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Silvestri I, Manigrasso J, Andreani A, Brindani N, Mas C, Reiser JB, Vidossich P, Martino G, McCarthy AA, De Vivo M, Marcia M. Targeting the conserved active site of splicing machines with specific and selective small molecule modulators. Nat Commun 2024; 15:4980. [PMID: 38898052 PMCID: PMC11187226 DOI: 10.1038/s41467-024-48697-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.
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Affiliation(s)
- Ilaria Silvestri
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
- Institute of Crystallography, National Research Council, Via Vivaldi 43, 81100, Caserta, Italy
| | - Jacopo Manigrasso
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alessandro Andreani
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Nicoletta Brindani
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Caroline Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | | | - Pietro Vidossich
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Gianfranco Martino
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Andrew A McCarthy
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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Faure C, Min Ng Y, Belle C, Soler-Lopez M, Khettabi L, Saïdi M, Berthet N, Maresca M, Philouze C, Rachidi W, Réglier M, du Moulinet d'Hardemare A, Jamet H. Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical tudies. Chembiochem 2024; 25:e202400235. [PMID: 38642076 DOI: 10.1002/cbic.202400235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/22/2024]
Abstract
The pigmentation of the skin, modulated by different actors in melanogenesis, is mainly due to the melanins (protective pigments). In humans, these pigments' precursors are synthetized by an enzyme known as tyrosinase (TyH). The regulation of the enzyme activity by specific modulators (inhibitors or activators) can offer a means to fight hypo- and hyper-pigmentations responsible for medical, psychological and societal handicaps. Herein, we report the investigation of phenylalanine derivatives as TyH modulators. Interacting with the binuclear copper active site of the enzyme, phenylalanine derivatives combine effects induced by combination with known resorcinol inhibitors and natural substrate/intermediate (amino acid part). Computational studies including docking, molecular dynamics and free energy calculations combined with biological activity assays on isolated TyH and in human melanoma MNT-1 cells, and X-ray crystallography analyses with the TyH analogue Tyrp1, provide conclusive evidence of the interactions of phenylalanine derivatives with human tyrosinase. In particular, our findings indicate that an analogue of L-DOPA, namely (S)-3-amino-tyrosine, stands out as an amino phenol derivative with inhibitory properties against TyH.
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Affiliation(s)
- Clarisse Faure
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Yi Min Ng
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Catherine Belle
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Lyna Khettabi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Mélissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 38053, Grenoble, France
| | - Nathalie Berthet
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Marc Maresca
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France)
| | - Christian Philouze
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
| | - Walid Rachidi
- IRIG-BGE U1038, INSERM, Univ. Grenoble Alpes, Biomics, 38054, Grenoble, France
| | - Marius Réglier
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France)
| | | | - Hélène Jamet
- Université Grenoble Alpes, CNRS, Department of Molecular Chemistry (DCM, UMR 5250), 38058, Grenoble Cedex 9, France
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3
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Lange RW, Bloch K, Heindl MR, Wollenhaupt J, Weiss MS, Brandstetter H, Klebe G, Falcone FH, Böttcher-Friebertshäuser E, Dahms SO, Steinmetzer T. Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors. ChemMedChem 2024; 19:e202400057. [PMID: 38385828 DOI: 10.1002/cmdc.202400057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
A 1H-isoindol-3-amine was identified as suitable P1 group for the proprotein convertase furin using a crystallographic screening with a set of 20 fragments known to occupy the S1 pocket of trypsin-like serine proteases. Its binding mode is very similar to that observed for the P1 group of benzamidine-derived peptidic furin inhibitors suggesting an aminomethyl substitution of this fragment to obtain a couplable P1 residue for the synthesis of substrate-analogue furin inhibitors. The obtained inhibitors possess a slightly improved picomolar inhibitory potency compared to their benzamidine-derived analogues. The crystal structures of two inhibitors in complex with furin revealed that the new P1 group is perfectly suited for incorporation in peptidic furin inhibitors. Selected inhibitors were tested for antiviral activity against respiratory syncytial virus (RSV) and a furin-dependent influenza A virus (SC35M/H7N7) in A549 human lung cells and demonstrated an efficient inhibition of virus activation and replication at low micromolar or even submicromolar concentrations. First results suggest that the Mas-related G-protein coupled receptor GPCR-X2 could be a potential off-target for certain benzamidine-derived furin inhibitors.
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Affiliation(s)
- Roman W Lange
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
| | - Konstantin Bloch
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, Marburg, Germany
| | - Miriam Ruth Heindl
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, 12489, Berlin, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, 12489, Berlin, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, A-5020, Salzburg, Austria Phone
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
| | - Franco H Falcone
- Institute of Parasitology, BFS, Justus Liebig University, 35392, Giessen, Germany
| | | | - Sven O Dahms
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, A-5020, Salzburg, Austria Phone
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6-10, D-35032, Marburg, Germany Phone
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4
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Vilela-Alves G, Rebelo Manuel R, Pedrosa N, Cardoso Pereira IA, Romão MJ, Mota C. Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2024; 80:98-106. [PMID: 38699971 PMCID: PMC11134731 DOI: 10.1107/s2053230x24003911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation.
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Affiliation(s)
- Guilherme Vilela-Alves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Maria João Romão
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cristiano Mota
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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5
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Petit-Hartlein I, Vermot A, Thepaut M, Humm AS, Dupeux F, Dupuy J, Chaptal V, Marquez JA, Smith SME, Fieschi F. X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX. eLife 2024; 13:RP93759. [PMID: 38640072 PMCID: PMC11031084 DOI: 10.7554/elife.93759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024] Open
Abstract
NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2's requirement for activation.
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Affiliation(s)
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | - Michel Thepaut
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | | | - Florine Dupeux
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
- European Molecular Biology LaboratoryGrenobleFrance
| | - Jerome Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
| | | | | | - Susan ME Smith
- Department of Molecular and Cellular Biology, Kennesaw State UniversityKennesawUnited States
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie StructuraleGrenobleFrance
- Institut Universitaire de FranceParisFrance
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6
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Nishio S, Emori C, Wiseman B, Fahrenkamp D, Dioguardi E, Zamora-Caballero S, Bokhove M, Han L, Stsiapanava A, Algarra B, Lu Y, Kodani M, Bainbridge RE, Komondor KM, Carlson AE, Landreh M, de Sanctis D, Yasumasu S, Ikawa M, Jovine L. ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat. Cell 2024; 187:1440-1459.e24. [PMID: 38490181 DOI: 10.1016/j.cell.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/07/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
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Affiliation(s)
- Shunsuke Nishio
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Benjamin Wiseman
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisa Dioguardi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Marcel Bokhove
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Alena Stsiapanava
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Blanca Algarra
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Yonggang Lu
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Mayo Kodani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Rachel E Bainbridge
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kayla M Komondor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne E Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | | | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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7
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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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8
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Yuzugullu Karakus Y, Goc G, Zengin Karatas M, Balci Unver S, Yorke BA, Pearson AR. Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase. Acta Crystallogr D Struct Biol 2024; 80:101-112. [PMID: 38265876 PMCID: PMC10836395 DOI: 10.1107/s2059798323011063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Catalase is an antioxidant enzyme that breaks down hydrogen peroxide (H2O2) into molecular oxygen and water. In all monofunctional catalases the pathway that H2O2 takes to the catalytic centre is via the `main channel'. However, the structure of this channel differs in large-subunit and small-subunit catalases. In large-subunit catalases the channel is 15 Å longer and consists of two distinct parts, including a hydrophobic lower region near the heme and a hydrophilic upper region where multiple H2O2 routes are possible. Conserved glutamic acid and threonine residues are located near the intersection of these two regions. Mutations of these two residues in the Scytalidium thermophilum catalase had no significant effect on catalase activity. However, the secondary phenol oxidase activity was markedly altered, with kcat and kcat/Km values that were significantly increased in the five variants E484A, E484I, T188D, T188I and T188F. These variants also showed a lower affinity for inhibitors of oxidase activity than the wild-type enzyme and a higher affinity for phenolic substrates. Oxidation of heme b to heme d did not occur in most of the studied variants. Structural changes in solvent-chain integrity and channel architecture were also observed. In summary, modification of the main-channel gate glutamic acid and threonine residues has a greater influence on the secondary activity of the catalase enzyme, and the oxidation of heme b to heme d is predominantly inhibited by their conversion to aliphatic and aromatic residues.
