1
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Roux A, Alsalman Z, Jiang T, Mulatier JC, Pitrat D, Dumont E, Riobé F, Gillet N, Girard E, Maury O. Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network. Chemistry 2024; 30:e202400900. [PMID: 38738452 DOI: 10.1002/chem.202400900] [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: 03/08/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
Crystallophores are lanthanide complexes that have demonstrated outstanding induction of crystallization for various proteins. This article explores the effect of tailored modifications of the crystallophore first generation and their impact on the nucleating properties and protein crystal structures. Through high-throughput crystallization experiments and dataset analysis, we evaluated the effectiveness of these variants, in comparison to the first crystallophore generation G1. In particular, the V1 variant, featuring a propanol pendant arm, demonstrated the ability to produce new crystallization conditions for the proteins tested (hen-egg white lysozyme, proteinase K and thaumatin). Structural analysis performed in the case of hen egg-white lysozyme along with Molecular Dynamics simulations, highlights V1's unique behavior, taking advantage of the flexibility of its propanol arm to explore different protein surfaces and form versatile supramolecular interactions.
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Affiliation(s)
- Amandine Roux
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
- Polyvalan SAS, Lyon, France
| | - Zaynab Alsalman
- Univ Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Tao Jiang
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
| | - Jean-Christophe Mulatier
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
| | - Delphine Pitrat
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
| | - Elise Dumont
- Univ. Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
- Institut Universitaire de France, 5 rue Descartes, 75005, Paris, France
| | - François Riobé
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
- Univ Bordeaux, Bordeaux INP, CNRS, Institut de Chimie de la Matière Condensée de Bordeaux, 33608, Pessac, France
| | - Natacha Gillet
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
| | - Eric Girard
- Univ Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Olivier Maury
- Univ. Lyon, École Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, 69007, Lyon, France
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2
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Dos Santos K, Bartocci A, Gillet N, Denis-Quanquin S, Roux A, Lin E, Xu Z, Finizola R, Chedozeau P, Chen X, Caradeuc C, Baudin M, Bertho G, Riobé F, Maury O, Dumont E, Giraud N. One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics. Phys Chem Chem Phys 2024; 26:14573-14581. [PMID: 38722087 DOI: 10.1039/d4cp00463a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.
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Affiliation(s)
- Karen Dos Santos
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
- Polyvalan SAS, Lyon, France
| | - Eugene Lin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Zeren Xu
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Raphael Finizola
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Pauline Chedozeau
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Xi Chen
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Cédric Caradeuc
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Mathieu Baudin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université 45 Rue d'Ulm, 75005 Paris, France
| | - Gildas Bertho
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - François Riobé
- Univ. Bordeaux CNRS, Bordeaux INP, ICMCB UMR 5026, F-33600 Pessac, France
| | - Olivier Maury
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France.
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Nicolas Giraud
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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3
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Müller MC, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol 2024; 7:111. [PMID: 38243071 PMCID: PMC10799026 DOI: 10.1038/s42003-023-05726-w] [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: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.
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Affiliation(s)
- Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Olivier N Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Microcosm Earth Center, Philipps-University Marburg and Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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4
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Gelder K, Oliveira-Filho ER, García-García JD, Hu Y, Bruner SD, Hanson AD. Directed Evolution of Aerotolerance in Sulfide-Dependent Thiazole Synthases. ACS Synth Biol 2023; 12:963-970. [PMID: 36920242 PMCID: PMC10127261 DOI: 10.1021/acssynbio.2c00512] [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: 09/26/2022] [Indexed: 03/16/2023]
Abstract
Sulfide-dependent THI4 thiazole synthases could potentially be used to replace plant cysteine-dependent suicide THI4s, whose high protein turnover rates make thiamin synthesis exceptionally energy-expensive. However, sulfide-dependent THI4s are anaerobic or microoxic enzymes and hence unadapted to the aerobic conditions in plants; they are also slow enzymes (kcat < 1 h-1). To improve aerotolerance and activity, we applied continuous directed evolution under aerobic conditions in the yeast OrthoRep system to two sulfide-dependent bacterial THI4s. Seven beneficial single mutations were identified, of which five lie in the active-site cleft predicted by structural modeling and two recapitulate features of naturally aerotolerant THI4s. That single mutations gave substantial improvements suggests that further advance under selection will be possible by stacking mutations. This proof-of-concept study established that the performance of sulfide-dependent THI4s in aerobic conditions is evolvable and, more generally, that yeast OrthoRep provides a plant-like bridge to adapt nonplant enzymes to work better in plants.
