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McGregor L, Acajjaoui S, Desfosses A, Saïdi M, Bacia-Verloop M, Schwarz JJ, Juyoux P, von Velsen J, Bowler MW, McCarthy AA, Kandiah E, Gutsche I, Soler-Lopez M. The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination. Nat Commun 2023; 14:8248. [PMID: 38086790 PMCID: PMC10716376 DOI: 10.1038/s41467-023-43865-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer's disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathogenesis, is poorly understood. Here we report the structural basis of the complex formation between the MCIA subunits ECSIT and ACAD9. ECSIT binding induces a major conformational change in the FAD-binding loop of ACAD9, releasing the FAD cofactor and converting ACAD9 from a fatty acid β-oxidation (FAO) enzyme to a CI assembly factor. We provide evidence that ECSIT phosphorylation downregulates its association with ACAD9 and is reduced in neuronal cells upon exposure to amyloid-β (Aβ) oligomers. These findings advance our understanding of the MCIA complex assembly and suggest a possible role for ECSIT in the reprogramming of bioenergetic pathways linked to Aβ toxicity, a hallmark of AD.
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Affiliation(s)
- Lindsay McGregor
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France
| | - Melissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France
| | - Jennifer J Schwarz
- European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany
| | - Pauline Juyoux
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Jill von Velsen
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Andrew A McCarthy
- European Molecular Biology Laboratory (EMBL), 38043, Grenoble, France
| | - Eaazhisai Kandiah
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS (IBS), 38044, Grenoble, France.
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38043, Grenoble, France.
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2
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Juyoux P, Galdadas I, Gobbo D, von Velsen J, Pelosse M, Tully M, Vadas O, Gervasio FL, Pellegrini E, Bowler MW. Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation. Science 2023; 381:1217-1225. [PMID: 37708276 PMCID: PMC7615176 DOI: 10.1126/science.add7859] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
The mitogen-activated protein kinase (MAPK) p38α is a central component of signaling in inflammation and the immune response and is, therefore, an important drug target. Little is known about the molecular mechanism of its activation by double phosphorylation from MAPK kinases (MAP2Ks), because of the challenge of trapping a transient and dynamic heterokinase complex. We applied a multidisciplinary approach to generate a structural model of p38α in complex with its MAP2K, MKK6, and to understand the activation mechanism. Integrating cryo-electron microscopy with molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and experiments in cells, we demonstrate a dynamic, multistep phosphorylation mechanism, identify catalytically relevant interactions, and show that MAP2K-disordered amino termini determine pathway specificity. Our work captures a fundamental step of cell signaling: a kinase phosphorylating its downstream target kinase.
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Affiliation(s)
- Pauline Juyoux
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Ioannis Galdadas
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Dorothea Gobbo
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jill von Velsen
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Martin Pelosse
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Mark Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Oscar Vadas
- Protein and peptide purification platform, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Department of Chemistry, University College London, London, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
- Swiss Institute of Bioinformatics, Geneva, Switzerland
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3
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Ma S, Mykhaylyk V, Bowler MW, Pinotsis N, Kozielski F. High-Confidence Placement of Fragments into Electron Density Using Anomalous Diffraction-A Case Study Using Hits Targeting SARS-CoV-2 Non-Structural Protein 1. Int J Mol Sci 2023; 24:11197. [PMID: 37446375 DOI: 10.3390/ijms241311197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
The identification of multiple simultaneous orientations of small molecule inhibitors binding to a protein target is a common challenge. It has recently been reported that the conformational heterogeneity of ligands is widely underreported in the Protein Data Bank, which is likely to impede optimal exploitation to improve affinity of these ligands. Significantly less is even known about multiple binding orientations for fragments (<300 Da), although this information would be essential for subsequent fragment optimisation using growing, linking or merging and rational structure-based design. Here, we use recently reported fragment hits for the SARS-CoV-2 non-structural protein 1 (nsp1) N-terminal domain to propose a general procedure for unambiguously identifying binding orientations of 2-dimensional fragments containing either sulphur or chloro substituents within the wavelength range of most tunable beamlines. By measuring datasets at two energies, using a tunable beamline operating in vacuum and optimised for data collection at very low X-ray energies, we show that the anomalous signal can be used to identify multiple orientations in small fragments containing sulphur and/or chloro substituents or to verify recently reported conformations. Although in this specific case we identified the positions of sulphur and chlorine in fragments bound to their protein target, we are confident that this work can be further expanded to additional atoms or ions which often occur in fragments. Finally, our improvements in the understanding of binding orientations will also serve to improve the rational optimisation of SARS-CoV-2 nsp1 fragment hits.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | | | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
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4
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Triandafillidis DP, Karavassili F, Spiliopoulou M, Valmas A, Athanasiadou M, Nikolaras G, Fili S, Kontou P, Bowler MW, Chasapis CT, Von Dreele RB, Fitch AN, Margiolaki I. The T 2 structure of polycrystalline cubic human insulin. Acta Crystallogr D Struct Biol 2023; 79:374-386. [PMID: 37039669 PMCID: PMC10167666 DOI: 10.1107/s2059798323001328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/13/2023] [Indexed: 04/12/2023] Open
Abstract
The polymorphism of human insulin upon pH variation was characterized via X-ray powder diffraction, employing a crystallization protocol previously established for co-crystallization with phenolic derivatives. Two distinct rhombohedral (R3) polymorphs and one cubic (I213) polymorph were identified with increasing pH, corresponding to the T6, T3R3f and T2 conformations of insulin, respectively. The structure of the cubic T2 polymorph was determined via multi-profile stereochemically restrained Rietveld refinement at 2.7 Å resolution. This constitutes the first cubic insulin structure to be determined from crystals grown in the presence of zinc ions, although no zinc binding was observed. The differences of the polycrystalline variant from other cubic insulin structures, as well as the nature of the pH-driven phase transitions, are discussed in detail.
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Affiliation(s)
- Dimitris P Triandafillidis
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Fotini Karavassili
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Maria Spiliopoulou
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Alexandros Valmas
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Maria Athanasiadou
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - George Nikolaras
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Stavroula Fili
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Paraskevi Kontou
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Matthew W Bowler
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Robert B Von Dreele
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Andrew N Fitch
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble CEDEX 9, France
| | - Irene Margiolaki
- Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
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5
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Kang-Pettinger T, Walker K, Brown R, Cowan R, Wright H, Baravalle R, Waters LC, Muskett FW, Bowler MW, Sawmynaden K, Coombs PJ, Carr MD, Hall G. Identification, binding, and structural characterization of single domain anti-PD-L1 antibodies inhibitory of immune regulatory proteins PD-1 and CD80. J Biol Chem 2022; 299:102769. [PMID: 36470427 PMCID: PMC9811221 DOI: 10.1016/j.jbc.2022.102769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Programmed death-ligand 1 (PD-L1) is a key immune regulatory protein that interacts with programmed cell death protein 1 (PD-1), leading to T-cell suppression. Whilst this interaction is key in self-tolerance, cancer cells evade the immune system by overexpressing PD-L1. Inhibition of the PD-1/PD-L1 pathway with standard monoclonal antibodies has proven a highly effective cancer treatment; however, single domain antibodies (VHH) may offer numerous potential benefits. Here, we report the identification and characterization of a diverse panel of 16 novel VHHs specific to PD-L1. The panel of VHHs demonstrate affinities of 0.7 nM to 5.1 μM and were able to completely inhibit PD-1 binding to PD-L1. The binding site for each VHH on PD-L1 was determined using NMR chemical shift perturbation mapping and revealed a common binding surface encompassing the PD-1-binding site. Additionally, we solved crystal structures of two representative VHHs in complex with PD-L1, which revealed unique binding modes. Similar NMR experiments were used to identify the binding site of CD80 on PD-L1, which is another immune response regulatory element and interacts with PD-L1 localized on the same cell surface. CD80 and PD-1 were revealed to share a highly overlapping binding site on PD-L1, with the panel of VHHs identified expected to inhibit CD80 binding. Comparison of the CD80 and PD-1 binding sites on PD-L1 enabled the identification of a potential antibody binding region able to confer specificity for the inhibition of PD-1 binding only, which may offer therapeutic benefits to counteract cancer cell evasion of the immune system.
