shastri
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Helena L Spiewak
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK.,Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Institute of Genetic Medicine, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Daniel J Mosby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Matthew J Harris
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,Department of Chemistry, King's College London, Britannia House, London, SE1 1DB, UK
| | - Sarah L Batters
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Thomas A Brooker
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK
| | - Svetomir B Tzokov
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Svetlana E Sedelnikova
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Patrick J Baker
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Per A Bullough
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - David W Rice
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Mark S Thomas
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK.
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25
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Campeotto I, Lebedev A, Schreurs AMM, Kroon-Batenburg LMJ, Lowe E, Phillips SEV, Murshudov GN, Pearson AR. Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools. Sci Rep 2018; 8:14876. [PMID: 30291262 PMCID: PMC6173773 DOI: 10.1038/s41598-018-32962-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Twinning is a crystal growth anomaly, which has posed a challenge in macromolecular crystallography (MX) since the earliest days. Many approaches have been used to treat twinned data in order to extract structural information. However, in most cases it is usually simpler to rescreen for new crystallization conditions that yield an untwinned crystal form or, if possible, collect data from non-twinned parts of the crystal. Here, we report 11 structures of engineered variants of the E. coli enzyme N-acetyl-neuraminic lyase which, despite twinning and incommensurate modulation, have been successfully indexed, solved and deposited. These structures span a resolution range of 1.45-2.30 Å, which is unusually high for datasets presenting such lattice disorders in MX and therefore these data provide an excellent test set for improving and challenging MX data processing programs.
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Affiliation(s)
- Ivan Campeotto
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK. .,Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK.
| | - Andrey Lebedev
- Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK
| | - Antoine M M Schreurs
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Loes M J Kroon-Batenburg
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Edward Lowe
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK
| | - Simon E V Phillips
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK
| | - Garib N Murshudov
- Structural Studies Division, MRC-LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Hamburg Centre for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
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26
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Perraud Q, Moynié L, Gasser V, Munier M, Godet J, Hoegy F, Mély Y, Mislin GLA, Naismith JH, Schalk IJ. A Key Role for the Periplasmic PfeE Esterase in Iron Acquisition via the Siderophore Enterobactin in Pseudomonas aeruginosa. ACS Chem Biol 2018; 13:2603-2614. [PMID: 30086222 DOI: 10.1021/acschembio.8b00543] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enterobactin (ENT) is a siderophore (iron-chelating compound) produced by Escherichia coli to gain access to iron, an indispensable nutrient for bacterial growth. ENT is used as an exosiderophore by Pseudomonas aeruginosa with transport of ferri-ENT across the outer membrane by the PfeA transporter. Next to the pfeA gene on the chromosome is localized a gene encoding for an esterase, PfeE, whose transcription is regulated, as for pfeA, by the presence of ENT in bacterial environment. Purified PfeE hydrolyzed ferri-ENT into three molecules of 2,3-DHBS (2,3-dihydroxybenzoylserine) still complexed with ferric iron, and complete dissociation of iron from ENT chelating groups was only possible in the presence of both PfeE and an iron reducer, such as DTT. The crystal structure of PfeE and an inactive PfeE mutant complexed with ferri-ENT or a nonhydrolyzable ferri-catechol complex allowed identification of the enzyme binding site and the catalytic triad. Finally, cell fractionation and fluorescence microscopy showed periplasmic localization of PfeE in P. aeruginosa cells. Thus, the molecular mechanism of iron dissociation from ENT in P. aeruginosa differs from that previously described in E. coli. In P. aeruginosa, siderophore hydrolysis occurs in the periplasm, with ENT never reaching the bacterial cytoplasm. In E. coli, ferri-ENT crosses the inner membrane via the ABC transporter FepBCD and ferri-ENT is hydrolyzed by the esterase Fes only once it is in the cytoplasm.
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Affiliation(s)
- Quentin Perraud
- Université de Strasbourg, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
- CNRS, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Lucile Moynié
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, United Kingdom
- Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, United Kingdom
| | - Véronique Gasser
- Université de Strasbourg, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
- CNRS, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Mathilde Munier
- Université de Strasbourg, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
- CNRS, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Julien Godet
- Université de Strasbourg, Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, F-67413 Illkirch, Strasbourg, France
| | - Françoise Hoegy
- Université de Strasbourg, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
- CNRS, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - Yves Mély
- Université de Strasbourg, Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, F-67413 Illkirch, Strasbourg, France
| | - Gaëtan. L. A. Mislin
- Université de Strasbourg, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
- CNRS, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, United Kingdom
- Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, United Kingdom
| | - Isabelle J. Schalk
- Université de Strasbourg, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
- CNRS, UMR7242, ESBS, 300 Bld Sébastien Brant, F-67413 Illkirch, Strasbourg, France
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27
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Owen HJ, Sun R, Ahmad A, Sedelnikova SE, Baker PJ, Thomas MS, Rice DW. TssA from Burkholderia cenocepacia: expression, purification, crystallization and crystallographic analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:536-542. [PMID: 30198885 PMCID: PMC6130427 DOI: 10.1107/s2053230x18009706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/06/2018] [Indexed: 01/16/2023] Open
Abstract
TssA is a core component of the type VI secretion system, and phylogenetic analysis of TssA subunits from different species has suggested that these proteins fall into three distinct clades. Whilst representatives of two clades, TssA1 and TssA2, have been the subjects of investigation, no members of the third clade (TssA3) have been studied. Constructs of TssA from Burkholderia cenocepacia, a representative of clade 3, were expressed, purified and subjected to crystallization trials. Data were collected from crystals of constructs of the N-terminal and C-terminal domains. Analysis of the data from the crystals of these constructs and preliminary structure determination indicates that the C-terminal domain forms an assembly of 32 subunits in D16 symmetry, whereas the N-terminal domain is not involved in subunit assocation.