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Affiliation(s)
- Kristen
Van Gelder
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Edmar R. Oliveira-Filho
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | | | - You Hu
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Andrew D. Hanson
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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5
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Tetreau G, Sawaya MR, De Zitter E, Andreeva EA, Banneville AS, Schibrowsky NA, Coquelle N, Brewster AS, Grünbein ML, Kovacs GN, Hunter MS, Kloos M, Sierra RG, Schiro G, Qiao P, Stricker M, Bideshi D, Young ID, Zala N, Engilberge S, Gorel A, Signor L, Teulon JM, Hilpert M, Foucar L, Bielecki J, Bean R, de Wijn R, Sato T, Kirkwood H, Letrun R, Batyuk A, Snigireva I, Fenel D, Schubert R, Canfield EJ, Alba MM, Laporte F, Després L, Bacia M, Roux A, Chapelle C, Riobé F, Maury O, Ling WL, Boutet S, Mancuso A, Gutsche I, Girard E, Barends TRM, Pellequer JL, Park HW, Laganowsky AD, Rodriguez J, Burghammer M, Shoeman RL, Doak RB, Weik M, Sauter NK, Federici B, Cascio D, Schlichting I, Colletier JP. De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals. Nat Commun 2022; 13:4376. [PMID: 35902572 PMCID: PMC9334358 DOI: 10.1038/s41467-022-31746-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.
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Affiliation(s)
- Guillaume Tetreau
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
| | - Elke De Zitter
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Elena A Andreeva
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Anne-Sophie Banneville
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Natalie A Schibrowsky
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Nicolas Coquelle
- Large-Scale Structures Group, Institut Laue-Langevin, F-38000, Grenoble, France
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marie Luise Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Marco Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Giorgio Schiro
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Pei Qiao
- Department of Chemistry, Texas A&M University, College Station, TX, 77845, USA
| | - Myriam Stricker
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Dennis Bideshi
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ninon Zala
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Sylvain Engilberge
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Alexander Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Mario Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Irina Snigireva
- European Synchrotron Radiation Facility (ESRF), BP 220, 38043, Grenoble, France
| | - Daphna Fenel
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Ethan J Canfield
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mario M Alba
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | | | | | - Maria Bacia
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | | | - François Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342, Lyon, France
| | - Wai Li Ling
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Adrian Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Irina Gutsche
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Eric Girard
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Hyun-Woo Park
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Arthur D Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77845, USA
| | - Jose Rodriguez
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Manfred Burghammer
- European Synchrotron Radiation Facility (ESRF), BP 220, 38043, Grenoble, France
| | - Robert L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - R Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Martin Weik
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, CA, 90095-1570, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jacques-Philippe Colletier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des martyrs, F-38000, Grenoble, France.
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6
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Yadav RK, Krishnan V. New structural insights into the
PI
‐2 pilus from
Streptococcus oralis
, an early dental plaque colonizer. FEBS J 2022; 289:6342-6366. [DOI: 10.1111/febs.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/20/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Rajnesh Kumari Yadav
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology NCR Biotech Science Cluster Faridabad India
- School of Biotechnology KIIT University Odisha India
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology NCR Biotech Science Cluster Faridabad India
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7
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Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen. Biomolecules 2021; 11:biom11111679. [PMID: 34827677 PMCID: PMC8615647 DOI: 10.3390/biom11111679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs.