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Affiliation(s)
- Tara Kang-Pettinger
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Kayleigh Walker
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Richard Brown
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Helena Wright
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Roberta Baravalle
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Lorna C. Waters
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Frederick W. Muskett
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | | | - Kovilen Sawmynaden
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Peter J. Coombs
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Mark D. Carr
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK,For correspondence: Gareth Hall; Mark D. Carr
| | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK,For correspondence: Gareth Hall; Mark D. Carr
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6
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Ma S, Damfo S, Lou J, Pinotsis N, Bowler MW, Haider S, Kozielski F. Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening. Int J Mol Sci 2022; 23:ijms232012448. [PMID: 36293303 PMCID: PMC9604401 DOI: 10.3390/ijms232012448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
The regular reappearance of coronavirus (CoV) outbreaks over the past 20 years has caused significant health consequences and financial burdens worldwide. The most recent and still ongoing novel CoV pandemic, caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has brought a range of devastating consequences. Due to the exceptionally fast development of vaccines, the mortality rate of the virus has been curbed to a significant extent. However, the limitations of vaccination efficiency and applicability, coupled with the still high infection rate, emphasise the urgent need for discovering safe and effective antivirals against SARS-CoV-2 by suppressing its replication or attenuating its virulence. Non-structural protein 1 (nsp1), a unique viral and conserved leader protein, is a crucial virulence factor for causing host mRNA degradation, suppressing interferon (IFN) expression and host antiviral signalling pathways. In view of the essential role of nsp1 in the CoV life cycle, it is regarded as an exploitable target for antiviral drug discovery. Here, we report a variety of fragment hits against the N-terminal domain of SARS-CoV-2 nsp1 identified by fragment-based screening via X-ray crystallography. We also determined the structure of nsp1 at atomic resolution (0.99 Å). Binding affinities of hits against nsp1 and potential stabilisation were determined by orthogonal biophysical assays such as microscale thermophoresis and thermal shift assays. We identified two ligand-binding sites on nsp1, one deep and one shallow pocket, which are not conserved between the three medically relevant SARS, SARS-CoV-2 and MERS coronaviruses. Our study provides an excellent starting point for the development of more potent nsp1-targeting inhibitors and functional studies on SARS-CoV-2 nsp1.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shymaa Damfo
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiaqi Lou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | | | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- Correspondence:
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7
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Swale C, Bellini V, Bowler MW, Flore N, Brenier-Pinchart MP, Cannella D, Belmudes L, Mas C, Couté Y, Laurent F, Scherf A, Bougdour A, Hakimi MA. Altiratinib blocks Toxoplasma gondii and Plasmodium falciparum development by selectively targeting a spliceosome kinase. Sci Transl Med 2022; 14:eabn3231. [PMID: 35921477 DOI: 10.1126/scitranslmed.abn3231] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Apicomplexa comprise a large phylum of single-celled, obligate intracellular protozoa that include Toxoplasma gondii, Plasmodium, and Cryptosporidium spp., which infect humans and animals and cause severe parasitic diseases. Available therapeutics against these diseases are limited by suboptimal efficacy and frequent side effects, as well as the emergence and spread of resistance. We use a drug repurposing strategy and identify altiratinib, a compound originally developed to treat glioblastoma, as a promising drug candidate with broad spectrum activity against apicomplexans. Altiratinib is parasiticidal and blocks the development of intracellular zoites in the nanomolar range and with a high selectivity index when used against T. gondii. We have identified TgPRP4K of T. gondii as the primary target of altiratinib using genetic target deconvolution, which highlighted key residues within the kinase catalytic site that conferred drug resistance when mutated. We have further elucidated the molecular basis of the inhibitory mechanism and species selectivity of altiratinib for TgPRP4K and for its Plasmodium falciparum counterpart, PfCLK3. Our data identified structural features critical for binding of the other PfCLK3 inhibitor, TCMDC-135051. Consistent with the splicing control activity of this kinase family, we have shown that altiratinib can cause global disruption of splicing, primarily through intron retention in both T. gondii and P. falciparum. Thus, our data establish parasitic PRP4K/CLK3 as a potential pan-apicomplexan target whose repertoire of inhibitors can be expanded by the addition of altiratinib.
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Affiliation(s)
- Christopher Swale
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Valeria Bellini
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Nardella Flore
- Institut Pasteur, Université de Paris, Unité de Biologie des Interactions Hôte-Parasite, CNRS ERL 9195, INSERM U1201, F-75015 Paris, France
| | - Marie-Pierre Brenier-Pinchart
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Dominique Cannella
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, 71 avenue des Martyrs, F-38042, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Fabrice Laurent
- INRAE, Université François Rabelais de Tours, Centre Val de Loire, UMR1282 ISP, Laboratoire Apicomplexes et Immunité Mucosale, 37380 Nouzilly, France
| | - Artur Scherf
- Institut Pasteur, Université de Paris, Unité de Biologie des Interactions Hôte-Parasite, CNRS ERL 9195, INSERM U1201, F-75015 Paris, France
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
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8
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Chu Yuan Kee MJ, Bharath SR, Wee S, Bowler MW, Gunaratne J, Pan S, Zhang L, Song H. Structural insights into the substrate-bound condensation domains of non-ribosomal peptide synthetase AmbB. Sci Rep 2022; 12:5353. [PMID: 35354859 PMCID: PMC8968710 DOI: 10.1038/s41598-022-09188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/15/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractNon-ribosomal peptide synthetases (NRPS) are multi-modular/domain enzymes that catalyze the synthesis of bioactive peptides. A crucial step in the process is peptide elongation accomplished by the condensation (C) domain with the aid of a peptidyl carrier or thiolation (T) domain. Here, we examined condensation reaction carried out by NRPS AmbB involved in biosynthesis of l-2-amino-4-methoxy-trans-3-butenoic acid (AMB) in P. aeruginosa. We determined crystal structures of the truncated T–C bidomain of AmbB in three forms, the apo enzyme with disordered T domain, the holo form with serine linked phosphopantetheine (Ppant) and a holo form with substrate (l-alanine) loaded onto Ppant. The two holo forms feature the T domain in a substrate-donation conformation. Mutagenesis combined with functional assays identified residues essential for the attachment of Ppant, anchoring the Ppant-l-Ala in the donor catalytic channel and the role of the conserved His953 in condensation activity. Altogether, these results provide structural insights into the condensation reaction at the donor site with a substrate-bound C domain of AmbB and lay the foundation for understanding the molecular mechanism of condensation which is crucial for AMB synthesis.
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9
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Bowler MW. Finding order in chaos - nanocrystals in amorphous protein gels. Acta Crystallogr F Struct Biol Commun 2021; 77:386-387. [PMID: 34726176 PMCID: PMC8561820 DOI: 10.1107/s2053230x21010852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Measurements of protein dense phases reveal the presence of highly ordered protein nanostructures. Such phases may be candidates for structural biology measurements on next-generation instruments for molecules that are difficult or impossible to crystallize.
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Affiliation(s)
- Matthew W. Bowler
- European Molecular Biology Laboratory, 71 Ave des Martyrs, Grenoble, CS 90181 F-38042, France
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10
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Farhat DC, Bowler MW, Communie G, Pontier D, Belmudes L, Mas C, Corrao C, Couté Y, Bougdour A, Lagrange T, Hakimi MA, Swale C. A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma. eLife 2021; 10:68312. [PMID: 34263725 PMCID: PMC8313237 DOI: 10.7554/elife.68312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
Correct 3’end processing of mRNAs is one of the regulatory cornerstones of gene expression. In a parasite that must adapt to the regulatory requirements of its multi-host life style, there is a need to adopt additional means to partition the distinct transcriptional signatures of the closely and tandemly arranged stage-specific genes. In this study, we report our findings in T. gondii of an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at these loci. We identify the core polyadenylation complex within T. gondii and establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of the T. gondii CPSF4-YTH in complex with an m6A-modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition is associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant model Arabidopsis thaliana. Nanopore direct RNA sequencing shows the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in both T. gondii and A. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in both T. gondii and A. thaliana, as a guardian against aberrant transcriptional read-throughs.