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Affiliation(s)
- Hayley J. Owen
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, England
| | - Ruyue Sun
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, England
| | - Asma Ahmad
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, England
| | - Svetlana E. Sedelnikova
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, England
| | - Patrick J. Baker
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, England
| | - Mark S. Thomas
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, England
| | - David W. Rice
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, England
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28
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Luscher A, Moynié L, Auguste PS, Bumann D, Mazza L, Pletzer D, Naismith JH, Köhler T. TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates. Antimicrob Agents Chemother 2018; 62:e00097-18. [PMID: 29555629 PMCID: PMC5971595 DOI: 10.1128/aac.00097-18] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
The conjugation of siderophores to antimicrobial molecules is an attractive strategy to overcome the low outer membrane permeability of Gram-negative bacteria. In this Trojan horse approach, the transport of drug conjugates is redirected via TonB-dependent receptors (TBDR), which are involved in the uptake of essential nutrients, including iron. Previous reports have demonstrated the involvement of the TBDRs PiuA and PirA from Pseudomonas aeruginosa and their orthologues in Acinetobacter baumannii in the uptake of siderophore-beta-lactam drug conjugates. By in silico screening, we further identified a PiuA orthologue, termed PiuD, present in clinical isolates, including strain LESB58. The piuD gene in LESB58 is located at the same genetic locus as piuA in strain PAO1. PiuD has a similar crystal structure as PiuA and is involved in the transport of the siderophore-drug conjugates BAL30072, MC-1, and cefiderocol in strain LESB58. To screen for additional siderophore-drug uptake systems, we overexpressed 28 of the 34 TBDRs of strain PAO1 and identified PfuA, OptE, OptJ, and the pyochelin receptor FptA as novel TBDRs conferring increased susceptibility to siderophore-drug conjugates. The existence of a TBDR repertoire in P. aeruginosa able to transport siderophore-drug molecules potentially decreases the likelihood of resistance emergence during therapy.
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Affiliation(s)
- Alexandre Luscher
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Lucile Moynié
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | | | - Dirk Bumann
- Biozentrum, University of Basel, Basel, Switzerland
| | - Lena Mazza
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | | | - James H Naismith
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | - Thilo Köhler
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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29
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Stangier MM, Kumar A, Chen X, Farcas AM, Barral Y, Steinmetz MO. Structure-Function Relationship of the Bik1-Bim1 Complex. Structure 2018; 26:607-618.e4. [PMID: 29576319 DOI: 10.1016/j.str.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/09/2018] [Accepted: 02/28/2018] [Indexed: 11/30/2022]
Abstract
In budding yeast, the microtubule plus-end tracking proteins Bik1 (CLIP-170) and Bim1 (EB1) form a complex that interacts with partners involved in spindle positioning, including Stu2 and Kar9. Here, we show that the CAP-Gly and coiled-coil domains of Bik1 interact with the C-terminal ETF peptide of Bim1 and the C-terminal tail region of Stu2, respectively. The crystal structures of the CAP-Gly domain of Bik1 (Bik1CG) alone and in complex with an ETF peptide revealed unique, functionally relevant CAP-Gly elements, establishing Bik1CG as a specific C-terminal phenylalanine recognition domain. Unlike the mammalian CLIP-170-EB1 complex, Bik1-Bim1 forms ternary complexes with the EB1-binding motifs SxIP and LxxPTPh, which are present in diverse proteins, including Kar9. Perturbation of the Bik1-Bim1 interaction in vivo affected Bik1 localization and astral microtubule length. Our results provide insight into the role of the Bik1-Bim1 interaction for cell division, and demonstrate that the CLIP-170-EB1 module is evolutionarily flexible.
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Affiliation(s)
- Marcel M Stangier
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Anil Kumar
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Xiuzhen Chen
- Institute of Biochemistry, ETH Zürich, 8049 Zürich, Switzerland
| | | | - Yves Barral
- Institute of Biochemistry, ETH Zürich, 8049 Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland; University of Basel, Biozentrum, 4056 Basel, Switzerland.