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Affiliation(s)
| | - Gunce Goc
- Department of Biology, Kocaeli University, Kabaoglu, Kocaeli, Izmit 41001, Türkiye
| | - Melis Zengin Karatas
- Department of Biology, Kocaeli University, Kabaoglu, Kocaeli, Izmit 41001, Türkiye
| | - Sinem Balci Unver
- Department of Biology, Kocaeli University, Kabaoglu, Kocaeli, Izmit 41001, Türkiye
| | - Briony A. Yorke
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Arwen R. Pearson
- The Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, HARBOR, Universitat Hamburg, 22761 Hamburg, Germany
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9
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Tamhaev R, Grosjean E, Ahamed H, Chebaiki M, Rodriguez F, Recchia D, Degiacomi G, Pasca MR, Maveyraud L, Mourey L, Lherbet C. Exploring the plasticity of the InhA substrate-binding site using new diaryl ether inhibitors. Bioorg Chem 2024; 143:107032. [PMID: 38128204 DOI: 10.1016/j.bioorg.2023.107032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a worldwide scourge with more than 10 million people affected yearly. Among the proteins essential for the survival of Mtb, InhA has been and is still clinically validated as a therapeutic target. A new family of direct diaryl ether inhibitors, not requiring prior activation by the catalase peroxidase enzyme KatG, has been designed with the ambition of fully occupying the InhA substrate-binding site. Thus, eleven compounds, featuring three pharmacophores within the same molecule, were synthesized. One of them, 5-(((4-(2-hydroxyphenoxy)benzyl)(octyl)amino)methyl)-2-phenoxyphenol (compound 21), showed good inhibitory activity against InhA with IC50 of 0.70 µM. The crystal structure of compound 21 in complex with InhA/NAD+ showed how the molecule fills the substrate-binding site as well as the minor portal of InhA. This study represents a further step towards the design of new inhibitors of InhA.
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Affiliation(s)
- Rasoul Tamhaev
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Emeline Grosjean
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Hikmat Ahamed
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Mélina Chebaiki
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Frédéric Rodriguez
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Deborah Recchia
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
| | - Christian Lherbet
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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10
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Seveso A, Mazurkewich S, Banerjee S, Poulsen JCN, Lo Leggio L, Larsbrink J. Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds. Appl Environ Microbiol 2024; 90:e0176823. [PMID: 38179933 PMCID: PMC10807430 DOI: 10.1128/aem.01768-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Lignocellulose is a renewable but complex material exhibiting high recalcitrance to enzymatic hydrolysis, which is attributed, in part, to the presence of covalent linkages between lignin and polysaccharides in the plant cell wall. Glucuronoyl esterases from carbohydrate esterase family 15 (CE15) have been proposed as an aid in reducing this recalcitrance by cleaving ester bonds found between lignin and glucuronoxylan. In the Bacteroidota phylum, some species organize genes related to carbohydrate metabolism in polysaccharide utilization loci (PULs) which encode all necessary proteins to bind, deconstruct, and respond to a target glycan. Bioinformatic analyses identified CE15 members in some PULs that appear to not target the expected glucuronoxylan. Here, five CE15 members from such PULs were investigated with the aim of gaining insights on their biological roles. The selected targets were characterized using glucuronoyl esterase model substrates and with a new synthetic molecule mimicking a putative ester linkage between pectin and lignin. The CE15 enzyme from Phocaeicola vulgatus was structurally determined by X-ray crystallography both with and without carbohydrate ligands with galacturonate binding in a distinct conformation than that of glucuronate. We further explored whether these CE15 enzymes could act akin to pectin methylesterases on pectin-rich biomass but did not find evidence to support the proposed activity. Based on the evidence gathered, the CE15 enzymes in the PULs expected to degrade pectin could be involved in cleavage of uronic acid esters in rhamnogalacturonans.IMPORTANCEThe plant cell wall is a highly complex matrix, and while most of its polymers interact non-covalently, there are also covalent bonds between lignin and carbohydrates. Bonds between xylan and lignin are known, such as the glucuronoyl ester bonds that are cleavable by CE15 enzymes. Our work here indicates that enzymes from CE15 may also have other activities, as we have discovered enzymes in PULs proposed to target other polysaccharides, including pectin. Our study represents the first investigation of such enzymes. Our first hypothesis that the enzymes would act as pectin methylesterases was shown to be false, and we instead propose that they may cleave other esters on complex pectins such as rhamnogalacturonan II. The work presents both the characterization of five novel enzymes and can also provide indirect information about the components of the cell wall itself, which is a highly challenging material to chemically analyze in fine detail.
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Affiliation(s)
- Andrea Seveso
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Sanchari Banerjee
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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11
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Eymery MC, Nguyen KA, Basu S, Hausmann J, Tran-Nguyen VK, Seidel HP, Gutierrez L, Boumendjel A, McCarthy AA. Discovery of potent chromone-based autotaxin inhibitors inspired by cannabinoids. Eur J Med Chem 2024; 263:115944. [PMID: 37976710 DOI: 10.1016/j.ejmech.2023.115944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Autotaxin (ATX) is an enzyme primarily known for the production of lysophosphatidic acid. Being involved in the development of major human diseases, such as cancer and neurodegenerative diseases, the enzyme has been featured in multiple studies as a pharmacological target. We previously found that the cannabinoid tetrahydrocannabinol (THC) could bind and act as an excellent inhibitor of ATX. This study aims to use the cannabinoid scaffold as a starting point to find cannabinoid-unrelated ATX inhibitors, following a funnel down approach in which large chemical libraries sharing chemical similarities with THC were screened to identify lead scaffold types for optimization. This approach allowed us to identify compounds bearing chromone and indole scaffolds as promising ATX inhibitors. Further optimization led to MEY-003, which is characterized by the direct linkage of an N-pentyl indole to the 5,7-dihydroxychromone moiety. This molecule has potent inhibitory activity towards ATX-β and ATX-ɣ as evidenced by enzymatic studies and its mode of action was rationalized by structural biology studies using macromolecular X-ray crystallography.
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Affiliation(s)
- Mathias Christophe Eymery
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France; Univ. Grenoble Alpes, INSERM U1039, LRB, 38000, Grenoble, France
| | - Kim-Anh Nguyen
- Univ. Grenoble Alpes, INSERM U1039, LRB, 38000, Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Jens Hausmann
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Viet-Khoa Tran-Nguyen
- Unité de Biologie Fonctionnelle et Adaptative (BFA), Université Paris Cité, 75013, Paris, France
| | - Hans Peter Seidel
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Lola Gutierrez
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | | | - Andrew Aloysius McCarthy
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
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12
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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13
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Taborda A, Frazão T, Rodrigues MV, Fernández-Luengo X, Sancho F, Lucas MF, Frazão C, Melo EP, Ventura MR, Masgrau L, Borges PT, Martins LO. Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms. Nat Commun 2023; 14:7289. [PMID: 37963862 PMCID: PMC10646112 DOI: 10.1038/s41467-023-42000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
C-glycosides are natural products with important biological activities but are recalcitrant to degradation. Glycoside 3-oxidases (G3Oxs) are recently identified bacterial flavo-oxidases from the glucose-methanol-coline (GMC) superfamily that catalyze the oxidation of C-glycosides with the concomitant reduction of O2 to H2O2. This oxidation is followed by C-C acid/base-assisted bond cleavage in two-step C-deglycosylation pathways. Soil and gut microorganisms have different oxidative enzymes, but the details of their catalytic mechanisms are largely unknown. Here, we report that PsG3Ox oxidizes at 50,000-fold higher specificity (kcat/Km) the glucose moiety of mangiferin to 3-keto-mangiferin than free D-glucose to 2-keto-glucose. Analysis of PsG3Ox X-ray crystal structures and PsG3Ox in complex with glucose and mangiferin, combined with mutagenesis and molecular dynamics simulations, reveal distinctive features in the topology surrounding the active site that favor catalytically competent conformational states suitable for recognition, stabilization, and oxidation of the glucose moiety of mangiferin. Furthermore, their distinction to pyranose 2-oxidases (P2Oxs) involved in wood decay and recycling is discussed from an evolutionary, structural, and functional viewpoint.