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Affiliation(s)
- Dayana C Farhat
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | | | | | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), Perpignan, France
| | - Lucid Belmudes
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, Grenoble, France
| | - Charlotte Corrao
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | - Alexandre Bougdour
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), Perpignan, France
| | - Mohamed-Ali Hakimi
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
| | - Christopher Swale
- IAB,Team Host-Pathogen Interactions & Immunity to Infection, INSERMU1209, CNRSUMR5309, Grenoble Alpes University, Grenoble, France
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11
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Bullen G, Galson JD, Hall G, Villar P, Moreels L, Ledsgaard L, Mattiuzzo G, Bentley EM, Masters EW, Tang D, Millett S, Tongue D, Brown R, Diamantopoulos I, Parthiban K, Tebbutt C, Leah R, Chaitanya K, Ergueta-Carballo S, Pazeraitis D, Surade SB, Ashiru O, Crippa L, Cowan R, Bowler MW, Campbell JI, Lee WYJ, Carr MD, Matthews D, Pfeffer P, Hufton SE, Sawmynaden K, Osbourn J, McCafferty J, Karatt-Vellatt A. Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses. Front Immunol 2021; 12:678570. [PMID: 34211469 PMCID: PMC8239432 DOI: 10.3389/fimmu.2021.678570] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
Passive immunization using monoclonal antibodies will play a vital role in the fight against COVID-19. The recent emergence of viral variants with reduced sensitivity to some current antibodies and vaccines highlights the importance of broad cross-reactivity. This study describes deep-mining of the antibody repertoires of hospitalized COVID-19 patients using phage display technology and B cell receptor (BCR) repertoire sequencing to isolate neutralizing antibodies and gain insights into the early antibody response. This comprehensive discovery approach has yielded a panel of potent neutralizing antibodies which bind distinct viral epitopes including epitopes conserved in SARS-CoV-1. Structural determination of a non-ACE2 receptor blocking antibody reveals a previously undescribed binding epitope, which is unlikely to be affected by the mutations in any of the recently reported major viral variants including B.1.1.7 (from the UK), B.1.351 (from South Africa) and B.1.1.28 (from Brazil). Finally, by combining sequences of the RBD binding and neutralizing antibodies with the B cell receptor repertoire sequencing, we also describe a highly convergent early antibody response. Similar IgM-derived sequences occur within this study group and also within patient responses described by multiple independent studies published previously.
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Affiliation(s)
| | | | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | | | | | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Emma M Bentley
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Wing-Yiu Jason Lee
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mark D Carr
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | - Paul Pfeffer
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Simon E Hufton
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | - Jane Osbourn
- Alchemab Therapeutics Ltd., London, United Kingdom
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12
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Naschberger A, Juyoux P, von Velsen J, Rupp B, Bowler MW. Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin. Acta Crystallogr D Struct Biol 2019; 75:1071-1083. [PMID: 31793901 PMCID: PMC6889915 DOI: 10.1107/s2059798319013500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/02/2019] [Indexed: 01/29/2023] Open
Abstract
Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.
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Affiliation(s)
- Andreas Naschberger
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
| | - Pauline Juyoux
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jill von Velsen
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Bernhard Rupp
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
- C.V.M.O., k. k. Hofkristallamt, 991 Audrey Place, Vista, California, USA
| | - Matthew W. Bowler
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
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13
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Svensson O, Gilski M, Nurizzo D, Bowler MW. A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples. IUCrJ 2019; 6:822-831. [PMID: 31576216 PMCID: PMC6760449 DOI: 10.1107/s2052252519008017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
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14
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Hutin S, Van Laer B, Mueller-Dieckmann C, Leonard G, Nurizzo D, Bowler MW. Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules. J Vis Exp 2019. [PMID: 30958484 DOI: 10.3791/59032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High-brilliance X-ray beams coupled with automation have led to the use of synchrotron-based macromolecular X-ray crystallography (MX) beamlines for even the most challenging projects in structural biology. However, most facilities still require the presence of a scientist on site to perform the experiments. A new generation of automated beamlines dedicated to the fully automatic characterization of, and data collection from, crystals of biological macromolecules has recently been developed. These beamlines represent a new tool for structural biologists to screen the results of initial crystallization trials and/or the collection of large numbers of diffraction data sets, without users having to control the beamline themselves. Here we show how to set up an experiment for automatic screening and data collection, how an experiment is performed at the beamline, how the resulting data sets are processed, and how, when possible, the crystal structure of the biological macromolecule is solved.
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Affiliation(s)
- Stephanie Hutin
- Structural Biology Group, European Synchrotron Radiation Facility
| | - Bart Van Laer
- Structural Biology Group, European Synchrotron Radiation Facility
| | | | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility
| | - Didier Nurizzo
- Structural Biology Group, European Synchrotron Radiation Facility
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15
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Oscarsson M, Beteva A, Flot D, Gordon E, Guijarro M, Leonard G, McSweeney S, Monaco S, Mueller-Dieckmann C, Nanao M, Nurizzo D, Popov AN, von Stetten D, Svensson O, Rey-Bakaikoa V, Chado I, Chavas LMG, Gadea L, Gourhant P, Isabet T, Legrand P, Savko M, Sirigu S, Shepard W, Thompson A, Mueller U, Nan J, Eguiraun M, Bolmsten F, Nardella A, Milàn-Otero A, Thunnissen M, Hellmig M, Kastner A, Schmuckermaier L, Gerlach M, Feiler C, Weiss MS, Bowler MW, Gobbo A, Papp G, Sinoir J, McCarthy AA, Karpics I, Nikolova M, Bourenkov G, Schneider T, Andreu J, Cuní G, Juanhuix J, Boer R, Fogh R, Keller P, Flensburg C, Paciorek W, Vonrhein C, Bricogne G, de Sanctis D. MXCuBE2: the dawn of MXCuBE Collaboration. J Synchrotron Radiat 2019; 26:393-405. [PMID: 30855248 PMCID: PMC6412183 DOI: 10.1107/s1600577519001267] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/23/2019] [Indexed: 05/22/2023]
Abstract
MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF - the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.
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Affiliation(s)
- Marcus Oscarsson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonia Beteva
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David Flot
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elspeth Gordon
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matias Guijarro
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon Leonard
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Stephanie Monaco
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Max Nanao
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Didier Nurizzo
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Alexander N. Popov
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David von Stetten
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | | | | | - Laurent Gadea
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | | | - Martin Savko
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | - Serena Sirigu
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | - Uwe Mueller
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | | | | | | | | | - Michael Hellmig
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Alexandra Kastner
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Lukas Schmuckermaier
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Martin Gerlach
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Christian Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ivars Karpics
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Marina Nikolova
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Gleb Bourenkov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Jordi Andreu
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Guifré Cuní
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Judith Juanhuix
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Roeland Boer
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Rasmus Fogh
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Peter Keller
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Claus Flensburg
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Wlodek Paciorek
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Clemens Vonrhein
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Gerard Bricogne
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Daniele de Sanctis
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
- Correspondence e-mail:
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16
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Yee AW, Aldeghi M, Blakeley MP, Ostermann A, Mas PJ, Moulin M, de Sanctis D, Bowler MW, Mueller-Dieckmann C, Mitchell EP, Haertlein M, de Groot BL, Boeri Erba E, Forsyth VT. A molecular mechanism for transthyretin amyloidogenesis. Nat Commun 2019; 10:925. [PMID: 30804345 PMCID: PMC6390107 DOI: 10.1038/s41467-019-08609-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/14/2019] [Indexed: 01/12/2023] Open
Abstract
Human transthyretin (TTR) is implicated in several fatal forms of amyloidosis. Many mutations of TTR have been identified; most of these are pathogenic, but some offer protective effects. The molecular basis underlying the vastly different fibrillation behaviours of these TTR mutants is poorly understood. Here, on the basis of neutron crystallography, native mass spectrometry and modelling studies, we propose a mechanism whereby TTR can form amyloid fibrils via a parallel equilibrium of partially unfolded species that proceeds in favour of the amyloidogenic forms of TTR. It is suggested that unfolding events within the TTR monomer originate at the C-D loop of the protein, and that destabilising mutations in this region enhance the rate of TTR fibrillation. Furthermore, it is proposed that the binding of small molecule drugs to TTR stabilises non-amyloidogenic states of TTR in a manner similar to that occurring for the protective mutants of the protein.
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Affiliation(s)
- Ai Woon Yee
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matteo Aldeghi
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Matthew P Blakeley
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, 85748, Garching, Germany
| | - Philippe J Mas
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
| | - Martine Moulin
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Daniele de Sanctis
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matthew W Bowler
- EMBL, Grenoble Outstation, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | | | - Edward P Mitchell
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Bert L de Groot
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | | | - V Trevor Forsyth
- Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK.