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30
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Kumar S, Hedrick V, Mattoo S. YopT domain of the PfhB2 toxin from Pasteurella multocida: protein expression, characterization, crystallization and crystallographic analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:128-134. [PMID: 29497015 PMCID: PMC5947697 DOI: 10.1107/s2053230x18000857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/13/2018] [Indexed: 11/10/2022] Open
Abstract
Pasteurella multocida causes respiratory-tract infections in a broad range of animals, as well as opportunistic infections in humans. P. multocida secretes a multidomain toxin called PfhB2, which contains a YopT-like cysteine protease domain at its C-terminus. The YopT domain of PfhB2 contains a well conserved Cys-His-Asp catalytic triad that defines YopT family members, and shares high sequence similarity with the prototype YopT from Yersinia sp. To date, only one crystal structure of a YopT family member has been reported; however, additional structural information is needed to help characterize the varied substrate specificity and enzymatic action of this large protease family. Here, a catalytically inactive C3733S mutant of PfhB2 YopT that provides enhanced protein stability was used with the aim of gaining structural insight into the diversity within the YopT protein family. To this end, the C3733S mutant of PfhB2 YopT has been successfully cloned, overexpressed, purified and crystallized. Diffraction data sets were collected from native crystals to 3.5 Å resolution and a single-wavelength anomalous data set was collected from an iodide-derivative crystal to 3.2 Å resolution. Data pertaining to crystals belonging to space group P31, with unit-cell parameters a = 136.9, b = 136.9, c = 74.7 Å for the native crystals and a = 139.2, b = 139.2, c = 74.7 Å for the iodide-derivative crystals, are discussed.
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Affiliation(s)
- Sanjeev Kumar
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
| | - Victoria Hedrick
- Bindley Biosciences Center, Purdue University, 1203 West State Street, West Lafayette, IN 47907, USA
| | - Seema Mattoo
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
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31
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Mota F, Fotinou C, Rana RR, Chan AWE, Yelland T, Arooz MT, O'Leary AP, Hutton J, Frankel P, Zachary I, Selwood D, Djordjevic S. Architecture and hydration of the arginine-binding site of neuropilin-1. FEBS J 2018; 285:1290-1304. [PMID: 29430837 PMCID: PMC5947257 DOI: 10.1111/febs.14405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/26/2018] [Accepted: 02/06/2018] [Indexed: 12/15/2022]
Abstract
Neuropilin‐1 (NRP1) is a transmembrane co‐receptor involved in binding interactions with variety of ligands and receptors, including receptor tyrosine kinases. Expression of NRP1 in several cancers correlates with cancer stages and poor prognosis. Thus, NRP1 has been considered a therapeutic target and is the focus of multiple drug discovery initiatives. Vascular endothelial growth factor (VEGF) binds to the b1 domain of NRP1 through interactions between the C‐terminal arginine of VEGF and residues in the NRP1‐binding site including Tyr297, Tyr353, Asp320, Ser346 and Thr349. We obtained several complexes of the synthetic ligands and the NRP1‐b1 domain and used X‐ray crystallography and computational methods to analyse atomic details and hydration profile of this binding site. We observed side chain flexibility for Tyr297 and Asp320 in the six new high‐resolution crystal structures of arginine analogues bound to NRP1. In addition, we identified conserved water molecules in binding site regions which can be targeted for drug design. The computational prediction of the VEGF ligand‐binding site hydration map of NRP1 was in agreement with the experimentally derived, conserved hydration structure. Displacement of certain conserved water molecules by a ligand's functional groups may contribute to binding affinity, whilst other water molecules perform as protein–ligand bridges. Our report provides a comprehensive description of the binding site for the peptidic ligands’ C‐terminal arginines in the b1 domain of NRP1, highlights the importance of conserved structural waters in drug design and validates the utility of the computational hydration map prediction method in the context of neuropilin. Database The structures were deposited to the PDB with accession numbers PDB ID: 5IJR, 5IYY, 5JHK, 5J1X, 5JGQ, 5JGI.
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Affiliation(s)
- Filipa Mota
- Magnus Life, Magnus Life Science, London, UK
| | | | | | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London, UK
| | | | - Mohamed T Arooz
- The Institute of Structural and Molecular Biology, University College London, UK
| | | | | | - Paul Frankel
- Magnus Life, Magnus Life Science, London, UK.,Centre for Cardiovascular Biology & Medicine, BHF Laboratories at University College London, UK
| | - Ian Zachary
- Centre for Cardiovascular Biology & Medicine, BHF Laboratories at University College London, UK
| | - David Selwood
- Wolfson Institute for Biomedical Research, University College London, UK
| | - Snezana Djordjevic
- The Institute of Structural and Molecular Biology, University College London, UK
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32
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Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G. DIALS: implementation and evaluation of a new integration package. Acta Crystallogr D Struct Biol 2018; 74:85-97. [PMID: 29533234 PMCID: PMC5947772 DOI: 10.1107/s2059798317017235] [Citation(s) in RCA: 670] [Impact Index Per Article: 111.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/30/2017] [Indexed: 01/07/2023] Open
Abstract
The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.
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Affiliation(s)
- Graeme Winter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - David G. Waterman
- STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - James M. Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Aaron S. Brewster
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Richard J. Gildea
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Markus Gerstel
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Luis Fuentes-Montero
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Melanie Vollmar
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tara Michels-Clark
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Iris D. Young
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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33
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Atherton J, Jiang K, Stangier MM, Luo Y, Hua S, Houben K, van Hooff JJ, Joseph AP, Scarabelli G, Grant BJ, Roberts AJ, Topf M, Steinmetz MO, Baldus M, Moores CA, Akhmanova A. A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. Nat Struct Mol Biol 2017; 24:931-943. [PMID: 28991265 PMCID: PMC6134180 DOI: 10.1038/nsmb.3483] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 09/12/2017] [Indexed: 12/12/2022]
Abstract
CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization and differentiation. Here, we found that the CAMSAP C-terminal CKK domain is widely present among eukaryotes and autonomously recognizes microtubule minus ends. Through a combination of structural approaches, we uncovered how mammalian CKK binds between two tubulin dimers at the interprotofilament interface on the outer microtubule surface. In vitro reconstitution assays combined with high-resolution fluorescence microscopy and cryo-electron tomography suggested that CKK preferentially associates with the transition zone between curved protofilaments and the regular microtubule lattice. We propose that minus-end-specific features of the interprotofilament interface at this site serve as the basis for CKK's minus-end preference. The steric clash between microtubule-bound CKK and kinesin motors explains how CKK protects microtubule minus ends against kinesin-13-induced depolymerization and thus controls the stability of free microtubule minus ends.