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Grants
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Fundação para a Ciência e Tecnologia, Portugal, grants 2022.02027.PTDC, UIDB/04612/2020 and UIDP/04612/2020, LA/P/0087/2020, PTDC/BII-BBF/29564/2017, and AAC 01/SAICT/2016 Fundação para a Ciência e Tecnologia, Portugal, Ph.D. fellowships 2020.07928, 2022.13872, and 2022.09426 Ministry of Science and Innovation, Spain, grant PID2021-126897NB-I00 and fellowship PRE2019-088412, funded by the MCIN/AEI/10.13039/501100011033/ FEDER, EU
- Fundação para a Ciência e Tecnologia (FCT), Portugal, grants UIDB/04326/2020, UIDP/043226/2020 and LA/P/0101/2020
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Affiliation(s)
- André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Tomás Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Miguel V Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | | | - Ferran Sancho
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | | | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Eduardo P Melo
- Centro de Ciências do Mar, Universidade do Algarve, 8005-139, Faro, Portugal
| | - M Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Laura Masgrau
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
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14
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Cao Y, Kümmel F, Logemann E, Gebauer JM, Lawson AW, Yu D, Uthoff M, Keller B, Jirschitzka J, Baumann U, Tsuda K, Chai J, Schulze-Lefert P. Structural polymorphisms within a common powdery mildew effector scaffold as a driver of coevolution with cereal immune receptors. Proc Natl Acad Sci U S A 2023; 120:e2307604120. [PMID: 37523523 PMCID: PMC10410722 DOI: 10.1073/pnas.2307604120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
In plants, host-pathogen coevolution often manifests in reciprocal, adaptive genetic changes through variations in host nucleotide-binding leucine-rich repeat immune receptors (NLRs) and virulence-promoting pathogen effectors. In grass powdery mildew (PM) fungi, an extreme expansion of a RNase-like effector family, termed RALPH, dominates the effector repertoire, with some members recognized as avirulence (AVR) effectors by cereal NLR receptors. We report the structures of the sequence-unrelated barley PM effectors AVRA6, AVRA7, and allelic AVRA10/AVRA22 variants, which are detected by highly sequence-related barley NLRs MLA6, MLA7, MLA10, and MLA22 and of wheat PM AVRPM2 detected by the unrelated wheat NLR PM2. The AVR effectors adopt a common scaffold, which is shared with the RNase T1/F1 family. We found striking variations in the number, position, and length of individual structural elements between RALPH AVRs, which is associated with a differentiation of RALPH effector subfamilies. We show that all RALPH AVRs tested have lost nuclease and synthetase activities of the RNase T1/F1 family and lack significant binding to RNA, implying that their virulence activities are associated with neo-functionalization events. Structure-guided mutagenesis identified six AVRA6 residues that are sufficient to turn a sequence-diverged member of the same RALPH subfamily into an effector specifically detected by MLA6. Similar structure-guided information for AVRA10 and AVRA22 indicates that MLA receptors detect largely distinct effector surface patches. Thus, coupling of sequence and structural polymorphisms within the RALPH scaffold of PMs facilitated escape from NLR recognition and potential acquisition of diverse virulence functions.
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Affiliation(s)
- Yu Cao
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Florian Kümmel
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Elke Logemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Jan M. Gebauer
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Aaron W. Lawson
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Dongli Yu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Matthias Uthoff
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich8008, Switzerland
| | - Jan Jirschitzka
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Jijie Chai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou310024, China
- Beijing Frontier Research Center for Biological Structure, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
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15
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Moussaoui D, Robblee JP, Robert-Paganin J, Auguin D, Fisher F, Fagnant PM, Macfarlane JE, Schaletzky J, Wehri E, Mueller-Dieckmann C, Baum J, Trybus KM, Houdusse A. Mechanism of small molecule inhibition of Plasmodium falciparum myosin A informs antimalarial drug design. Nat Commun 2023; 14:3463. [PMID: 37308472 PMCID: PMC10261046 DOI: 10.1038/s41467-023-38976-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Malaria results in more than 500,000 deaths per year and the causative Plasmodium parasites continue to develop resistance to all known agents, including different antimalarial combinations. The class XIV myosin motor PfMyoA is part of a core macromolecular complex called the glideosome, essential for Plasmodium parasite mobility and therefore an attractive drug target. Here, we characterize the interaction of a small molecule (KNX-002) with PfMyoA. KNX-002 inhibits PfMyoA ATPase activity in vitro and blocks asexual blood stage growth of merozoites, one of three motile Plasmodium life-cycle stages. Combining biochemical assays and X-ray crystallography, we demonstrate that KNX-002 inhibits PfMyoA using a previously undescribed binding mode, sequestering it in a post-rigor state detached from actin. KNX-002 binding prevents efficient ATP hydrolysis and priming of the lever arm, thus inhibiting motor activity. This small-molecule inhibitor of PfMyoA paves the way for the development of alternative antimalarial treatments.
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Affiliation(s)
- Dihia Moussaoui
- Structural Motility, Institut Curie, Université Paris Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248, Paris, France
- Structural Biology group, European Synchrotron Radiation Facility (ESRF), 71, Avenue des Martyrs, 38000, Grenoble, France
| | - James P Robblee
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT, USA
| | - Julien Robert-Paganin
- Structural Motility, Institut Curie, Université Paris Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248, Paris, France
| | - Daniel Auguin
- Structural Motility, Institut Curie, Université Paris Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248, Paris, France
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, INRAE, USC1328, Orléans, France
| | - Fabio Fisher
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Patricia M Fagnant
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT, USA
| | - Jill E Macfarlane
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT, USA
| | - Julia Schaletzky
- Center for Emerging and Neglected Diseases, Drug Discovery Center, Berkeley, CA, USA
| | - Eddie Wehri
- Center for Emerging and Neglected Diseases, Drug Discovery Center, Berkeley, CA, USA
| | - Christoph Mueller-Dieckmann
- Structural Biology group, European Synchrotron Radiation Facility (ESRF), 71, Avenue des Martyrs, 38000, Grenoble, France
| | - Jake Baum
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK
- School of Medical Sciences, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Kathleen M Trybus
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT, USA.
| | - Anne Houdusse
- Structural Motility, Institut Curie, Université Paris Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248, Paris, France.
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16
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Elchennawi I, Carpentier P, Caux C, Ponge M, Ollagnier de Choudens S. Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex. Biomolecules 2023; 13:biom13050732. [PMID: 37238602 DOI: 10.3390/biom13050732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464(sufS) and Rv1465(sufU). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents.
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Affiliation(s)
- Ingie Elchennawi
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Philippe Carpentier
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Christelle Caux
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Marine Ponge
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
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17
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Gadella TWJ, van Weeren L, Stouthamer J, Hink MA, Wolters AHG, Giepmans BNG, Aumonier S, Dupuy J, Royant A. mScarlet3: a brilliant and fast-maturing red fluorescent protein. Nat Methods 2023; 20:541-545. [PMID: 36973546 DOI: 10.1038/s41592-023-01809-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/27/2023] [Indexed: 03/29/2023]
Abstract
We report the evolution of mScarlet3, a cysteine-free monomeric red fluorescent protein with fast and complete maturation, as well as record brightness, quantum yield (75%) and fluorescence lifetime (4.0 ns). The mScarlet3 crystal structure reveals a barrel rigidified at one of its heads by a large hydrophobic patch of internal residues. mScarlet3 behaves well as a fusion tag, displays no apparent cytotoxicity and it surpasses existing red fluorescent proteins as a Förster resonance energy transfer acceptor and as a reporter in transient expression systems.