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France.
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17
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Li Y, Muir KW, Bowler MW, Metz J, Haering CH, Panne D. Structural basis for Scc3-dependent cohesin recruitment to chromatin. eLife 2018; 7:e38356. [PMID: 30109982 PMCID: PMC6120753 DOI: 10.7554/elife.38356] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
The cohesin ring complex is required for numerous chromosomal transactions including sister chromatid cohesion, DNA damage repair and transcriptional regulation. How cohesin engages its chromatin substrate has remained an unresolved question. We show here, by determining a crystal structure of the budding yeast cohesin HEAT-repeat subunit Scc3 bound to a fragment of the Scc1 kleisin subunit and DNA, that Scc3 and Scc1 form a composite DNA interaction module. The Scc3-Scc1 subcomplex engages double-stranded DNA through a conserved, positively charged surface. We demonstrate that this conserved domain is required for DNA binding by Scc3-Scc1 in vitro, as well as for the enrichment of cohesin on chromosomes and for cell viability. These findings suggest that the Scc3-Scc1 DNA-binding interface plays a central role in the recruitment of cohesin complexes to chromosomes and therefore for cohesin to faithfully execute its functions during cell division.
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Affiliation(s)
- Yan Li
- European Molecular Biology LaboratoryGrenobleFrance
| | - Kyle W Muir
- European Molecular Biology LaboratoryGrenobleFrance
| | | | - Jutta Metz
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Christian H Haering
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Daniel Panne
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUnited Kingdom
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18
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Xu X, Li Y, Bharath SR, Ozturk MB, Bowler MW, Loo BZL, Tergaonkar V, Song H. Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1. Nat Commun 2018; 9:3183. [PMID: 30093619 PMCID: PMC6085347 DOI: 10.1038/s41467-018-05644-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Transcriptional factors ETS1/2 and p52 synergize downstream of non-canonical NF-κB signaling to drive reactivation of the −146C>T mutant TERT promoter in multiple cancer types, but the mechanism underlying this cooperativity remains unknown. Here we report the crystal structure of a ternary p52/ETS1/−146C>T TERT promoter complex. While p52 needs to associate with consensus κB sites on the DNA to function during non-canonical NF-κB signaling, we show that p52 can activate the −146C>T TERT promoter without binding DNA. Instead, p52 interacts with ETS1 to form a heterotetramer, counteracting autoinhibition of ETS1. Analogous to observations with the GABPA/GABPB heterotetramer, the native flanking ETS motifs are required for sustained activation of the −146C>T TERT promoter by the p52/ETS1 heterotetramer. These observations provide a unifying mechanism for transcriptional activation by GABP and ETS1, and suggest that genome-wide targets of non-canonical NF-κB signaling are not limited to those driven by consensus κB sequences. Incessant telomere synthesis in cancer cells depends on specific mutations in the TERT promoter, enabling its activation by transcription factors ETS1 and p52. Here, the authors elucidate the structural basis for p52/ETS1 binding to mutant TERT, suggesting a general mechanism for TERT reactivation in cancer.
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Affiliation(s)
- Xueyong Xu
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Yinghui Li
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Mert Burak Ozturk
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, France.,Unit of Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, France
| | - Bryan Zong Lin Loo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore. .,Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, 5001, SA, Australia.
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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19
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Johnson LA, Robertson AJ, Baxter NJ, Trevitt CR, Bisson C, Jin Y, Wood HP, Hounslow AM, Cliff MJ, Blackburn GM, Bowler MW, Waltho JP. van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luke A. Johnson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Angus J. Robertson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola J. Baxter
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Clare R. Trevitt
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Yi Jin
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Henry P. Wood
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Andrea M. Hounslow
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - G. Michael Blackburn
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Jonathan P. Waltho
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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20
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Kokotidou C, Jonnalagadda SVR, Orr AA, Seoane-Blanco M, Apostolidou CP, van Raaij MJ, Kotzabasaki M, Chatzoudis A, Jakubowski JM, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Llamas-Saiz AL, Tamamis P, Mitraki A. A novel amyloid designable scaffold and potential inhibitor inspired by GAIIG of amyloid beta and the HIV-1 V3 loop. FEBS Lett 2018; 592:1777-1788. [PMID: 29772603 DOI: 10.1002/1873-3468.13096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
The GAIIG sequence, common to the amyloid beta peptide (residues 29-33) and to the HIV-1 gp120 (residues 24-28 in a typical V3 loop), self-assembles into amyloid fibrils, as suggested by theory and the experiments presented here. The longer YATGAIIGNII sequence from the V3 loop also self-assembles into amyloid fibrils, of which the first three and the last two residues are outside the amyloid GAIIG core. We postulate that this sequence, with suitably selected modifications at the flexible positions, can serve as a designable scaffold for novel amyloid-based materials. Moreover, we report the single crystal X-ray structure of the beta-breaker peptide GAIPIG at 1.05 Å resolution. The structural information provided in this study could serve as the basis for structure-based design of potential inhibitors of amyloid formation.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | | | - Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Mateo Seoane-Blanco
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Chrysanthi Pinelopi Apostolidou
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Madrid, Spain
| | - Marianna Kotzabasaki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Apostolos Chatzoudis
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece
| | - Joseph M Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Estelle Mossou
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - V Trevor Forsyth
- Institut Laue Langevin, Grenoble Cedex 9, France.,Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK
| | - Edward P Mitchell
- Faculty of Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire, UK.,European Synchrotron Radiation Facility, Grenoble Cedex 9, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble, France.,Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Antonio L Llamas-Saiz
- X-Ray Unit, RIAIDT, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion, Greece.,Institute of Electronic Structure and Laser (IESL), FORTH, Heraklion, Greece
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21
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Svensson O, Gilski M, Nurizzo D, Bowler MW. Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1. Acta Crystallogr D Struct Biol 2018; 74:433-440. [PMID: 29717714 PMCID: PMC5930350 DOI: 10.1107/s2059798318003728] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/03/2018] [Indexed: 12/11/2022] Open
Abstract
Macromolecular crystallography is now a mature and widely used technique that is essential in the understanding of biology and medicine. Increases in computing power combined with robotics have not only enabled large numbers of samples to be screened and characterized but have also enabled better decisions to be taken on data collection itself. This led to the development of MASSIF-1 at the ESRF, the first beamline in the world to run fully automatically while making intelligent decisions taking user requirements into account. Since opening in late 2014, the beamline has processed over 42 000 samples. Improvements have been made to the speed of the sample-handling robotics and error management within the software routines. The workflows initially put into place, while highly innovative at the time, have been expanded to include increased complexity and additional intelligence using the information gathered during characterization; this includes adapting the beam diameter dynamically to match the diffraction volume within the crystal. Complex multi-position and multi-crystal data collections have now also been integrated into the selection of experiments available. This has led to increased data quality and throughput, allowing even the most challenging samples to be treated automatically.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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22
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Skubák P, Araç D, Bowler MW, Correia AR, Hoelz A, Larsen S, Leonard GA, McCarthy AA, McSweeney S, Mueller-Dieckmann C, Otten H, Salzman G, Pannu NS. A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model. IUCrJ 2018; 5:166-171. [PMID: 29765606 PMCID: PMC5947721 DOI: 10.1107/s2052252517017961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/15/2017] [Indexed: 05/07/2023]
Abstract
Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F1-ATPase data set and a 4.5 Å resolution SecYEG-SecA complex data set. All of the models were automatically built by the method to Rfree values of between 28.9 and 39.9% and were free from the initial model bias.