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Affiliation(s)
- Joseph Atherton
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Kai Jiang
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Marcel M. Stangier
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Yanzhang Luo
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Shasha Hua
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Jolien J.E. van Hooff
- Hubrecht Institute, Utrecht, the Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Agnel-Praveen Joseph
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Guido Scarabelli
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Barry J. Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Anthony J. Roberts
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
- University of Basel, Biozentrum, Basel, Switzerland
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Carolyn A. Moores
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
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34
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Abstract
The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most commonly used software in the field.
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35
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Kolappan S, Lo KY, Shen CLJ, Guttman JA, Craig L. Structure of the conserved Francisella virulence protein FvfA. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:814-821. [PMID: 28994410 DOI: 10.1107/s205979831701333x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/18/2017] [Indexed: 11/10/2022]
Abstract
Francisella tularensis is a potent human pathogen that invades and survives in macrophage and epithelial cells. Two identical proteins, FTT_0924 from F. tularensis subsp. tularensis and FTL_1286 from F. tularensis subsp. holarctica LVS, have previously been identified as playing a role in protection of the bacteria from osmotic shock and its survival in macrophages. FTT_0924 has been shown to localize to the inner membrane, with its C-terminus exposed to the periplasm. Here, crystal structures of the F. novicida homologue FTN_0802, which we call FvfA, in two crystal forms are reported at 1.8 Å resolution. FvfA differs from FTT_0924 and FTL_1286 by a single amino acid. FvfA has a DUF1471 fold that closely resembles the Escherichia coli outer membrane lipoprotein RscF, a component of a phosphorelay pathway involved in protecting bacteria from outer membrane perturbation. The structural and functional similarities and differences between these proteins and their implications for F. tularensis pathogenesis are discussed.
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Affiliation(s)
- Subramania Kolappan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Karen Y Lo
- Department of Biological Sciences, Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Chiao Ling Jennifer Shen
- Department of Biological Sciences, Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Julian A Guttman
- Department of Biological Sciences, Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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36
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Elegheert J, Cvetkovska V, Clayton AJ, Heroven C, Vennekens KM, Smukowski SN, Regan MC, Jia W, Smith AC, Furukawa H, Savas JN, de Wit J, Begbie J, Craig AM, Aricescu AR. Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins. Neuron 2017; 95:896-913.e10. [PMID: 28817804 PMCID: PMC5563082 DOI: 10.1016/j.neuron.2017.07.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 06/22/2017] [Accepted: 07/28/2017] [Indexed: 01/30/2023]
Abstract
Neuroligin-neurexin (NL-NRX) complexes are fundamental synaptic organizers in the central nervous system. An accurate spatial and temporal control of NL-NRX signaling is crucial to balance excitatory and inhibitory neurotransmission, and perturbations are linked with neurodevelopmental and psychiatric disorders. MDGA proteins bind NLs and control their function and interaction with NRXs via unknown mechanisms. Here, we report crystal structures of MDGA1, the NL1-MDGA1 complex, and a spliced NL1 isoform. Two large, multi-domain MDGA molecules fold into rigid triangular structures, cradling a dimeric NL to prevent NRX binding. Structural analyses guided the discovery of a broad, splicing-modulated interaction network between MDGA and NL family members and helped rationalize the impact of autism-linked mutations. We demonstrate that expression levels largely determine whether MDGAs act selectively or suppress the synapse organizing function of multiple NLs. These results illustrate a potentially brain-wide regulatory mechanism for NL-NRX signaling modulation. The MDGA1 extracellular region has an unusual triangular multi-domain arrangement The NL1-MDGA1 complex structure reveals how MDGA proteins block neurexin binding MDGA1 and MDGA2 bind all NL isoforms, a process fine-tuned by alternative splicing MDGA1 and MDGA2 suppress NL synaptogenic activity in a concentration-dependent manner
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Affiliation(s)
- Jonathan Elegheert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Vedrana Cvetkovska
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Amber J Clayton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christina Heroven
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Kristel M Vennekens
- VIB Center for Brain and Disease Research, Herestraat 49, B-3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Samuel N Smukowski
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Michael C Regan
- Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Wanyi Jia
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alexandra C Smith
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Hiro Furukawa
- Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joris de Wit
- VIB Center for Brain and Disease Research, Herestraat 49, B-3000 Leuven, Belgium; Department of Neurosciences, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Jo Begbie
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2B5, Canada.