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Affiliation(s)
- Theodorus W J Gadella
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Laura van Weeren
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Jente Stouthamer
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark A Hink
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Anouk H G Wolters
- Biomedical Sciences of Cells & Systems, University of Groningen UMC Groningen, Groningen, the Netherlands
| | - Ben N G Giepmans
- Biomedical Sciences of Cells & Systems, University of Groningen UMC Groningen, Groningen, the Netherlands
| | - Sylvain Aumonier
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Jérôme Dupuy
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France
- European Synchrotron Radiation Facility, Grenoble, France
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18
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Jing L, Wei W, Meng B, Chantegreil F, Nachon F, Martínez A, Wu G, Zhao H, Song Y, Kang D, Brazzolotto X, Zhan P, Liu X. Rapid discovery and crystallography study of highly potent and selective butylcholinesterase inhibitors based on oxime-containing libraries and conformational restriction strategies. Bioorg Chem 2023; 134:106465. [PMID: 36933339 DOI: 10.1016/j.bioorg.2023.106465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
Butyrylcholinesterase is regarded as a promising drug target in advanced Alzheimer's disease. In order to identify highly selective and potent BuChE inhibitors, a 53-membered compound library was constructed via the oxime-based tethering approach based on microscale synthesis. Although A2Q17 and A3Q12 exhibited higher BuChE selectivity versus acetylcholinesterase, the inhibitory activities were unsatisfactory and A3Q12 did not inhibit Aβ1-42 peptide self-induced aggregation. With A2Q17 and A3Q12 as leads, a novel series of tacrine derivatives with nitrogen-containing heterocycles were designed based on conformation restriction strategy. The results demonstrated that 39 (IC50 = 3.49 nM) and 43 (IC50 = 7.44 nM) yielded much improved hBuChE inhibitory activity compared to the lead A3Q12 (IC50 = 63 nM). Besides, the selectivity indexes (SI = AChE IC50 / BChE IC50) of 39 (SI = 33) and 43 (SI = 20) were also higher than A3Q12 (SI = 14). The results of the kinetic study showed that 39 and 43 exhibited a mixed-type inhibition against eqBuChE with respective Ki values of 1.715 nM and 0.781 nM. And 39 and 43 could inhibit Aβ1-42 peptide self-induced aggregation into fibril. X-ray crystallography structures of 39 or 43 complexes with BuChE revealed the molecular basis for their high potency. Thus, 39 and 43 are deserve for further study to develop potential drug candidates for the treatment of Alzheimer's disease.
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Affiliation(s)
- Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Wenxiu Wei
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Bairu Meng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Fabien Chantegreil
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place du Général Valérie André, 91220, Brétigny-sur-Orge, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place du Général Valérie André, 91220, Brétigny-sur-Orge, France
| | - Ana Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China
| | - Huajun Zhao
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Ji'nan, Shandong, PR China.
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
| | - Xavier Brazzolotto
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place du Général Valérie André, 91220, Brétigny-sur-Orge, France.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong, PR China.
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19
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Vilela-Alves G, Manuel RR, Oliveira AR, Pereira IC, Romão MJ, Mota C. Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci 2022; 24:ijms24010476. [PMID: 36613918 PMCID: PMC9820355 DOI: 10.3390/ijms24010476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO2 to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies.
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Affiliation(s)
- Guilherme Vilela-Alves
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Inês Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria João Romão
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Correspondence:
| | - Cristiano Mota
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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20
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Gijsbers A, Eymery M, Gao Y, Menart I, Vinciauskaite V, Siliqi D, Peters PJ, McCarthy A, Ravelli RBG. The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in Mycobacterium tuberculosis. J Biol Chem 2022; 299:102761. [PMID: 36463964 PMCID: PMC9811218 DOI: 10.1016/j.jbc.2022.102761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Pathogenic species from the Mycobacterium genus are responsible for a number of adverse health conditions in humans and animals that threaten health security and the economy worldwide. Mycobacteria have up to five specialized secretion systems (ESX-1 to ESX-5) that transport virulence factors across their complex cell envelope to facilitate manipulation of their environment. In pathogenic species, these virulence factors influence the immune system's response and are responsible for membrane disruption and contributing to cell death. While structural details of these secretion systems have been recently described, gaps still remain in the structural understanding of the secretion mechanisms of most substrates. Here, we describe the crystal structure of Mycobacterium tuberculosis ESX-1 secretion-associated substrate EspB bound to its chaperone EspK. We found that EspB interacts with the C-terminal domain of EspK through its helical tip. Furthermore, cryogenic electron microscopy, size exclusion chromatography analysis, and small-angle X-ray scattering experiments show that EspK keeps EspB in its secretion-competent monomeric form and prevents its oligomerization. The structure presented in this study suggests an additional secretion mechanism in ESX-1, analogous to the chaperoning of proline-glutamate (PE)-proline-proline-glutamate (PPE) proteins by EspG, where EspK facilitates the secretion of EspB in Mycobacterium species.
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Affiliation(s)
- Abril Gijsbers
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | | | - Ye Gao
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Isabella Menart
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Vanesa Vinciauskaite
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | | | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Molecular Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands.
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21
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Minazzato G, Gasparrini M, Heroux A, Sernova NV, Rodionov DA, Cianci M, Sorci L, Raffaelli N. Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis. J Struct Biol 2022; 214:107917. [PMID: 36332744 DOI: 10.1016/j.jsb.2022.107917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/13/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Nicotinamide-adenine dinucleotide (NAD) is centrally important to metabolic reactions that involve redox chemistry. In bacteria, NAD biosynthesis is controlled by different transcription factors, depending on the species. Among the four regulators identified so far, the protein NadQ is reported to act as a repressor of the de novo NAD biosynthetic pathway in proteobacteria. Using comparative genomics, a systematic reconstruction of NadQ regulons in thousands of fully sequenced bacterial genomes has been performed, confirming that NadQ is present in α-proteobacteria and some β- and γ-proteobacteria, including pathogens like Bordetella pertussis and Neisseria meningitidis, where it likely controls de novo NAD biosynthesis. Through mobility shift assay and mutagenesis, the DNA binding activity of NadQ from Agrobacterium tumefaciens was experimentally validated and determined to be suppressed by ATP. The crystal structures of NadQ in native form and in complex with ATP were determined, indicating that NadQ is a dimer, with each monomer composed of an N-terminal Nudix domain hosting the effector binding site and a C-terminal winged helix-turn-helix domain that binds DNA. Within the dimer, we found one ATP molecule bound, at saturating concentration of the ligand, in keeping with an intrinsic asymmetry of the quaternary structure. Overall, this study provided the basis for depicting a working model of NadQ regulation mechanism.
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Affiliation(s)
- Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Annie Heroux
- Elettra - Sincrotrone Trieste S.C.P.A., Basovizza, Italy
| | - Natalia V Sernova
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Materials, Environmental Sciences and Urban Planning, Division of Bioinformatics and Biochemistry, Polytechnic University of Marche, Ancona, Italy.
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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22
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Ferrario E, Miggiano R, Rizzi M, Ferraris DM. The integration of AlphaFold-predicted and crystal structures of human trans-3-hydroxy-l-proline dehydratase reveals a regulatory catalytic mechanism. Comput Struct Biotechnol J 2022; 20:3874-3883. [PMID: 35891782 PMCID: PMC9309405 DOI: 10.1016/j.csbj.2022.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Computational methods for protein structure prediction have made significant strides forward, as evidenced by the last development of the neural network AlphaFold, which outperformed the CASP14 competitors by consistently predicting the structure of target proteins. Here we show an integrated structural investigation that combines the AlphaFold and crystal structures of human trans-3-Hydroxy-l-proline dehydratase, an enzyme involved in hydroxyproline catabolism and whose structure had never been reported before, identifying a structural element, absent in the AlphaFold model but present in the crystal structure, that was subsequently proved to be functionally relevant. Although the AlphaFold model lacked information on protein oligomerization, the native dimer was reconstructed using template-based and ab initio computational approaches. Moreover, molecular phasing of the diffraction data using the AlphaFold model resulted in dimer reconstruction and straightforward structure solution. Our work adds to the integration of AlphaFold with experimental structural and functional data for protein analysis, crystallographic phasing and structure solution.