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Affiliation(s)
- Pavol Skubák
- Department of Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Demet Araç
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ana R. Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Andre Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Sine Larsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
- Department of Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | | | - Harm Otten
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Navraj S. Pannu
- Department of Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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23
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Ampaw A, Carroll M, von Velsen J, Bhattasali D, Cohen A, Bowler MW, Jakeman DL. Observing enzyme ternary transition state analogue complexes by 19F NMR spectroscopy. Chem Sci 2017; 8:8427-8434. [PMID: 29619190 PMCID: PMC5863612 DOI: 10.1039/c7sc04204c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/23/2017] [Indexed: 11/21/2022] Open
Abstract
Ternary transition state analogue (TSA) complexes probing the isomerization of β-d-glucose 1-phosphate (G1P) into d-glucose 6-phosphate (G6P) catalyzed by catalytically active, fluorinated (5-fluorotryptophan), β-phosphoglucomutase (βPGM) have been observed directly by 19F NMR spectroscopy. In these complexes MgF3- and AlF4- are surrogates for the transferring phosphate. However, the relevance of these metal fluorides as TSA complexes has been queried. The 1D 19F spectrum of a ternary TSA complex presented a molar equivalence between fluorinated enzyme, metal fluoride and non-isomerizable fluoromethylenephosphonate substrate analogue. Ring flips of the 5-fluoroindole ring remote from the active site were observed by both 19F NMR and X-ray crystallography, but did not perturb function. This data unequivocally demonstrates that the concentration of the metal fluoride complexes is equivalent to the concentration of enzyme and ligand in the TSA complex in aqueous solution.
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Affiliation(s)
- Anna Ampaw
- Department of Chemistry , Dalhousie University , Halifax , NS , Canada B3H 4R2 .
| | - Madison Carroll
- Department of Chemistry , Dalhousie University , Halifax , NS , Canada B3H 4R2 .
| | - Jill von Velsen
- European Molecular Biology Laboratory , Grenoble Outstation , 71 avenue des Martyrs , CS 90181 F-38042 Grenoble , France
| | | | - Alejandro Cohen
- Proteomics and Mass Spectrometry Core Facility , Life Sciences Research Institute , Dalhousie University , Halifax , NS , Canada B3H 4R2
| | - Matthew W Bowler
- European Molecular Biology Laboratory , Grenoble Outstation , 71 avenue des Martyrs , CS 90181 F-38042 Grenoble , France
| | - David L Jakeman
- Department of Chemistry , Dalhousie University , Halifax , NS , Canada B3H 4R2 .
- College of Pharmacy , Dalhousie University , Halifax , NS , Canada B3H 4R2
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24
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Naschberger A, Orry A, Lechner S, Bowler MW, Nurizzo D, Novokmet M, Keller MA, Oemer G, Seppi D, Haslbeck M, Pansi K, Dieplinger H, Rupp B. Structural Evidence for a Role of the Multi-functional Human Glycoprotein Afamin in Wnt Transport. Structure 2017; 25:1907-1915.e5. [PMID: 29153507 DOI: 10.1016/j.str.2017.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/14/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022]
Abstract
Afamin, a human plasma glycoprotein and putative transporter of hydrophobic molecules, has been shown to act as extracellular chaperone for poorly soluble, acylated Wnt proteins, forming a stable, soluble complex with functioning Wnt proteins. The 2.1-Å crystal structure of glycosylated human afamin reveals an almost exclusively hydrophobic binding cleft capable of harboring large hydrophobic moieties. Lipid analysis confirms the presence of lipids, and density in the primary binding pocket of afamin was modeled as palmitoleic acid, presenting the native O-acylation on serine 209 in human Wnt3a. The modeled complex between the experimental afamin structure and a Wnt3a homology model based on the XWnt8-Fz8-CRD fragment complex crystal structure is compelling, with favorable interactions comparable with the crystal structure complex. Afamin readily accommodates the conserved palmitoylated serine 209 of Wnt3a, providing a structural basis how afamin solubilizes hydrophobic and poorly soluble Wnt proteins.
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Affiliation(s)
- Andreas Naschberger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria; Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Andrew Orry
- MolSoft LLC, 11199 Sorrento Valley Road, San Diego, CA 92121, USA
| | - Stefan Lechner
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Didier Nurizzo
- Structural Biology Group, ESRF, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Mislav Novokmet
- Genos, Glycoscience Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia
| | - Markus A Keller
- Division of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Straße 1, 6020 Innsbruck, Austria
| | - Gregor Oemer
- Genos, Glycoscience Laboratory, Hondlova 2/11, 10000 Zagreb, Croatia
| | - Daniele Seppi
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Martin Haslbeck
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Kathrin Pansi
- Division of Biological Chemistry, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Hans Dieplinger
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria; k.-k. Hofkristallamt, San Diego, CA 92084, USA.
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25
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Papp G, Felisaz F, Sorez C, Lopez-Marrero M, Janocha R, Manjasetty B, Gobbo A, Belrhali H, Bowler MW, Cipriani F. FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography. Acta Crystallogr D Struct Biol 2017; 73:841-851. [PMID: 28994413 PMCID: PMC5633909 DOI: 10.1107/s2059798317013596] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/22/2017] [Indexed: 11/23/2022]
Abstract
A sample changer based on a six-axis industrial robot and a new sample-storage dewar with an ice-cleaning feature have been developed to open automated X-ray crystallography beamlines to new sample-holder models, such as miniSPINE and NewPin, while remaining compatible with the widespread SPINE sample-holder standard. Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Papp et al. (2017, Acta Cryst., D73, 829–840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting. In this context, a versatile and fast sample changer, FlexED8, has been developed that is compatible with the highly successful SPINE sample holder and with the miniSPINE and NewPin sample holders. Based on a six-axis industrial robot, FlexED8 is equipped with a tool changer and includes a novel open sample-storage dewar with a built-in ice-filtering system. With seven versatile puck slots, it can hold up to 112 SPINE sample holders in uni-pucks, or 252 miniSPINE or NewPin sample holders, with 36 samples per puck. Additionally, a double gripper, compatible with the SPINE sample holders and uni-pucks, allows a reduction in the sample-exchange time from 40 s, the typical time with a standard single gripper, to less than 5 s. Computer vision-based sample-transfer monitoring, sophisticated error handling and automatic error-recovery procedures ensure high reliability. The FlexED8 sample changer has been successfully tested under real conditions on a beamline.
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Affiliation(s)
- Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Marcos Lopez-Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Babu Manjasetty
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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26
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Papp G, Rossi C, Janocha R, Sorez C, Lopez-Marrero M, Astruc A, McCarthy A, Belrhali H, Bowler MW, Cipriani F. Towards a compact and precise sample holder for macromolecular crystallography. Acta Crystallogr D Struct Biol 2017; 73:829-840. [PMID: 28994412 PMCID: PMC5633908 DOI: 10.1107/s2059798317013742] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022]
Abstract
Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of miniSPINE was tested at different institutes using evaluation kits, and pilot beamlines are being equipped with compatible robotics for large-scale evaluation. A companion paper describes a new sample changer FlexED8 (Papp et al., 2017, Acta Cryst., D73, 841-851).
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Affiliation(s)
- Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Christopher Rossi
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Robert Janocha
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Clement Sorez
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Marcos Lopez-Marrero
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Anthony Astruc
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Andrew McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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27
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, 19 F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017; 56:9732-9735. [PMID: 28498638 PMCID: PMC5575484 DOI: 10.1002/anie.201703074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 11/08/2022]
Abstract
We report X-ray crystallographic and 19 F NMR studies of the G-protein RhoA complexed with MgF3- , GDP, and RhoGAP, which has the mutation Arg85'Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X-ray data show how Tyr34 maintains solvent exclusion and the core H-bond network in the active site by relocating to replace the missing Arg85' sidechain. The 19 F NMR data show deshielding effects that indicate the main function of Arg85' is electronic polarization of the transferring phosphoryl group, primarily mediated by H-bonding to O3G and thence to PG . DFT calculations identify electron-density redistribution and pinpoint why the TS for guanosine 5'-triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85'Ala relative to wild-type (WT) RhoGAP. This study demonstrates that 19 F NMR measurements, in combination with X-ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site-specific modifications.
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Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Robert W Molt
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,ENSCO, Inc., Melbourne, FL, 32940, USA
| | - Erika Pellegrini
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
| | - Matthew W Bowler
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France.,European Molecular Biology Laboratory, Grenoble Outstation CS90181, 38042, Grenoble, Cedex 9, France
| | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography,
19
F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yi Jin
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- School of ChemistryCardiff University Cardiff CF10 3AT UK
| | - Robert W. Molt
- School of ChemistryCardiff University Cardiff CF10 3AT UK
- Department of Biochemistry and Molecular BiologyIndiana University School of Medicine Indianapolis IN 46202 USA
- ENSCO, Inc. Melbourne FL 32940 USA
| | - Erika Pellegrini
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
| | | | - Matthew W. Bowler
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
- European Molecular Biology Laboratory, Grenoble Outstation CS90181 38042 Grenoble, Cedex 9 France
| | | | - G. Michael Blackburn
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
| | - Jonathan P. Waltho
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- Manchester Institute of Biotechnology Manchester M1 7DN UK
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29
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Bowler MG, Bowler DR, Bowler MW. Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments. J Appl Crystallogr 2017; 50:631-638. [PMID: 28381983 PMCID: PMC5377353 DOI: 10.1107/s1600576717003636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/07/2017] [Indexed: 11/16/2022] Open
Abstract
The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F68, 111-114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.