| | - A Radu Aricescu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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37
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Ge C, Tong D, Liang B, Lönnblom E, Schneider N, Hagert C, Viljanen J, Ayoglu B, Stawikowska R, Nilsson P, Fields GB, Skogh T, Kastbom A, Kihlberg J, Burkhardt H, Dobritzsch D, Holmdahl R. Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage. JCI Insight 2017; 2:93688. [PMID: 28679953 DOI: 10.1172/jci.insight.93688] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/23/2017] [Indexed: 12/29/2022] Open
Abstract
Today, it is known that autoimmune diseases start a long time before clinical symptoms appear. Anti-citrullinated protein antibodies (ACPAs) appear many years before the clinical onset of rheumatoid arthritis (RA). However, it is still unclear if and how ACPAs are arthritogenic. To better understand the molecular basis of pathogenicity of ACPAs, we investigated autoantibodies reactive against the C1 epitope of collagen type II (CII) and its citrullinated variants. We found that these antibodies are commonly occurring in RA. A mAb (ACC1) against citrullinated C1 was found to cross-react with several noncitrullinated epitopes on native CII, causing proteoglycan depletion of cartilage and severe arthritis in mice. Structural studies by X-ray crystallography showed that such recognition is governed by a shared structural motif "RG-TG" within all the epitopes, including electrostatic potential-controlled citrulline specificity. Overall, we have demonstrated a molecular mechanism that explains how ACPAs trigger arthritis.
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Affiliation(s)
- Changrong Ge
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Dongmei Tong
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong, Southern Medical University, Guangzhou, China
| | - Bibo Liang
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong, Southern Medical University, Guangzhou, China
| | - Erik Lönnblom
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nadine Schneider
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology, and Division of Rheumatology, University Hospital Frankfurt Goethe University, Frankfurt, Germany
| | - Cecilia Hagert
- Medicity Research Laboratory, University of Turku, Turku, Finland; National Doctoral Programme in Informational and Structural Biology, Turku, Finland
| | - Johan Viljanen
- Section of Organic Chemistry, Department of Chemistry - Biomedicinskt centrum, Uppsala University, Uppsala, Sweden
| | - Burcu Ayoglu
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roma Stawikowska
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida, USA
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida, USA
| | - Thomas Skogh
- Department of Rheumatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Alf Kastbom
- Department of Rheumatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jan Kihlberg
- Section of Organic Chemistry, Department of Chemistry - Biomedicinskt centrum, Uppsala University, Uppsala, Sweden
| | - Harald Burkhardt
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology, and Division of Rheumatology, University Hospital Frankfurt Goethe University, Frankfurt, Germany
| | - Doreen Dobritzsch
- Section of Biochemistry, Department of Chemistry - Biomedicinskt centrum, Uppsala University, Uppsala, Sweden
| | - Rikard Holmdahl
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Medicity Research Laboratory, University of Turku, Turku, Finland; National Doctoral Programme in Informational and Structural Biology, Turku, Finland.,Center for Medical Immunopharmacology Research, Southern Medical University, Guangzhou, China
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38
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Fukuzawa T, Sampei Z, Haraya K, Ruike Y, Shida-Kawazoe M, Shimizu Y, Gan SW, Irie M, Tsuboi Y, Tai H, Sakiyama T, Sakamoto A, Ishii S, Maeda A, Iwayanagi Y, Shibahara N, Shibuya M, Nakamura G, Nambu T, Hayasaka A, Mimoto F, Okura Y, Hori Y, Habu K, Wada M, Miura T, Tachibana T, Honda K, Tsunoda H, Kitazawa T, Kawabe Y, Igawa T, Hattori K, Nezu J. Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases. Sci Rep 2017; 7:1080. [PMID: 28439081 PMCID: PMC5430875 DOI: 10.1038/s41598-017-01087-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/23/2017] [Indexed: 12/25/2022] Open
Abstract
Dysregulation of the complement system is linked to the pathogenesis of a variety of hematological disorders. Eculizumab, an anti-complement C5 monoclonal antibody, is the current standard of care for paroxysmal nocturnal hemoglobinuria (PNH) and atypical hemolytic uremic syndrome (aHUS). However, because of high levels of C5 in plasma, eculizumab has to be administered biweekly by intravenous infusion. By applying recycling technology through pH-dependent binding to C5, we generated a novel humanized antibody against C5, SKY59, which has long-lasting neutralization of C5. In cynomolgus monkeys, SKY59 suppressed C5 function and complement activity for a significantly longer duration compared to a conventional antibody. Furthermore, epitope mapping by X-ray crystal structure analysis showed that a histidine cluster located on C5 is crucial for the pH-dependent interaction with SKY59. This indicates that the recycling effect of SKY59 is driven by a novel mechanism of interaction with its antigen and is distinct from other known pH-dependent antibodies. Finally, SKY59 showed neutralizing effect on C5 variant p.Arg885His, while eculizumab does not inhibit complement activity in patients carrying this mutation. Collectively, these results suggest that SKY59 is a promising new anti-C5 agent for patients with PNH and other complement-mediated disorders.