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Affiliation(s)
- Eugenio Ferrario
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
| | - Riccardo Miggiano
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
- IXTAL srl, Via Bovio 6, 28100 Novara, Italy
| | - Menico Rizzi
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
| | - Davide M. Ferraris
- University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy
- IXTAL srl, Via Bovio 6, 28100 Novara, Italy
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23
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Okumura H, Sakai N, Murakami H, Mizuno N, Nakamura Y, Ueno G, Masunaga T, Kawamura T, Baba S, Hasegawa K, Yamamoto M, Kumasaka T. In situ crystal data-collection and ligand-screening system at SPring-8. Acta Crystallogr F Struct Biol Commun 2022; 78:241-251. [PMID: 35647681 PMCID: PMC9158660 DOI: 10.1107/s2053230x22005283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
An in situ X-ray diffraction measurement system using a crystallization plate has been constructed at the SPring-8 protein crystallography beamline. Utilizing small-wedge measurements and incorporating a liquid dispenser to prepare protein–ligand complex crystals, this system will make ligand screening possible. In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein–ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser.
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24
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Structural insights into the mechanism of archaellar rotational switching. Nat Commun 2022; 13:2857. [PMID: 35606361 PMCID: PMC9126983 DOI: 10.1038/s41467-022-30358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Signal transduction via phosphorylated CheY towards the flagellum and the archaellum involves a conserved mechanism of CheY phosphorylation and subsequent conformational changes within CheY. This mechanism is conserved among bacteria and archaea, despite substantial differences in the composition and architecture of archaellum and flagellum, respectively. Phosphorylated CheY has higher affinity towards the bacterial C-ring and its binding leads to conformational changes in the flagellar motor and subsequent rotational switching of the flagellum. In archaea, the adaptor protein CheF resides at the cytoplasmic face of the archaeal C-ring formed by the proteins ArlCDE and interacts with phosphorylated CheY. While the mechanism of CheY binding to the C-ring is well-studied in bacteria, the role of CheF in archaea remains enigmatic and mechanistic insights are absent. Here, we have determined the atomic structures of CheF alone and in complex with activated CheY by X-ray crystallography. CheF forms an elongated dimer with a twisted architecture. We show that CheY binds to the C-terminal tail domain of CheF leading to slight conformational changes within CheF. Our structural, biochemical and genetic analyses reveal the mechanistic basis for CheY binding to CheF and allow us to propose a model for rotational switching of the archaellum. Signal transduction via phosphorylated CheY is conserved in bacteria and archaea. In this study, the authors employ structural biochemistry combined with cell biology to delineate the mechanism of CheY recognition by the adaptor protein CheF.
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25
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Stsiapanava A, Xu C, Nishio S, Han L, Yamakawa N, Carroni M, Tunyasuvunakool K, Jumper J, de Sanctis D, Wu B, Jovine L. Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH. Nat Struct Mol Biol 2022; 29:190-193. [PMID: 35273390 PMCID: PMC8930769 DOI: 10.1038/s41594-022-00729-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/21/2022] [Indexed: 12/25/2022]
Abstract
Glycoprotein 2 (GP2) and uromodulin (UMOD) filaments protect against gastrointestinal and urinary tract infections by acting as decoys for bacterial fimbrial lectin FimH. By combining AlphaFold2 predictions with X-ray crystallography and cryo-EM, we show that these proteins contain a bipartite decoy module whose new fold presents the high-mannose glycan recognized by FimH. The structure rationalizes UMOD mutations associated with kidney diseases and visualizes a key epitope implicated in cast nephropathy. AlphaFold2 predictions, X-ray crystallography and cryo-EM analyses reveal how related human glycoproteins GP2 and uromodulin catch pathogenic bacteria by presenting a high-mannose glycan that acts as a decoy for fimbrial adhesin FimH.
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Affiliation(s)
- Alena Stsiapanava
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Chenrui Xu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Shunsuke Nishio
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nao Yamakawa
- US 41-UMS 2014-PLBS, Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | | | | | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. .,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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26
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Nanao M, Basu S, Zander U, Giraud T, Surr J, Guijarro M, Lentini M, Felisaz F, Sinoir J, Morawe C, Vivo A, Beteva A, Oscarsson M, Caserotto H, Dobias F, Flot D, Nurizzo D, Gigmes J, Foos N, Siebrecht R, Roth T, Theveneau P, Svensson O, Papp G, Lavault B, Cipriani F, Barrett R, Clavel C, Leonard G. ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:581-590. [PMID: 35254323 PMCID: PMC8900849 DOI: 10.1107/s1600577522000984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/28/2022] [Indexed: 05/30/2023]
Abstract
ID23-2 is a fixed-energy (14.2 keV) microfocus beamline at the European Synchrotron Radiation Facility (ESRF) dedicated to macromolecular crystallography. The optics and sample environment have recently been redesigned and rebuilt to take full advantage of the upgrade of the ESRF to the fourth generation Extremely Brilliant Source (ESRF-EBS). The upgraded beamline now makes use of two sets of compound refractive lenses and multilayer mirrors to obtain a highly intense (>1013 photons s-1) focused microbeam (minimum size 1.5 µm × 3 µm full width at half-maximum). The sample environment now includes a FLEX-HCD sample changer/storage system, as well as a state-of-the-art MD3Up high-precision multi-axis diffractometer. Automatic data reduction and analysis are also provided for more advanced protocols such as synchrotron serial crystallographic experiments.
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Affiliation(s)
- Max Nanao
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Franck Felisaz
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christian Morawe
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Amparo Vivo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Marcus Oscarsson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Jonathan Gigmes
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Nicolas Foos
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Thomas Roth
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gergely Papp
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | | | - Florent Cipriani
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ray Barrett
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Carole Clavel
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
| | - Gordon Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, F-38000 Grenoble, France
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27
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Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
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28
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Merlo R, Mattossovich R, Genta M, Valenti A, Di Mauro G, Minassi A, Miggiano R, Perugino G. First thermostable CLIP-tag by rational design applied to an archaeal O-alkyl-guanine-DNA-alkyl-transferase. Comput Struct Biotechnol J 2022; 20:5275-5286. [PMID: 36212535 PMCID: PMC9519396 DOI: 10.1016/j.csbj.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Self-labelling protein tags (SLPs) are resourceful tools that revolutionized sensor imaging, having the versatile ability of being genetically fused with any protein of interest and undergoing activation with alternative probes specifically designed for each variant (namely, SNAP-tag, CLIP-tag and Halo-tag). Commercially available SLPs are highly useful in studying molecular aspects of mesophilic organisms, while they fail in characterizing model organisms that thrive in harsh conditions. By applying an integrated computational and structural approach, we designed a engineered variant of the alkylguanine-DNA-alkyl-transferase (OGT) from the hyper-thermophilic archaeon Saccharolobus solfataricus (SsOGT), with no DNA-binding activity, able to covalently react with O6-benzyl-cytosine (BC-) derivatives, obtaining the first thermostable CLIP-tag, named SsOGT-MC8. The presented construct is able to recognize and to covalently bind BC- substrates with a marked specificity, displaying a very low activity on orthogonal benzyl-guanine (BG-) substrate and showing a remarkable thermal stability that broadens the applicability of SLPs. The rational mutagenesis that, starting from SsOGT, led to the production of SsOGT-MC8 was first evaluated by structural predictions to precisely design the chimeric construct, by mutating specific residues involved in protein stability and substrate recognition. The final construct was further validated by biochemical characterization and X-ray crystallography, allowing us to present here the first structural model of a CLIP-tag establishing the molecular determinants of its activity, as well as proposing a general approach for the rational engineering of any O6-alkylguanine-DNA-alkyl-transferase turning it into a SNAP- and a CLIP-tag variant.
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29
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Goodfellow BJ, Freire F, Carvalho AL, Aveiro SS, Charbonnier P, Moulis JM, Delgado L, Ferreira GC, Rodrigues JE, Poussin-Courmontagne P, Birck C, McEwen A, Macedo AL. The SOUL family of heme-binding proteins: Structure and function 15 years later. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992-4007.e10. [PMID: 34562373 DOI: 10.1016/j.molcel.2021.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 01/29/2023]
Abstract
ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Connolley
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Helge Feddersen
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | | | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Seán Murray
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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31
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Mota C, Diniz A, Coelho C, Santos-Silva T, Esmaeeli M, Leimkühler S, Cabrita EJ, Marcelo F, Romão MJ. Interrogating the Inhibition Mechanisms of Human Aldehyde Oxidase by X-ray Crystallography and NMR Spectroscopy: The Raloxifene Case. J Med Chem 2021; 64:13025-13037. [PMID: 34415167 DOI: 10.1021/acs.jmedchem.1c01125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery.