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Affiliation(s)
- Michael G. Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, UK
| | - David R. Bowler
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, Grenoble F-38042, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, 71 avenue des Martyrs, CS 90181, Grenoble F-38042, France
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30
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Deidda G, Jonnalagadda SVR, Spies JW, Ranella A, Mossou E, Forsyth VT, Mitchell EP, Bowler MW, Tamamis P, Mitraki A. Self-Assembled Amyloid Peptides with Arg-Gly-Asp (RGD) Motifs As Scaffolds for Tissue Engineering. ACS Biomater Sci Eng 2016; 3:1404-1416. [DOI: 10.1021/acsbiomaterials.6b00570] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Graziano Deidda
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
| | - Sai Vamshi R. Jonnalagadda
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Jacob W. Spies
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anthi Ranella
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
| | - Estelle Mossou
- Institut Laue Langevin, 6 rue
Jules Horowitz, 38042 Grenoble Cedex 9, France
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - V. Trevor Forsyth
- Institut Laue Langevin, 6 rue
Jules Horowitz, 38042 Grenoble Cedex 9, France
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Edward P. Mitchell
- Faculty of
Natural Sciences/Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble Cedex 9, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble, France
- Unit
for Virus Host Cell Interactions, Université Grenoble Alpes−EMBL-CNRS, 71 avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 70013, Greece
- Institute
of Electronic Structure and Laser (IESL), Foundation for Research and Technology−Hellas (FORTH), Heraklion 70013, Greece
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31
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Pellegrini E, Palencia A, Braun L, Kapp U, Bougdour A, Belrhali H, Bowler MW, Hakimi MA. Structural Basis for the Subversion of MAP Kinase Signaling by an Intrinsically Disordered Parasite Secreted Agonist. Structure 2016; 25:16-26. [PMID: 27889209 PMCID: PMC5222587 DOI: 10.1016/j.str.2016.10.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 01/07/2023]
Abstract
The causative agent of toxoplasmosis, the intracellular parasite Toxoplasma gondii, delivers a protein, GRA24, into the cells it infects that interacts with the mitogen-activated protein (MAP) kinase p38α (MAPK14), leading to activation and nuclear translocation of the host kinase and a subsequent inflammatory response that controls the progress of the parasite. The purification of a recombinant complex of GRA24 and human p38α has allowed the molecular basis of this activation to be determined. GRA24 is shown to be intrinsically disordered, binding two kinases that act independently, and is the only factor required to bypass the canonical mitogen-activated protein kinase activation pathway. An adapted kinase interaction motif (KIM) forms a highly stable complex that competes with cytoplasmic regulatory partners. In addition, the recombinant complex forms a powerful in vitro tool to evaluate the specificity and effectiveness of p38α inhibitors that have advanced to clinical trials, as it provides a hitherto unavailable stable and highly active form of p38α. Toxoplasmosis controls its host immune response via a protein effector, GRA24 A recombinant complex of GRA24 and MAPK p38α demonstrates how the protein works An adapted KIM domain ensures activation and a sustained inflammatory response The recombinant complex is useful in the evaluation of p38 inhibitors
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Affiliation(s)
- Erika Pellegrini
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Andrés Palencia
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Laurence Braun
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Ulrike Kapp
- Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Alexandre Bougdour
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France.
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France.
| | - Mohamed-Ali Hakimi
- IAB, Team Host-Pathogen Interactions & Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France.
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32
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Affiliation(s)
- Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Shunfu Piao
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Vanessa Qianmin Tan
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France.,Unit of Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore
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33
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Nurizzo D, Bowler MW, Caserotto H, Dobias F, Giraud T, Surr J, Guichard N, Papp G, Guijarro M, Mueller-Dieckmann C, Flot D, McSweeney S, Cipriani F, Theveneau P, Leonard GA. RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments. Acta Crystallogr D Struct Biol 2016; 72:966-75. [PMID: 27487827 PMCID: PMC4973212 DOI: 10.1107/s205979831601158x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/15/2016] [Indexed: 11/11/2022]
Abstract
An industrial six-axis robot has been combined with a high-accuracy air-bearing rotation axis to create a single device with the capabilities of both transferring cryocooled protein crystals from a sample-containing dewar and collecting complete X-ray diffraction data sets. Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically.
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Affiliation(s)
- Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - John Surr
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Nicolas Guichard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | | | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Florent Cipriani
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Gordon A Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
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34
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Tang X, Zhu Y, Baker SL, Bowler MW, Chen BJ, Chen C, Hogg JR, Goff SP, Song H. Structural basis of suppression of host translation termination by Moloney Murine Leukemia Virus. Nat Commun 2016; 7:12070. [PMID: 27329342 PMCID: PMC4917968 DOI: 10.1038/ncomms12070] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/25/2016] [Indexed: 01/24/2023] Open
Abstract
Retroviral reverse transcriptase (RT) of Moloney murine leukemia virus (MoMLV) is expressed in the form of a large Gag–Pol precursor protein by suppression of translational termination in which the maximal efficiency of stop codon read-through depends on the interaction between MoMLV RT and peptidyl release factor 1 (eRF1). Here, we report the crystal structure of MoMLV RT in complex with eRF1. The MoMLV RT interacts with the C-terminal domain of eRF1 via its RNase H domain to sterically occlude the binding of peptidyl release factor 3 (eRF3) to eRF1. Promotion of read-through by MoMLV RNase H prevents nonsense-mediated mRNA decay (NMD) of mRNAs. Comparison of our structure with that of HIV RT explains why HIV RT cannot interact with eRF1. Our results provide a mechanistic view of how MoMLV manipulates the host translation termination machinery for the synthesis of its own proteins. Retroviral reverse transcriptase from Moloney Murine Leukemia Virus (MoMLV) requires interaction with peptidyl release factor 1. Here, the authors report the crystal structure of this complex, and provide insights into how MoMLV uses the host translation machinery to synthesize its own proteins.
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Affiliation(s)
- Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yiping Zhu
- Department of Biochemistry and Molecular Biophysics, Columbia University, HHSC 1310C, 701 West 168th Street, New York, New York 10032, USA.,Howard Hughes Medical Institute, Columbia University, HHSC 1310C, 701 West 168th Street, New York, NY 10032, USA
| | - Stacey L Baker
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble F-38042, France.,Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, Grenoble F-38042, France
| | - Benjamin Jieming Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Chen Chen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University, HHSC 1310C, 701 West 168th Street, New York, New York 10032, USA.,Howard Hughes Medical Institute, Columbia University, HHSC 1310C, 701 West 168th Street, New York, NY 10032, USA
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.,Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore
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35
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Na Z, Yeo SP, Bharath SR, Bowler MW, Balıkçı E, Wang CI, Song H. Structural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab. Cell Res 2016; 27:147-150. [PMID: 27325296 PMCID: PMC5223238 DOI: 10.1038/cr.2016.77] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Zhenkun Na
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Siok Ping Yeo
- Singapore Immunology Network, 8a Biomedical Grove, Singapore 138648, Singapore
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France.,Unit of Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France
| | - Esra Balıkçı
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, 8a Biomedical Grove, Singapore 138648, Singapore
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore
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36
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Bowler MW, Svensson O, Nurizzo D. Fully automatic macromolecular crystallography: the impact of MASSIF-1 on the optimum acquisition and quality of data. CRYSTALLOGR REV 2016. [DOI: 10.1080/0889311x.2016.1155050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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37
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Bowler MW, Nurizzo D, Barrett R, Beteva A, Bodin M, Caserotto H, Delagenière S, Dobias F, Flot D, Giraud T, Guichard N, Guijarro M, Lentini M, Leonard GA, McSweeney S, Oskarsson M, Schmidt W, Snigirev A, von Stetten D, Surr J, Svensson O, Theveneau P, Mueller-Dieckmann C. MASSIF-1: a beamline dedicated to the fully automatic characterization and data collection from crystals of biological macromolecules. J Synchrotron Radiat 2015; 22:1540-7. [PMID: 26524320 PMCID: PMC4629869 DOI: 10.1107/s1600577515016604] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/05/2015] [Indexed: 05/22/2023]
Abstract
MASSIF-1 (ID30A-1) is an ESRF undulator beamline operating at a fixed wavelength of 0.969 Å (12.8 keV) that is dedicated to the completely automatic characterization of and data collection from crystals of biological macromolecules. The first of the ESRF Upgrade MASSIF beamlines to be commissioned, it has been open since September 2014, providing a unique automated data collection service to academic and industrial users. Here, the beamline characteristics and details of the new service are outlined.