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Affiliation(s)
- Taku Fukuzawa
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Zenjiro Sampei
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Kenta Haraya
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Yoshinao Ruike
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Meiri Shida-Kawazoe
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yuichiro Shimizu
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Siok Wan Gan
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Yoshinori Tsuboi
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Hitoshi Tai
- Chugai Research Institute for Medical Science, Inc., Gotemba, Shizuoka, Japan
| | - Tetsushi Sakiyama
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Akihisa Sakamoto
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Shinya Ishii
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Atsuhiko Maeda
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yuki Iwayanagi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Norihito Shibahara
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Mitsuko Shibuya
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Genki Nakamura
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Takeru Nambu
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Akira Hayasaka
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Futa Mimoto
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Yuu Okura
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Yuji Hori
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Kiyoshi Habu
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Manabu Wada
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Takaaki Miura
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Tatsuhiko Tachibana
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Kiyofumi Honda
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore
| | - Hiroyuki Tsunoda
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Takehisa Kitazawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Yoshiki Kawabe
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan.,Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Tomoyuki Igawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Kunihiro Hattori
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Junichi Nezu
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07-11 to 16, Synapse, 138623, Singapore.
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Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Nat Chem Biol 2017; 13:660-667. [PMID: 28414710 DOI: 10.1038/nchembio.2361] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/12/2017] [Indexed: 02/05/2023]
Abstract
Biotin is an essential vitamin in plants and mammals, functioning as the carbon dioxide carrier within central lipid metabolism. Bacterial pimeloyl-CoA synthetase (BioW) acts as a highly specific substrate-selection gate, ensuring the integrity of the carbon chain in biotin synthesis. BioW catalyzes the condensation of pimelic acid (C7 dicarboxylic acid) with CoASH in an ATP-dependent manner to form pimeloyl-CoA, the first dedicated biotin building block. Multiple structures of Bacillus subtilis BioW together capture all three substrates, as well as the intermediate pimeloyl-adenylate and product pyrophosphate (PPi), indicating that the enzyme uses an internal ruler to select the correct dicarboxylic acid substrate. Both the catalytic mechanism and the surprising stability of the adenylate intermediate were rationalized through site-directed mutagenesis. Building on this understanding, BioW was engineered to synthesize high-value heptanoyl (C7) and octanoyl (C8) monocarboxylic acid-CoA and C8 dicarboxylic-CoA products, highlighting the enzyme's synthetic potential.
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 PMCID: PMC5376230 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D. Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ernest S. Burgie
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Christopher J. Pollock
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Claudiu A. Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation
Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, 12489
Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
- Department of Biochemistry, University of Oxford, South Parks Road,
Oxford OX1 3QU, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Christian G. Roessler
- National Synchrotron Light Source II, Brookhaven National
Laboratory, Upton, NY, 11973, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raymond G. Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Peter T. Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - James M. Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu
Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum,
Umeå Universitet, SE 90187 Umeå, Sweden
- Department of Chemistry – Ångström,
Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory,
Menlo Park, CA 94025, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University,
University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania
State University, University Park, PA 16802, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University,
SE-106 91 Stockholm, Sweden
- Department of Chemistry, Stanford University, Stanford, CA 94305,
USA
| | - George N. Phillips
- Department of BioSciences, Rice Univ. Houston, TX 77005, USA
- Department of Chemistry, Rice Univ. Houston, TX 77005, USA
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St.
Louis, Missouri 63130, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Allen M. Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus,
Didcot, OX110DE, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, Berkeley, CA 94720, USA
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Structure and Function of the PiuA and PirA Siderophore-Drug Receptors from Pseudomonas aeruginosa and Acinetobacter baumannii. Antimicrob Agents Chemother 2017; 61:AAC.02531-16. [PMID: 28137795 DOI: 10.1128/aac.02531-16] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/27/2017] [Indexed: 01/06/2023] Open
Abstract
The outer membrane of Gram-negative bacteria presents an efficient barrier to the permeation of antimicrobial molecules. One strategy pursued to circumvent this obstacle is to hijack transport systems for essential nutrients, such as iron. BAL30072 and MC-1 are two monobactams conjugated to a dihydroxypyridone siderophore that are active against Pseudomonas aeruginosa and Acinetobacter baumannii Here, we investigated the mechanism of action of these molecules in A. baumannii We identified two novel TonB-dependent receptors, termed Ab-PiuA and Ab-PirA, that are required for the antimicrobial activity of both agents. Deletion of either piuA or pirA in A. baumannii resulted in 4- to 8-fold-decreased susceptibility, while their overexpression in the heterologous host P. aeruginosa increased susceptibility to the two siderophore-drug conjugates by 4- to 32-fold. The crystal structures of PiuA and PirA from A. baumannii and their orthologues from P. aeruginosa were determined. The structures revealed similar architectures; however, structural differences between PirA and PiuA point to potential differences between their cognate siderophore ligands. Spontaneous mutants, selected upon exposure to BAL30072, harbored frameshift mutations in either the ExbD3 or the TonB3 protein of A. baumannii, forming the cytoplasmic-membrane complex providing the energy for the siderophore translocation process. The results of this study provide insight for the rational design of novel siderophore-drug conjugates against problematic Gram-negative pathogens.