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Affiliation(s)
- Cristiano Mota
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Ana Diniz
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Catarina Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Teresa Santos-Silva
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Mariam Esmaeeli
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Eurico J Cabrita
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
| | - Maria João Romão
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal
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32
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Czyzewski A, Krawiec F, Brzezinski D, Porebski PJ, Minor W. Detecting anomalies in X-ray diffraction images using convolutional neural networks. EXPERT SYSTEMS WITH APPLICATIONS 2021; 174:114740. [PMID: 34366575 PMCID: PMC8341115 DOI: 10.1016/j.eswa.2021.114740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Our understanding of life is based upon the interpretation of macromolecular structures and their dynamics. Almost 90% of currently known macromolecular models originated from electron density maps constructed using X-ray diffraction images. Even though diffraction images are critical for structure determination, due to their vast amounts and noisy, non-intuitive nature, their quality is rarely inspected. In this paper, we use recent advances in machine learning to automatically detect seven types of anomalies in X-ray diffraction images. For this purpose, we utilize a novel X-ray beam center detection algorithm, propose three different image representations, and compare the predictive performance of general-purpose classifiers and deep convolutional neural networks (CNNs). In benchmark tests on a set of 6,311 X-ray diffraction images, the proposed CNN achieved between 87% and 99% accuracy depending on the type of anomaly. Experimental results show that the proposed anomaly detection system can be considered suitable for early detection of sub-optimal data collection conditions and malfunctions at X-ray experimental stations.
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Affiliation(s)
- Adam Czyzewski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Faustyna Krawiec
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Dariusz Brzezinski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Center for Biocrystallographic Research, Institute of
Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-714, Poland
- Center for Artificial Intelligence and Machine Learning,
Poznan University of Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Przemyslaw Jerzy Porebski
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
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33
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Lima GMA, Jagudin E, Talibov VO, Benz LS, Marullo C, Barthel T, Wollenhaupt J, Weiss MS, Mueller U. FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. Acta Crystallogr D Struct Biol 2021; 77:799-808. [PMID: 34076593 PMCID: PMC8171072 DOI: 10.1107/s2059798321003818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/08/2021] [Indexed: 01/13/2023] Open
Abstract
Crystallographic fragment screening (CFS) has become one of the major techniques for screening compounds in the early stages of drug-discovery projects. Following the advances in automation and throughput at modern macromolecular crystallography beamlines, the bottleneck for CFS has shifted from collecting data to organizing and handling the analysis of such projects. The complexity that emerges from the use of multiple methods for processing and refinement and to search for ligands requires an equally sophisticated solution to summarize the output, allowing researchers to focus on the scientific questions instead of on software technicalities. FragMAXapp is the fragment-screening project-management tool designed to handle CFS projects at MAX IV Laboratory. It benefits from the powerful computing infrastructure of large-scale facilities and, as a web application, it is accessible from everywhere.
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Affiliation(s)
| | - Elmir Jagudin
- BioMAX, MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | | | - Laila S. Benz
- Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | | | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
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34
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Salinas-Garcia MC, Plaza-Garrido M, Camara-Artigas A. The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain. Acta Crystallogr D Struct Biol 2021; 77:854-866. [PMID: 34076598 PMCID: PMC8171063 DOI: 10.1107/s2059798321004344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 03/26/2023] Open
Abstract
Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.
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Affiliation(s)
- M. Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
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35
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Goc G, Balci S, Yorke BA, Pearson AR, Yuzugullu Karakus Y. Probing the role of Val228 on the catalytic activity of Scytalidium catalase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140662. [PMID: 33887466 DOI: 10.1016/j.bbapap.2021.140662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022]
Abstract
Scytalidium catalase is a homotetramer including heme d in each subunit. Its primary function is the dismutation of H2O2 to water and oxygen, but it is also able to oxidase various small organic compounds including catechol and phenol. The crystal structure of Scytalidium catalase reveals the presence of three linked channels providing access to the exterior like other catalases reported so far. The function of these channels has been extensively studied, revealing the possible routes for substrate flow and product release. In this report, we have focussed on the semi-conserved residue Val228, located near to the vinyl groups of the heme at the opening of the lateral channel. Its replacement with Ala, Ser, Gly, Cys, Phe and Ile were tested. We observed a significant decrease in catalytic efficiency in all mutants with the exception of a remarkable increase in oxidase activity when Val228 was mutated to either Ala, Gly or Ser. The reduced catalytic efficiencies are characterized in terms of the restriction of hydrogen peroxide as electron acceptor in the active centre resulting from the opening of lateral channel inlet by introducing the smaller side chain residues. On the other hand, the increased oxidase activity is explained by allowing the suitable electron donor to approach more closely to the heme. The crystal structures of V228C and V228I were determined at 1.41 and 1.47 Å resolution, respectively. The lateral channels of the V228C and V228I presented a broadly identical chain of arranged waters to that observed for wild-type enzyme.
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Affiliation(s)
- Gunce Goc
- Department of Biology, Kocaeli University, Umuttepe, Kocaeli 41380, Turkey
| | - Sinem Balci
- Department of Biology, Kocaeli University, Umuttepe, Kocaeli 41380, Turkey
| | - Briony A Yorke
- School of Chemistry and Bioscience, Faculty of Life Sciences, University of Bradford, Bradford West Yorkshire BD7 1DP, UK
| | - Arwen R Pearson
- The Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, 22761, Germany
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36
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Xiao X, Willemse J, Voskamp P, Li X, Prota AE, Lamers M, Pannu N, Abrahams JP, van Wezel GP. Ectopic positioning of the cell division plane is associated with single amino acid substitutions in the FtsZ-recruiting SsgB in Streptomyces. Open Biol 2021; 11:200409. [PMID: 33622102 PMCID: PMC8061694 DOI: 10.1098/rsob.200409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In most bacteria, cell division begins with the polymerization of the GTPase FtsZ at mid-cell, which recruits the division machinery to initiate cell constriction. In the filamentous bacterium Streptomyces, cell division is positively controlled by SsgB, which recruits FtsZ to the future septum sites and promotes Z-ring formation. Here, we show that various amino acid (aa) substitutions in the highly conserved SsgB protein result in ectopically placed septa that sever spores diagonally or along the long axis, perpendicular to the division plane. Fluorescence microscopy revealed that between 3.3% and 9.8% of the spores of strains expressing SsgB E120 variants were severed ectopically. Biochemical analysis of SsgB variant E120G revealed that its interaction with FtsZ had been maintained. The crystal structure of Streptomyces coelicolor SsgB was resolved and the key residues were mapped on the structure. Notably, residue substitutions (V115G, G118V, E120G) that are associated with septum misplacement localize in the α2-α3 loop region that links the final helix and the rest of the protein. Structural analyses and molecular simulation revealed that these residues are essential for maintaining the proper angle of helix α3. Our data suggest that besides altering FtsZ, aa substitutions in the FtsZ-recruiting protein SsgB also lead to diagonally or longitudinally divided cells in Streptomyces.
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Affiliation(s)
- Xiansha Xiao
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300RA Leiden, The Netherlands
| | - Xinmeng Li
- LIC/Energy and Sustainability, Leiden University, PO Box 9502, 2300RA Leiden, The Netherlands
| | | | - Meindert Lamers
- Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Navraj Pannu
- Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300RA Leiden, The Netherlands
| | - Jan Pieter Abrahams
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands.,Paul Scherrer Institute, CH-5232 Villigen, Switzerland.,Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Gilles P van Wezel
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
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37
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van der Linden PJEM, Popov AM, Pontoni D. Accurate and rapid 3D printing of microfluidic devices using wavelength selection on a DLP printer. LAB ON A CHIP 2020; 20:4128-4140. [PMID: 33057528 DOI: 10.1039/d0lc00767f] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The use of microfluidics on synchrotron X-ray beamlines represents an advanced sample preparation and delivery platform for state-of-the-art X-ray characterization of micro-samples. The recent developments of 3D printing technologies have opened possibilities for rapid fabrication of complex microfluidic devices. One of the major challenges in 3D printing of microfluidic devices using a digital light processing (DLP) desktop printer is that the static liquid resin trapped in the channels, once the "ceiling" is printed, still receives small doses of light through the subsequently printed layers. This easily triggers partial polymerisation of the resin which impedes its flushing out of the channels after completion of the printing session. We show here that it is possible to gain better control over the resin polymerisation and improve the quality of the microfluidic devices by efficiently reducing the penetration depth of the UV LED light through wavelength selection combined with a careful choice of absorber and photo-initiator materials. We produced and tested several structures using a slightly modified desktop printer at 385 nm wavelength with 37 × 37 μm2 pixel resolution at a printed layer thickness of 25 μm. The structures include particle filters, mixers, droplet generators and droplet storage traps with features below 100 μm. We demonstrate crystallisation of model inorganic and organic compounds in trapped droplets and assess the feasibility of in-device X-ray diffraction experiments. This research opens the path for the use of 3D printed microfluidic devices on X-ray beamlines.