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Affiliation(s)
- Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, F-38042 Grenoble, France
- Unit for Virus Host Cell Interactions, Université Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Marjolaine Bodin
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Solange Delagenière
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Fabian Dobias
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Nicolas Guichard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Mattias Guijarro
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Marcus Oskarsson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Werner Schmidt
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Anatoli Snigirev
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - David von Stetten
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, F-38043 Grenoble, France
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38
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Bowler MW, Nurizzo D. MASSIF1: fully automated macromolecular crystallography. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315095947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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39
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Svensson O, Malbet-Monaco S, Popov A, Nurizzo D, Bowler MW. Fully automatic characterization and data collection from crystals of biological macromolecules. Acta Crystallogr D Biol Crystallogr 2015; 71:1757-67. [PMID: 26249356 PMCID: PMC4528805 DOI: 10.1107/s1399004715011918] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/22/2015] [Indexed: 11/24/2022]
Abstract
Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Stéphanie Malbet-Monaco
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Alexander Popov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
- Unit for Virus–Host Cell Interactions, Université Grenoble Alpes–EMBL–CNRS, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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Farci D, Bowler MW, Esposito F, McSweeney S, Tramontano E, Piano D. Purification and characterization of DR_2577 (SlpA) a major S-layer protein from Deinococcus radiodurans. Front Microbiol 2015; 6:414. [PMID: 26074883 PMCID: PMC4419837 DOI: 10.3389/fmicb.2015.00414] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/20/2015] [Indexed: 11/25/2022] Open
Abstract
The protein DR_2577 is a major Surface layer component of the radio-resistant bacterium Deinococcus radiodurans. In the present study DR_2577 has been purified and its oligomeric profile characterized by means of size exclusion chromatography and gel electrophoresis. DR_2577 was found to be organized into three hierarchical orders characterized by monomers, stable dimers formed by the occurrence of disulfide bonds, and hexamers resulting from a combination of dimers. The structural implications of these findings are discussed providing new elements for a more integrated model of this S-layer.
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Affiliation(s)
- Domenica Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy
| | - Matthew W Bowler
- Laboratory of Synchrotron Crystallography, Department of Structural Biology, European Molecular Biology Laboratory Grenoble, France ; Unit for Virus Host Cell Interactions, Laboratory of Structural Biology of RNA-Protein Complexes in Gene Expression and Host-Pathogen Interactions, University Grenoble Alpes-EMBL-Centre National de la Recherche Scientifique Grenoble, France
| | - Francesca Esposito
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato Cagliari, Italy
| | - Sean McSweeney
- Department of Photon Sciences, Brookhaven National Laboratory Upton, NY, USA
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato Cagliari, Italy
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari Cagliari, Italy ; Laboratory of Structural Biology, International Institute of Molecular and Cell Biology Warsaw, Poland
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Koromyslova AD, Leuthold MM, Bowler MW, Hansman GS. The sweet quartet: Binding of fucose to the norovirus capsid. Virology 2015; 483:203-8. [PMID: 25980740 DOI: 10.1016/j.virol.2015.04.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 03/24/2015] [Accepted: 04/07/2015] [Indexed: 11/16/2022]
Abstract
Human noroviruses bind histo-blood group antigens (HBGAs) and this interaction is thought to be important for an infection. We identified two additional fucose-binding pockets (termed fucose-3/4 sites) on a genogroup II human (GII.10) norovirus-protruding (P) dimer using X-ray crystallography. Fucose-3/4 sites were located between two previously determined HBGA binding pockets (termed fucose-1/2 sites). We found that four fucose molecules were capable of binding altogether at fucose-1/2/3/4 sites on the P dimer, though the fucose molecules bound in a dose-dependent and step-wise manner. We also showed that HBGA B-trisaccharide molecules bound in a similar way at the fucose-1/2 sites. Interestingly, we discovered that the monomers of the P dimer were asymmetrical in an unliganded state and when a single B-trisaccharide molecule bound, but were symmetrical when two B-trisaccharide molecules bound. We postulate that the symmetrical dimers might favor HBGA binding interactions at fucose-1/2 sites.
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Affiliation(s)
- Anna D Koromyslova
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany
| | - Mila M Leuthold
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble, F-38042, France; Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 Avenue des Martyrs, CS 90181, Grenoble F-38042, France
| | - Grant S Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany.
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De Maria Antolinos A, Pernot P, Brennich ME, Kieffer J, Bowler MW, Delageniere S, Ohlsson S, Malbet Monaco S, Ashton A, Franke D, Svergun D, McSweeney S, Gordon E, Round A. ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments. ACTA ACUST UNITED AC 2015; 71:76-85. [PMID: 25615862 PMCID: PMC4304688 DOI: 10.1107/s1399004714019609] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/29/2014] [Indexed: 11/15/2022]
Abstract
The ISPyB information-management system for crystallography has been adapted to include data from small-angle X-ray scattering of macromolecules in solution experiments. Logging experiments with the laboratory-information management system ISPyB (Information System for Protein crystallography Beamlines) enhances the automation of small-angle X-ray scattering of biological macromolecules in solution (BioSAXS) experiments. The ISPyB interface provides immediate user-oriented online feedback and enables data cross-checking and downstream analysis. To optimize data quality and completeness, ISPyBB (ISPyB for BioSAXS) makes it simple for users to compare the results from new measurements with previous acquisitions from the same day or earlier experiments in order to maximize the ability to collect all data required in a single synchrotron visit. The graphical user interface (GUI) of ISPyBB has been designed to guide users in the preparation of an experiment. The input of sample information and the ability to outline the experimental aims in advance provides feedback on the number of measurements required, calculation of expected sample volumes and time needed to collect the data: all of this information aids the users to better prepare for their trip to the synchrotron. A prototype version of the ISPyBB database is now available at the European Synchrotron Radiation Facility (ESRF) beamline BM29 and is already greatly appreciated by academic users and industrial clients. It will soon be available at the PETRA III beamline P12 and the Diamond Light Source beamlines I22 and B21.
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Affiliation(s)
| | - Petra Pernot
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Martha E Brennich
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Jérôme Kieffer
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Solange Delageniere
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Staffan Ohlsson
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Stephanie Malbet Monaco
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Alun Ashton
- DLS, Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
| | - Daniel Franke
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Elspeth Gordon
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, CS 40220, 38042 Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181, 38042 Grenoble, France
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Jin Y, Bhattasali D, Pellegrini E, Forget SM, Baxter NJ, Cliff MJ, Bowler MW, Jakeman DL, Blackburn GM, Waltho JP. α-Fluorophosphonates reveal how a phosphomutase conserves transition state conformation over hexose recognition in its two-step reaction. Proc Natl Acad Sci U S A 2014; 111:12384-9. [PMID: 25104750 PMCID: PMC4151737 DOI: 10.1073/pnas.1402850111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
β-Phosphoglucomutase (βPGM) catalyzes isomerization of β-D-glucose 1-phosphate (βG1P) into D-glucose 6-phosphate (G6P) via sequential phosphoryl transfer steps using a β-D-glucose 1,6-bisphosphate (βG16BP) intermediate. Synthetic fluoromethylenephosphonate and methylenephosphonate analogs of βG1P deliver novel step 1 transition state analog (TSA) complexes for βPGM, incorporating trifluoromagnesate and tetrafluoroaluminate surrogates of the phosphoryl group. Within an invariant protein conformation, the β-D-glucopyranose ring in the βG1P TSA complexes (step 1) is flipped over and shifted relative to the G6P TSA complexes (step 2). Its equatorial hydroxyl groups are hydrogen-bonded directly to the enzyme rather than indirectly via water molecules as in step 2. The (C)O-P bond orientation for binding the phosphate in the inert phosphate site differs by ∼ 30° between steps 1 and 2. By contrast, the orientations for the axial O-Mg-O alignment for the TSA of the phosphoryl group in the catalytic site differ by only ∼ 5°, and the atoms representing the five phosphorus-bonded oxygens in the two transition states (TSs) are virtually superimposable. The conformation of βG16BP in step 1 does not fit into the same invariant active site for step 2 by simple positional interchange of the phosphates: the TS alignment is achieved by conformational change of the hexose rather than the protein.