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Blundell KLIM, Pal M, Roe SM, Pearl LH, Prodromou C. The structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90. PLoS One 2017; 12:e0173543. [PMID: 28278223 PMCID: PMC5344419 DOI: 10.1371/journal.pone.0173543] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/22/2017] [Indexed: 01/06/2023] Open
Abstract
Tetratricopeptide (TPR) domains are known protein interaction domains. We show that the TPR domain of FKBP8 selectively binds Hsp90, and interactions upstream of the conserved MEEVD motif are critical for tight binding. In contrast FKBP8 failed to bind intact Hsp70. The PPIase domain was not essential for the interaction with Hsp90 and binding was completely encompassed by the TPR domain alone. The conformation adopted by Hsp90 peptides, containing the conserved MEEVD motif, in the crystal structure were similar to that seen for the TPR domains of CHIP, AIP and Tah1. The carboxylate clamp interactions with bound Hsp90 peptide were a critical component of the interaction and mutation of Lys 307, involved in the carboxylate clamp, completely disrupted the interaction with Hsp90. FKBP8 binding to Hsp90 did not substantially influence its ATPase activity.
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Affiliation(s)
- Katie L. I. M. Blundell
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, England
| | - Mohinder Pal
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, England
| | - S. Mark Roe
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, England
| | - Laurence H. Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, England
| | - Chrisostomos Prodromou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, England
- * E-mail:
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43
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Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria. J Bacteriol 2017; 199:JB.00746-16. [PMID: 27994018 DOI: 10.1128/jb.00746-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/13/2016] [Indexed: 01/24/2023] Open
Abstract
Brucella abortus σE1 is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226, is among the most highly activated gene sets in the σE1 regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription of yehZYXW is activated by the general stress sigma factor σS in Enterobacteriaceae, which suggests a functional role for this transport system in bacterial stress response across the classes Alphaproteobacteria and Gammaproteobacteria We present evidence that B. abortus YehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σE1-null strain. The sole in vitro phenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li+ ion concentrations. A crystal structure of B. abortus YehZ revealed a class II periplasmic binding protein fold with significant structural homology to Archaeoglobus fulgidus ProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers.IMPORTANCEBrucella abortus σE1 regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σE1 remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σE1 Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure of B. abortus YehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.
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Abstract
Indexing is an essential step in analysis of diffraction patterns. Diffraction of monochromatic radiation by a single crystal provides approximate positions of some nodes of the reciprocal lattice of the crystal, and the indexing problem lies in determining a lattice matching these positions. Ind_X is a program for indexing diffraction data given in the form of several approximate reciprocal lattice nodes. The applied method relies on testing potential volumes of the primitive cell of the reciprocal lattice. A subset of reciprocal lattice vectors supporting a given test volume is used to obtain tentative lattice bases. These are bases of low-index superlattices of lattices based on triplets of supporting vectors. The Ind_X solution of the indexing problem consists of a list of best bases. The method turns out to be quite robust to data inaccuracies and spurious reflections. The program is relatively versatile, easily operated and freely accessible.
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Nguyen V, Wilson C, Hoemberger M, Stiller JB, Agafonov RV, Kutter S, English J, Theobald DL, Kern D. Evolutionary drivers of thermoadaptation in enzyme catalysis. Science 2017; 355:289-294. [PMID: 28008087 PMCID: PMC5649376 DOI: 10.1126/science.aah3717] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/21/2016] [Indexed: 11/02/2022]
Abstract
With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme's key kinetic obstacle-how to maintain catalytic speed on a cooler Earth-by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness.
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Affiliation(s)
- Vy Nguyen
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Christopher Wilson
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Marc Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - John B Stiller
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Roman V Agafonov
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Steffen Kutter
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Justin English
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | | | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA.
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Thayer J, Damiani D, Ford C, Dubrovin M, Gaponenko I, O’Grady CP, Kroeger W, Pines J, Lane TJ, Salnikov A, Schneider D, Tookey T, Weaver M, Yoon CH, Perazzo A. Data systems for the Linac coherent light source. ADVANCED STRUCTURAL AND CHEMICAL IMAGING 2017; 3:3. [PMID: 28261541 PMCID: PMC5313569 DOI: 10.1186/s40679-016-0037-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/28/2016] [Indexed: 11/10/2022]
Abstract
The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available.
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Affiliation(s)
- J. Thayer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - D. Damiani
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - C. Ford
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - M. Dubrovin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - I. Gaponenko
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - C. P. O’Grady
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - W. Kroeger
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - J. Pines
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - T. J. Lane
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - A. Salnikov
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - D. Schneider
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - T. Tookey
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - M. Weaver
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - C. H. Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
| | - A. Perazzo
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 USA
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Scarborough NM, Godaliyadda GMDP, Ye DH, Kissick DJ, Zhang S, Newman JA, Sheedlo MJ, Chowdhury AU, Fischetti RF, Das C, Buzzard GT, Bouman CA, Simpson GJ. Dynamic X-ray diffraction sampling for protein crystal positioning. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:188-195. [PMID: 28009558 PMCID: PMC5182024 DOI: 10.1107/s160057751601612x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/11/2016] [Indexed: 05/31/2023]
Abstract
A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.