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Affiliation(s)
- Peter J E M van der Linden
- Partnership for Soft Condensed Matter (PSCM), ESRF - The European Synchrotron, 71 avenue des Martyrs, 38043 Grenoble, France.
| | - Anton M Popov
- ESRF- The European Synchrotron, 71 avenue des Martyrs, 38043 Grenoble, France
| | - Diego Pontoni
- Partnership for Soft Condensed Matter (PSCM), ESRF - The European Synchrotron, 71 avenue des Martyrs, 38043 Grenoble, France.
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38
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Membrane protein crystallography in the era of modern structural biology. Biochem Soc Trans 2020; 48:2505-2524. [DOI: 10.1042/bst20200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]
Abstract
The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.
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Münzker L, Petrick JK, Schleberger C, Clavel D, Cornaciu I, Wilcken R, Márquez JA, Klebe G, Marzinzik A, Jahnke W. Fragment-Based Discovery of Non-bisphosphonate Binders of Trypanosoma brucei Farnesyl Pyrophosphate Synthase. Chembiochem 2020; 21:3096-3111. [PMID: 32537808 DOI: 10.1002/cbic.202000246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/29/2020] [Indexed: 12/26/2022]
Abstract
Trypanosoma brucei is the causative agent of human African trypanosomiasis (HAT). Nitrogen-containing bisphosphonates, a current treatment for bone diseases, have been shown to block the growth of the T. brucei parasites by inhibiting farnesyl pyrophosphate synthase (FPPS); however, due to their poor pharmacokinetic properties, they are not well suited for antiparasitic therapy. Recently, an allosteric binding pocket was discovered on human FPPS, but its existence on trypanosomal FPPS was unclear. We applied NMR and X-ray fragment screening to T. brucei FPPS and report herein on four fragments bound to this previously unknown allosteric site. Surprisingly, non-bisphosphonate active-site binders were also identified. Moreover, fragment screening revealed a number of additional binding sites. In an early structure-activity relationship (SAR) study, an analogue of an active-site binder was unexpectedly shown to bind to the allosteric site. Overlaying identified fragment binders of a parallel T. cruzi FPPS fragment screen with the T. brucei FPPS structure, and medicinal chemistry optimisation based on two binders revealed another example of fragment "pocket hopping". The discovery of binders with new chemotypes sets the framework for developing advanced compounds with pharmacokinetic properties suitable for the treatment of parasitic infections by inhibition of FPPS in T. brucei parasites.
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Affiliation(s)
- Lena Münzker
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Joy Kristin Petrick
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Christian Schleberger
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Damien Clavel
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France
| | - Irina Cornaciu
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France.,ALPX, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France
| | - Rainer Wilcken
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - José A Márquez
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France.,ALPX, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France
| | - Gerhard Klebe
- Institut für Pharmazie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Marzinzik
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
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Lambert GG, Depernet H, Gotthard G, Schultz DT, Navizet I, Lambert T, Adams SR, Torreblanca-Zanca A, Chu M, Bindels DS, Levesque V, Nero Moffatt J, Salih A, Royant A, Shaner NC. Aequorea's secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing. PLoS Biol 2020; 18:e3000936. [PMID: 33137097 PMCID: PMC7660908 DOI: 10.1371/journal.pbio.3000936] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/12/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022] Open
Abstract
Using mRNA sequencing and de novo transcriptome assembly, we identified, cloned, and characterized 9 previously undiscovered fluorescent protein (FP) homologs from Aequorea victoria and a related Aequorea species, with most sequences highly divergent from A. victoria green fluorescent protein (avGFP). Among these FPs are the brightest green fluorescent protein (GFP) homolog yet characterized and a reversibly photochromic FP that responds to UV and blue light. Beyond green emitters, Aequorea species express purple- and blue-pigmented chromoproteins (CPs) with absorbances ranging from green to far-red, including 2 that are photoconvertible. X-ray crystallography revealed that Aequorea CPs contain a chemically novel chromophore with an unexpected crosslink to the main polypeptide chain. Because of the unique attributes of several of these newly discovered FPs, we expect that Aequorea will, once again, give rise to an entirely new generation of useful probes for bioimaging and biosensing.
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Affiliation(s)
- Gerard G. Lambert
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Hadrien Depernet
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Darrin T. Schultz
- University of California Santa Cruz, Santa Cruz, California, United States of America
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi-Echelle, Université Gustave Eiffel, Université Paris Est Creteil, Marne-la-Vallée, France
| | - Talley Lambert
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen R. Adams
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Albertina Torreblanca-Zanca
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Meihua Chu
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Daphne S. Bindels
- Nikon Imaging Center, University of California San Diego, La Jolla, California, United States of America
| | - Vincent Levesque
- Birch Aquarium at Scripps, La Jolla, California, United States of America
| | | | - Anya Salih
- Confocal Facility, Western Sydney University, Penrith, New South Wales, Australia
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Nathan C. Shaner
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
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Plaza-Garrido M, Salinas-Garcia MC, Alba-Elena D, Martínez JC, Camara-Artigas A. Lysozyme crystals dyed with bromophenol blue: where has the dye gone? ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:845-856. [PMID: 32876060 DOI: 10.1107/s2059798320008803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/30/2020] [Indexed: 11/10/2022]
Abstract
Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices α1 (residues 4-15) and α3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.
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Affiliation(s)
- Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - M Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Daniel Alba-Elena
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Jose C Martínez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
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Gavira JA, Rodriguez-Ruiz I, Martinez-Rodriguez S, Basu S, Teychené S, McCarthy AA, Mueller-Dieckman C. Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Acta Crystallogr D Struct Biol 2020; 76:751-758. [PMID: 32744257 DOI: 10.1107/s2059798320008475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Sample handling and manipulation for cryoprotection currently remain critical factors in X-ray structural determination. While several microchips for macromolecular crystallization have been proposed during the last two decades to partially overcome crystal-manipulation issues, increased background noise originating from the scattering of chip-fabrication materials has so far limited the attainable resolution of diffraction data. Here, the conception and use of low-cost, X-ray-transparent microchips for in situ crystallization and direct data collection, and structure determination at atomic resolution close to 1.0 Å, is presented. The chips are fabricated by a combination of either OSTEMER and Kapton or OSTEMER and Mylar materials for the implementation of counter-diffusion crystallization experiments. Both materials produce a sufficiently low scattering background to permit atomic resolution diffraction data collection at room temperature and the generation of 3D structural models of the tested model proteins lysozyme, thaumatin and glucose isomerase. Although the high symmetry of the three model protein crystals produced almost complete data sets at high resolution, the potential of in-line data merging and scaling of the multiple crystals grown along the microfluidic channels is also presented and discussed.
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Affiliation(s)
- Jose A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Spain
| | - Isaac Rodriguez-Ruiz
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INP, INSA, UPS Toulouse, Toulouse, France
| | - Sergio Martinez-Rodriguez
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Spain
| | - Shibom Basu
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Sébastien Teychené
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INP, INSA, UPS Toulouse, Toulouse, France
| | - Andrew A McCarthy
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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Martiel I, Buntschu D, Meier N, Gobbo A, Panepucci E, Schneider R, Heimgartner P, Müller D, Bühlmann K, Birri M, Kaminski JW, Leuenberger J, Oliéric V, Glettig W, Wang M. The TELL automatic sample changer for macromolecular crystallography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:860-863. [PMID: 32381791 PMCID: PMC7285676 DOI: 10.1107/s1600577520002416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
In this paper, the design and functionalities of the high-throughput TELL sample exchange system for macromolecular crystallography is presented. TELL was developed at the Paul Scherrer Institute with a focus on speed, storage capacity and reliability to serve the three macromolecular crystallography beamlines of the Swiss Light Source, as well as the SwissMX instrument at SwissFEL.