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8
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Roux A, Talon R, Alsalman Z, Engilberge S, D'Aléo A, Di Pietro S, Robin A, Bartocci A, Pilet G, Dumont E, Wagner T, Shima S, Riobé F, Girard E, Maury O. Influence of Divalent Cations in the Protein Crystallization Process Assisted by Lanthanide-Based Additives. Inorg Chem 2021; 60:15208-15214. [PMID: 34597021 DOI: 10.1021/acs.inorgchem.1c01635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of lanthanide complexes as powerful auxiliaries for biocrystallography prompted us to systematically analyze the influence of the commercial crystallization kit composition on the efficiency of two lanthanide additives: [Eu(DPA)3]3- and Tb-Xo4. This study reveals that the tris(dipicolinate) complex presents a lower chemical stability and a strong tendency toward false positives, which are detrimental for its use in a high-throughput robotized crystallization platform. In particular, the crystal structures of (Mg(H2O)6)3[Eu(DPA)3]2·7H2O (1), {(Ca(H2O)4)3[Eu(DPA)3]2}n·10nH2O (2), and {Cu(DPA)(H2O)2}n (3), resulting from spontaneous crystallization in the presence of a divalent alkaline-earth cation and transmetalation, are reported. On the other hand, Tb-Xo4 is perfectly soluble in the crystallization media, stable in the presence of alkaline-earth dications, and slowly decomposes (within days) by transmetalation with transition metals. The original structure of [Tb4L4(H2O)4]Cl4·15H2O (4) is also described, where L represents a bis(pinacolato)triazacyclononane ligand. This paper also highlights a potential synergy of interactions between Tb-Xo4 and components of the crystallization mixtures, leading to the formation of complex adducts like {AdkA/Tb-Xo4/Mg2+/glycerol} in the protein binding sites. The observation of such multicomponent adducts illustrated the complexity and versatility of the supramolecular chemistry occurring at the surface of the proteins.
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Affiliation(s)
- Amandine Roux
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France.,Polyvalan, Lyon F-69342, France
| | - Romain Talon
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Zaynab Alsalman
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | | | - Anthony D'Aléo
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Sebastiano Di Pietro
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Adeline Robin
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Alessio Bartocci
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Guillaume Pilet
- CNRS UMR 5615, Université Lyon, Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, Villeurbanne Cedex F-69622, France
| | - Elise Dumont
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France.,Institut Universitaire de France, 1 rue Descartes, Paris 75005, France
| | - Tristan Wagner
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg D-35043, Germany.,Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, 1-Celsiusstrasse, Bremen 35043, Germany
| | - Seigo Shima
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, Marburg D-35043, Germany
| | - François Riobé
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
| | - Eric Girard
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble F-38000, France
| | - Olivier Maury
- Laboratoire de Chimie, ENS de Lyon, CNRS, UMR 5182, Université Lyon, Lyon F-69342, France
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9
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Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. Biochem J 2021; 478:3265-3279. [PMID: 34409984 PMCID: PMC8454699 DOI: 10.1042/bcj20210565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O2-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O2-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.
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10
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Denis-Quanquin S, Bartocci A, Szczepaniak F, Riobé F, Maury O, Dumont E, Giraud N. Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration. Phys Chem Chem Phys 2021; 23:11224-11232. [PMID: 34010374 DOI: 10.1039/d0cp06570f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex-protein interaction or self-assembly processes.
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Affiliation(s)
- Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Alessio Bartocci
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Florence Szczepaniak
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Francois Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. and Institut Universitaire de France, 5 rue Descartes, 75005, Paris, France
| | - Nicolas Giraud
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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11
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Kovalenko V, Popov A, Santoni G, Loiko N, Tereshkina K, Tereshkin E, Krupyanskii Y. Multi-crystal data collection using synchrotron radiation as exemplified with low-symmetry crystals of Dps. Acta Crystallogr F Struct Biol Commun 2020; 76:568-576. [PMID: 33135675 PMCID: PMC7605109 DOI: 10.1107/s2053230x20012571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/15/2020] [Indexed: 11/10/2022] Open
Abstract
Multi-crystal data collection using synchrotron radiation was successfully applied to determine the three-dimensional structure of a triclinic crystal form of Dps from Escherichia coli at 2.0 Å resolution. The final data set was obtained by combining 261 partial diffraction data sets measured from crystals with an average size of approximately 5 µm. The most important features of diffraction data measurement and processing for low-symmetry crystals are discussed.
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Affiliation(s)
- Vladislav Kovalenko
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Alexander Popov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gianluca Santoni
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Natalia Loiko
- Survival of Microorganisms, FRC ‘Fundamentals of Biotechnology’, 33 Leninsky Prospect, Building 2, Moscow 119071, Russian Federation
| | - Ksenia Tereshkina
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Eduard Tereshkin
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
| | - Yurii Krupyanskii
- Structure of Matter, Semenov FRC for Chemical Physics, RAS, 4 Kosygina Street, Moscow 119991, Russian Federation
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12
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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13
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Haroun M. In Silico Design, Synthesis and Evaluation of Novel Series of Benzothiazole- Based Pyrazolidinediones as Potent Hypoglycemic Agents. Med Chem 2020; 16:812-825. [DOI: 10.2174/1573406416666191227113716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/26/2019] [Accepted: 10/29/2019] [Indexed: 12/30/2022]
Abstract
Background:
The discovery of novel ligand binding domain (LBD) of peroxisome proliferator-
activated receptor γ (PPARγ) has recently attracted attention to few research groups in order
to develop more potent and safer antidiabetic agents.