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Affiliation(s)
| | | | - Dong Hye Ye
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - David J. Kissick
- GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Shijie Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Justin A. Newman
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Michael J. Sheedlo
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Azhad U. Chowdhury
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Robert F. Fischetti
- GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Gregery T. Buzzard
- Department of Mathematics, Purdue University, West Lafayette, IN 47907, USA
| | - Charles A. Bouman
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Scarborough NM, Godaliyadda GMDP, Ye DH, Kissick DJ, Zhang S, Newman JA, Sheedlo MJ, Chowdhury A, Fischetti RF, Das C, Buzzard GT, Bouman CA, Simpson GJ. Synchrotron X-Ray Diffraction Dynamic Sampling for Protein Crystal Centering. IS&T INTERNATIONAL SYMPOSIUM ON ELECTRONIC IMAGING 2017. [PMID: 29527589 DOI: 10.2352/issn.2470-1173.2017.17.coimg-415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
A supervised learning approach for dynamic sampling (SLADS) was developed to reduce X-ray exposure prior to data collection in protein structure determination. Implementation of this algorithm allowed reduction of the X-ray dose to the central core of the crystal by up to 20-fold compared to current raster scanning approaches. This dose reduction corresponds directly to a reduction on X-ray damage to the protein crystals prior to data collection for structure determination. Implementation at a beamline at Argonne National Laboratory suggests promise for the use of the SLADS approach to aid in the analysis of X-ray labile crystals. The potential benefits match a growing need for improvements in automated approaches for microcrystal positioning.
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Affiliation(s)
| | | | - Dong Hye Ye
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907
| | - David J Kissick
- GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439
| | - Shijie Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Justin A Newman
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Michael J Sheedlo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Azhad Chowdhury
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Robert F Fischetti
- GM/CA@APS, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Gregery T Buzzard
- Department of Mathematics, Purdue University, West Lafayette, IN, 47907
| | - Charles A Bouman
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907
| | - Garth J Simpson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
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Muenzner J, Traub LM, Kelly BT, Graham SC. Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin. Traffic 2016; 18:44-57. [PMID: 27813245 PMCID: PMC5182127 DOI: 10.1111/tra.12457] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/31/2016] [Accepted: 10/31/2016] [Indexed: 12/17/2022]
Abstract
Short peptide motifs in unstructured regions of clathrin‐adaptor proteins recruit clathrin to membranes to facilitate post‐Golgi membrane transport. Three consensus clathrin‐binding peptide sequences have been identified and structural studies show that each binds distinct sites on the clathrin heavy chain N‐terminal domain (NTD). A fourth binding site for adaptors on NTD has been functionally identified but not structurally characterised. We have solved high resolution structures of NTD bound to peptide motifs from the cellular clathrin adaptors β2 adaptin and amphiphysin plus a putative viral clathrin adaptor, hepatitis D virus large antigen (HDAg‐L). Surprisingly, with each peptide we observe simultaneous peptide binding at multiple sites on NTD and viral peptides binding to the same sites as cellular peptides. Peptides containing clathrin‐box motifs (CBMs) with the consensus sequence LΦxΦ[DE] bind at the ‘arrestin box’ on NTD, between β‐propeller blades 4 and 5, which had previously been thought to bind a distinct consensus sequence. Further, we structurally define the fourth peptide binding site on NTD, which we term the Royle box. In vitro binding assays show that clathrin is more readily captured by cellular CBMs than by HDAg‐L, and site‐directed mutagenesis confirms that multiple binding sites on NTD contribute to efficient capture by CBM peptides.
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Affiliation(s)
- Julia Muenzner
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Linton M Traub
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Bernard T Kelly
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
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Grabe GJ, Zhang Y, Przydacz M, Rolhion N, Yang Y, Pruneda JN, Komander D, Holden DW, Hare SA. The Salmonella Effector SpvD Is a Cysteine Hydrolase with a Serovar-specific Polymorphism Influencing Catalytic Activity, Suppression of Immune Responses, and Bacterial Virulence. J Biol Chem 2016; 291:25853-25863. [PMID: 27789710 PMCID: PMC5207060 DOI: 10.1074/jbc.m116.752782] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/26/2016] [Indexed: 12/02/2022] Open
Abstract
Many bacterial pathogens secrete virulence (effector) proteins that interfere with immune signaling in their host. SpvD is a Salmonella enterica effector protein that we previously demonstrated to negatively regulate the NF-κB signaling pathway and promote virulence of S. enterica serovar Typhimurium in mice. To shed light on the mechanistic basis for these observations, we determined the crystal structure of SpvD and show that it adopts a papain-like fold with a characteristic cysteine-histidine-aspartate catalytic triad comprising Cys-73, His-162, and Asp-182. SpvD possessed an in vitro deconjugative activity on aminoluciferin-linked peptide and protein substrates in vitro A C73A mutation abolished SpvD activity, demonstrating that an intact catalytic triad is required for its function. Taken together, these results strongly suggest that SpvD is a cysteine protease. The amino acid sequence of SpvD is highly conserved across different S. enterica serovars, but residue 161, located close to the catalytic triad, is variable, with serovar Typhimurium SpvD having an arginine and serovar Enteritidis a glycine at this position. This variation affected hydrolytic activity of the enzyme on artificial substrates and can be explained by substrate accessibility to the active site. Interestingly, the SpvDG161 variant more potently inhibited NF-κB-mediated immune responses in cells in vitro and increased virulence of serovar Typhimurium in mice. In summary, our results explain the biochemical basis for the effect of virulence protein SpvD and demonstrate that a single amino acid polymorphism can affect the overall virulence of a bacterial pathogen in its host.
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Affiliation(s)
| | - Yue Zhang
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
| | - Michal Przydacz
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
| | | | - Yi Yang
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
| | - Jonathan N Pruneda
- the Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom
| | - David Komander
- the Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom
| | | | - Stephen A Hare
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
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