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Affiliation(s)
- Isabelle Martiel
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Dominik Buntschu
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Nathalie Meier
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Alexandre Gobbo
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Ezequiel Panepucci
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Roman Schneider
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Peter Heimgartner
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - David Müller
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Kevin Bühlmann
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Mario Birri
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Jakub W. Kaminski
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - James Leuenberger
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Vincent Oliéric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Wayne Glettig
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen, Switzerland
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von Stetten D, Carpentier P, Flot D, Beteva A, Caserotto H, Dobias F, Guijarro M, Giraud T, Lentini M, McSweeney S, Royant A, Petitdemange S, Sinoir J, Surr J, Svensson O, Theveneau P, Leonard GA, Mueller-Dieckmann C. ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:844-851. [PMID: 32381789 PMCID: PMC7206554 DOI: 10.1107/s1600577520004002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/20/2020] [Indexed: 05/05/2023]
Abstract
ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 1013 photons s-1), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.
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Affiliation(s)
- David von Stetten
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biosciences et Biotechnologies de Grenoble (BIG) – Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CNRS, CEA, 38000 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonia Beteva
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Hugo Caserotto
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matias Guijarro
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Mario Lentini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antoine Royant
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Jeremy Sinoir
- EMBL Outstation Grenoble, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - John Surr
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Pascal Theveneau
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
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Tarkowski ŁP, Tsirkone VG, Osipov EM, Beelen S, Lammens W, Vergauwen R, Van den Ende W, Strelkov SV. Crystal structure of Arabidopsis thaliana neutral invertase 2. Acta Crystallogr F Struct Biol Commun 2020; 76:152-157. [PMID: 32134001 PMCID: PMC7057345 DOI: 10.1107/s2053230x2000179x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/07/2020] [Indexed: 11/11/2022] Open
Abstract
The metabolism of sucrose is of crucial importance for life on Earth. In plants, enzymes called invertases split sucrose into glucose and fructose, contributing to the regulation of metabolic fluxes. Invertases differ in their localization and pH optimum. Acidic invertases present in plant cell walls and vacuoles belong to glycoside hydrolase family 32 (GH32) and have an all-β structure. In contrast, neutral invertases are located in the cytosol and organelles such as chloroplasts and mitochondria. These poorly understood enzymes are classified into a separate GH100 family. Recent crystal structures of the closely related neutral invertases InvA and InvB from the cyanobacterium Anabaena revealed a predominantly α-helical fold with unique features compared with other sucrose-metabolizing enzymes. Here, a neutral invertase (AtNIN2) from the model plant Arabidopsis thaliana was heterologously expressed, purified and crystallized. As a result, the first neutral invertase structure from a higher plant has been obtained at 3.4 Å resolution. The hexameric AtNIN2 structure is highly similar to that of InvA, pointing to high evolutionary conservation of neutral invertases.
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Affiliation(s)
- Łukasz P. Tarkowski
- Molecular Plant Biology Laboratory, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium
| | - Vicky G. Tsirkone
- Molecular Plant Biology Laboratory, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium
| | - Evgenii M. Osipov
- Molecular Plant Biology Laboratory, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium
| | - Steven Beelen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, O&N II, bus 822, 3000 Leuven, Belgium
| | - Willem Lammens
- Molecular Plant Biology Laboratory, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium
| | - Rudy Vergauwen
- Molecular Plant Biology Laboratory, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium
| | - Wim Van den Ende
- Molecular Plant Biology Laboratory, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, O&N II, bus 822, 3000 Leuven, Belgium
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46
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Oliveira AR, Mota C, Mourato C, Domingos RM, Santos MFA, Gesto D, Guigliarelli B, Santos-Silva T, Romão MJ, Cardoso Pereira IA. Toward the Mechanistic Understanding of Enzymatic CO2 Reduction. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00086] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Cristiano Mota
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cláudia Mourato
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Renato M. Domingos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Marino F. A. Santos
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Diana Gesto
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Bruno Guigliarelli
- Aix Marseille Université, CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Teresa Santos-Silva
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria João Romão
- UCIBIO, Applied Molecular Biosciences Unit, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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47
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Salinas-Garcia MC, Plaza-Garrido M, Alba-Elena D, Camara-Artigas A. Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content. Acta Crystallogr F Struct Biol Commun 2019; 75:687-696. [PMID: 31702582 PMCID: PMC6839823 DOI: 10.1107/s2053230x19013189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
A new crystal form of lysozyme with a very low solvent content (26.35%) has been obtained in the orthorhombic space group P212121 (with unit-cell parameters a = 30.04, b = 51.68, c = 61.53 Å). The lysozyme structure obtained from these crystals does not show the typical overall fold. Instead, major conformational changes take place in some elements of the secondary structure and in the hydrophobic core of the protein. At the end of the central α-helix (α2), Glu35 is usually buried in the catalytic site and shows an abnormally high pKa value, which is key to the activity of the enzyme. The high pKa value of this glutamate residue is favoured by the hydrophobic environment, particularly by its neighbour Trp108, which is important for structural stability and saccharide binding. In this new structure, Trp108 shows a 90° rotation of its side chain, which results in the rearrangement of the hydrophobic core. Conformational changes also result in the exposure of Glu35 to the solvent, which impairs the catalytic site by increasing the distance between Glu35 and Asp52 and lowering the pKa value of the glutamate. Altogether, this new lysozyme structure reveals major conformational changes in the hydrophobic core and catalytic site that might play a role in the folding and bactericidal function of the protein.
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Affiliation(s)
- M. Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Daniel Alba-Elena
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain
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48
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Garcia-Bonete MJ, Katona G. Bayesian machine learning improves single-wavelength anomalous diffraction phasing. Acta Crystallogr A Found Adv 2019; 75:851-860. [PMID: 31692460 PMCID: PMC6833979 DOI: 10.1107/s2053273319011446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/14/2019] [Indexed: 11/25/2022] Open
Abstract
Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.
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Affiliation(s)
- Maria-Jose Garcia-Bonete
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, 40530, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, 40530, Sweden
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49
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Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
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Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
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50
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Ahmed YL, Thoms M, Mitterer V, Sinning I, Hurt E. Crystal structures of Rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin-ligand-type complexes. Nat Commun 2019; 10:3050. [PMID: 31296859 PMCID: PMC6624252 DOI: 10.1038/s41467-019-10922-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/10/2019] [Indexed: 01/08/2023] Open
Abstract
The Rea1 AAA+-ATPase dislodges assembly factors from pre-60S ribosomes upon ATP hydrolysis, thereby driving ribosome biogenesis. Here, we present crystal structures of Rea1-MIDAS, the conserved domain at the tip of the flexible Rea1 tail, alone and in complex with its substrate ligands, the UBL domains of Rsa4 or Ytm1. These complexes have structural similarity to integrin α-subunit domains when bound to extracellular matrix ligands, which for integrin biology is a key determinant for force-bearing cell-cell adhesion. However, the presence of additional motifs equips Rea1-MIDAS for its tasks in ribosome maturation. One loop insert cofunctions as an NLS and to activate the mechanochemical Rea1 cycle, whereas an additional β-hairpin provides an anchor to hold the ligand UBL domains in place. Our data show the versatility of the MIDAS fold for mechanical force transmission in processes as varied as integrin-mediated cell adhesion and mechanochemical removal of assembly factors from pre-ribosomes.
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Affiliation(s)
| | - Matthias Thoms
- Heidelberg University Biochemistry Center, D-69120, Heidelberg, Germany.,Gene Center, University of Munich, D-81377, Munich, Germany
| | - Valentin Mitterer
- Heidelberg University Biochemistry Center, D-69120, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center, D-69120, Heidelberg, Germany.
| | - Ed Hurt
- Heidelberg University Biochemistry Center, D-69120, Heidelberg, Germany.
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