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Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Debabrata Bhattasali
- Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2
| | - Erika Pellegrini
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; Structural Biology Group, European Synchrotron Radiation Facility, 38042 Grenoble, Cedex 9, France; European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France
| | - Stephanie M Forget
- Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J Cliff
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom; and
| | - Matthew W Bowler
- Structural Biology Group, European Synchrotron Radiation Facility, 38042 Grenoble, Cedex 9, France; European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France; Unit of Virus Host Cell Interactions, University of Grenoble Alpes-European Molecular Biology Laboratory-Centre National de la Recherche Scientifique, 38042 Grenoble, Cedex 9, France
| | - David L Jakeman
- Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2;
| | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom; and
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Farci D, Bowler MW, Kirkpatrick J, McSweeney S, Tramontano E, Piano D. New features of the cell wall of the radio-resistant bacterium Deinococcus radiodurans. Biochim Biophys Acta 2014; 1838:1978-84. [PMID: 24589688 DOI: 10.1016/j.bbamem.2014.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/07/2014] [Accepted: 02/19/2014] [Indexed: 11/27/2022]
Abstract
We have analyzed the cell wall of the radio-resistant bacterium Deinococcus radiodurans. Unexpectedly, the bacterial envelope appears to be organized in different complexes of high molecular weight. Each complex is composed of several proteins, most of which are coded by genes of unknown function and the majority are constituents of the inner/outer membrane system. One of the most abundant complexes is constituted by the gene DR_0774. This protein is a type of secretin which is a known subunit of the homo-oligomeric channel that represents the main bulk of the type IV piliation family. Finally, a minor component of the pink envelope consists of several inner-membrane proteins. The implications of these findings are discussed.
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Affiliation(s)
- Domenica Farci
- Department of Life and Environmental Sciences, Laboratory of Plant Physiology, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France; Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Joanna Kirkpatrick
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38000 Grenoble, France
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042 Monserrato, Cagliari, Italy
| | - Dario Piano
- Department of Life and Environmental Sciences, Laboratory of Plant Physiology, University of Cagliari, V.le S. Ingnazio da Laconi 13, 09123 Cagliari, Italy.
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Bowler MG, Bowler MW. Measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies. Acta Crystallogr F Struct Biol Commun 2013; 70:127-32. [PMID: 24419635 DOI: 10.1107/s2053230x13032007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022]
Abstract
The advent of micro-focused X-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. In particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. However, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be performed. For the automation of this process for large-scale screening, and to provide an indication of the best strategy for data collection, a metric of crystal variability could be useful. Here, measures of the intrinsic variability within protein crystals are presented and their implications for optimal data-collection strategies are discussed.
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Affiliation(s)
- Michael G Bowler
- Department of Physics, University of Oxford, Keble Road, Oxford OX1 3RH, England
| | - Matthew W Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France
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46
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Monaco S, Gordon E, Bowler MW, Delagenière S, Guijarro M, Spruce D, Svensson O, McSweeney SM, McCarthy AA, Leonard G, Nanao MH. Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF. J Appl Crystallogr 2013; 46:804-810. [PMID: 23682196 PMCID: PMC3654316 DOI: 10.1107/s0021889813006195] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/04/2013] [Indexed: 12/02/2022] Open
Abstract
The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.
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Affiliation(s)
- Stéphanie Monaco
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Elspeth Gordon
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France
- Unit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Solange Delagenière
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Matias Guijarro
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Darren Spruce
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Olof Svensson
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Sean M. McSweeney
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France
- Unit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043, Grenoble, France
| | - Max H. Nanao
- European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042, Grenoble, France
- Unit of Virus Host–Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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Ferrer JL, Larive NA, Bowler MW, Nurizzo D. Recent progress in robot-based systems for crystallography and their contribution to drug discovery. Expert Opin Drug Discov 2013; 8:835-47. [PMID: 23656378 DOI: 10.1517/17460441.2013.793666] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION X-ray crystallography is the main tool for macromolecular structure solution at atomic resolution. It provides key information for the understanding of protein function, opening opportunities for the modulation of enzymatic mechanisms, and protein-ligand interactions. As a consequence, macromolecular crystallography plays an essential role in drug design, as well as in the a posteriori validation of drug mechanisms. AREAS COVERED The demand for method developments and also tools for macromolecular crystallography has significantly increased over the past 10 years. As a consequence, access to the facilities required for these investigations, such as synchrotron beamlines, became more difficult and significant efforts were dedicated to the automation of the experimental setup in laboratories. In this article, the authors describe how this was accomplished and how robot-based systems contribute to the enhancement of the macromolecular structure solution pipeline. EXPERT OPINION The evolution in robot technology, together with progress in X-ray beam performance and software developments, contributes to a new era in macromolecular X-ray crystallography. Highly integrated experimental environments open new possibilities for crystallography experiments. It is likely that it will also change the way this technique will be used in the future, opening the field to a larger community.
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Affiliation(s)
- Jean-Luc Ferrer
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier (UJF), Institut de Biologie Structurale Jean-Pierre Ebel (IBS), F-38027 Grenoble Cedex 1, France.
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Abstract
Early studies on chemical synthesis of biological molecules can be seen to progress to preparation and biological evaluation of phosphonates as analogues of biological phosphates, with emphasis on their isosteric and isopolar character. Work with such mimics progressed into structural studies with a range of nucleotide-utilising enzymes. The arrival of metal fluorides as analogues of the phosphoryl group, PO(3)(-), for transition state (TS) analysis of enzyme reactions stimulated the symbiotic deployment of (19)F NMR and protein crystallography. Characteristics of enzyme transition state analogues are reviewed for a range of reactions. From the available MF(x) species, trifluoroberyllate gives tetrahedral mimics of ground states (GS) in which phosphate is linked to carboxylate and phosphate oxyanions. Tetrafluoroaluminate is widely employed as a TS mimic, but it necessarily imposes octahedral geometry on the assembled complexes, whereas phosphoryl transfer involves trigonal bipyramidal (tbp) geometry. Trifluoromagnesate (MgF(3)(-)) provides the near-ideal solution, delivering tbp geometry and correct anionic charge. Some of the forty reported tbp structures assigned as having AlF(3)(0) cores have been redefined as trifluoromagnesate complexes. Transition state analogues for a range of kinases, mutases, and phosphatases provide a detailed description of mechanism for phosphoryl group transfer, supporting the concept of charge balance in their TS and of concerted-associative pathways for biocatalysis. Above all, superposition of GS and TS structures reveals that in associative phosphoryl transfer, the phosphorus atom migrates through a triangle of three, near-stationary, equatorial oxygens. The extension of these studies to near attack conformers further illuminates enzyme catalysis of phosphoryl transfer.
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Affiliation(s)
- G M Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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Theveneau P, Baker R, Barrett R, Beteva A, Bowler MW, Carpentier P, Caserotto H, Sanctis DD, Dobias F, Flot D, Guijarro M, Giraud T, Lentini M, Leonard GA, Mattenet M, McCarthy AA, McSweeney SM, Morawe C, Nanao M, Nurizzo D, Ohlsson S, Pernot P, Popov AN, Round A, Royant A, Schmid W, Snigirev A, Surr J, Mueller-Dieckmann C. The Upgrade Programme for the Structural Biology beamlines at the European Synchrotron Radiation Facility – High throughput sample evaluation and automation. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/425/1/012001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Jin Y, Cliff MJ, Baxter NJ, Dannatt HRW, Hounslow AM, Bowler MW, Blackburn GM, Waltho JP. Charge-Balanced Metal Fluoride Complexes for Protein Kinase A with Adenosine Diphosphate and Substrate Peptide SP20. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204266] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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