Objective:
This study is focused on docking-based design and synthesis of novel compounds combining
benzothiazole and pyrazolidinedione scaffold as potential antidiabetic agents.
Methods:
Several benzothiazole-pyrazolidinedione hybrids were synthesized and tested for their in
vivo anti-hyperglycemic activity. Interactions profile of title compounds against PPARγ was examined
through molecular modelling approach.
Results:
All tested compounds exhibited anti-hyperglycemic activity similar or superior to the reference
drug Rosiglitazone. Introducing chlorine atom and alkyl group at position-6 and -5 respectively
on benzothiazole core resulted in enhancing the anti-hyperglycemic effect. Docking study
revealed that such groups demonstrated favorable hydrophobic interactions with novel LBD Ω-
pocket of PPARγ protein.
Conclusion:
Among the tested compounds, N-(6-chloro-5-methylbenzo[d]thiazol-2-yl-4-(4((3,5-
dioxopyrazolidin-4-ylidene)methyl)phenoxy)butanamide 5b was found to be the most potent compound
and provided valuable insights to further develop novel hybrids as anti-hyperglycemic
agents.
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Affiliation(s)
- Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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14
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Engilberge S, Wagner T, Carpentier P, Girard E, Shima S. Krypton-derivatization highlights O 2-channeling in a four-electron reducing oxidase. Chem Commun (Camb) 2020; 56:10863-10866. [DOI: 10.1039/d0cc04557h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kr-derivatization and X-ray structures indicated O2-channel and gating-loop that prevent side-reaction in reduction of O2 to water in F420H2 oxidase.
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Affiliation(s)
| | - Tristan Wagner
- Microbial Metabolism Group
- Max-Planck-Institut für Marine Mikrobiologie
- Celsiusstraße 1
- Bremen
- Germany
| | - Philippe Carpentier
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM)
- Université Grenoble Alpes, CNRS, CEA
- Grenoble
- France
- European Synchrotron Radiation Facility (ESRF)
| | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS
- F-38000 Grenoble
- France
| | - Seigo Shima
- Microbial Protein Structure Group
- Max Planck Institute for Terrestrial Microbiology
- Karl-von-Frisch Straße 10
- 35043 Marburg
- Germany
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15
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Kumari Yadav R, Krishnan V. The adhesive PitA pilus protein from the early dental plaque colonizer Streptococcus oralis: expression, purification, crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2020; 76:8-13. [PMID: 31929180 PMCID: PMC6957113 DOI: 10.1107/s2053230x1901642x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/05/2019] [Indexed: 11/10/2022] Open
Abstract
PitA is the putative tip adhesin of the pilus islet 2 (PI-2)-encoded sortase-dependent pilus in the Gram-positive Streptococcus oralis, an opportunistic pathogen that often flourishes within the diseased human oral cavity. Early colonization by S. oralis and its interaction with Actinomyces oris seeds the development of oral biofilm or dental plaque. Here, the PI-2 pilus plays a vital role in mediating adherence to host surfaces and other bacteria. A recombinant form of the PitA adhesin has now been produced and crystallized. Owing to the large size (∼100 kDa), flexibility and complicated folding of PitA, obtaining diffraction-quality crystals has been a challenge. However, by the use of limited proteolysis with α-chymotrypsin, the diffraction quality of the PitA crystals was considerably enhanced to 2.16 Å resolution. These crystals belonged to space group P1, with unit-cell parameters a = 61.48, b = 70.87, c = 82.46 Å, α = 80.08, β = 87.02, γ = 87.70°. The anomalous signal from the terbium derivative of α-chymotrypsin-treated PitA crystals prepared with terbium crystallophore (Tb-Xo4) was sufficient to obtain an interpretable electron-density map via terbium SAD phasing.
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Affiliation(s)
- Rajnesh Kumari Yadav
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121 001, India
- School of Biotechnology, KIIT University, Odisha 751 024, India
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121 001, India
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