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Froudas K, Vassaki M, Papadopoulos K, Tsangarakis C, Chen X, Shepard W, Fairen-Jimenez D, Tampaxis C, Charalambopoulou G, Steriotis TA, Trikalitis PN. Expanding the Reticular Chemistry Building Block Library toward Highly Connected Nets: Ultraporous MOFs Based on 18-Connected Ternary, Trigonal Prismatic Superpolyhedra. J Am Chem Soc 2024; 146:8961-8970. [PMID: 38428926 PMCID: PMC10996011 DOI: 10.1021/jacs.3c12679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
The chemistry of metal-organic frameworks (MOFs) continues to expand rapidly, providing materials with diverse structures and properties. The reticular chemistry approach, where well-defined structural building blocks are combined together to form crystalline open framework solids, has greatly accelerated the discovery of new and important materials. However, its full potential toward the rational design of MOFs relies on the availability of highly connected building blocks because these greatly reduce the number of possible structures. Toward this, building blocks with connectivity greater than 12 are highly desirable but extremely rare. We report here the discovery of novel 18-connected, trigonal prismatic, ternary building blocks (tbb's) and their assembly into unique MOFs, denoted as Fe-tbb-MOF-x (x: 1, 2, 3), with hierarchical micro- and mesoporosity. The remarkable tbb is an 18-c supertrigonal prism, with three points of extension at each corner, consisting of triangular (3-c) and rectangular (4-c) carboxylate-based organic linkers and trigonal prismatic [Fe3(μ3-Ο)(-COO)6]+ clusters. The tbb's are linked together by an 18-c cluster made of 4-c ligands and a crystallographically distinct Fe3(μ3-Ο) trimer, forming overall a 3-D (3,4,4,6,6)-c five nodal net. The hierarchical, highly porous nature of Fe-tbb-MOF-x (x: 1, 2, 3) was confirmed by recording detailed sorption isotherms of Ar, CH4, and CO2 at 87, 112, and 195 K, respectively, revealing an ultrahigh BET area (4263-4847 m2 g-1) and pore volume (1.95-2.29 cm3 g-1). Because of the observed ultrahigh porosities, the H2 and CH4 storage properties of Fe-tbb-MOF-x were investigated, revealing well-balanced high gravimetric and volumetric deliverable capacities for cryoadsorptive H2 storage (11.6 wt %/41.4 g L-1, 77 K/100 bar-160 K/5 bar), as well as CH4 storage at near ambient temperatures (367 mg g-1/160 cm3 STP cm-3, 5-100 bar at 298 K), placing these materials among the top performing MOFs. The present work opens new directions to apply reticular chemistry for the construction of novel MOFs with tunable porosities based on contracted or expanded tbb analogues.
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Affiliation(s)
| | - Maria Vassaki
- Department
of Chemistry, University of Crete, Heraklion 71003, Greece
| | | | | | - Xu Chen
- Department
of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - William Shepard
- Synchrotron
SOLEIL-UR1, L’Orme des Merisiers, Saint-Aubin, BP 48, Gif-Sur-Yvette 91192, France
| | - David Fairen-Jimenez
- Department
of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Christos Tampaxis
- National
Center for Scientific Research “Demokritos”, Athens 15341, Greece
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2
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Falaise C, Khlifi S, Bauduin P, Schmid P, Degrouard J, Leforestier A, Shepard W, Marrot J, Haouas M, Landy D, Mellot-Draznieks C, Cadot E. Cooperative Self-Assembly Process Involving Giant Toroidal Polyoxometalate as a Membrane Building Block in Nanoscale Vesicles. J Am Chem Soc 2024; 146:1501-1511. [PMID: 38189235 DOI: 10.1021/jacs.3c11004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The self-assembly of organic amphiphilic species into various aggregates such as spherical or elongated micelles and cylinders up to the formation of lyotropic hexagonal or lamellar phases results from cooperative processes orchestrated by the hydrophobic effect, while those involving ionic inorganic polynuclear entities and nonionic organic components are still intriguing. Herein, we report on the supramolecular behavior of giant toroidal molybdenum blue-type polyoxometalate, namely, the {Mo154} species in the presence of n-octyl-β-glucoside (C8G1), widely used as a surfactant in biochemistry. Structural investigations were carried out using a set of complementary multiscale methods including single-crystal X-ray diffraction analysis supported by molecular modeling, small-angle X-ray scattering and cryo-TEM observations. In addition, liquid NMR, viscosimetry, surface tension measurement, and isothermal titration calorimetry provided further information to decipher the complex aggregation pathway. Elucidation of the assembly process reveals a rich scenario where the presence of the large {Mo154} anion disrupts the self-assembly of the C8G1, well-known to produce micelles, and induces striking successive phase transitions from fluid-to-gel and from gel-to-fluid. Herein, intimate organic-inorganic primary interactions arising from the superchaotropic nature of the {Mo154} lead to versatile nanoscopic hybrid C8G1-{Mo154} aggregates including crystalline discrete assemblies, smectic lamellar liquid crystals, and large uni- or multilamellar vesicles where the large torus {Mo154} acts a trans-membrane component.
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Affiliation(s)
- Clément Falaise
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles 78035, France
| | - Soumaya Khlifi
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles 78035, France
| | - Pierre Bauduin
- ICSM, CEA, CNRS, ENSCM, Université Montpellier, Marcoule 34199, France
| | - Philipp Schmid
- ICSM, CEA, CNRS, ENSCM, Université Montpellier, Marcoule 34199, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay 91405, France
| | - Amélie Leforestier
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay 91405, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles 78035, France
| | - Mohamed Haouas
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles 78035, France
| | - David Landy
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV, EA 4492), ULCO, Dunkerque 59140, France
| | - Caroline Mellot-Draznieks
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France, Sorbonne Université, PSL Research University, Paris, Cedex 05 75231, France
| | - Emmanuel Cadot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles 78035, France
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3
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Chen X, Mendes B, Zhuang Y, Conniot J, Mercado Argandona S, Melle F, Sousa DP, Perl D, Chivu A, Patra HK, Shepard W, Conde J, Fairen-Jimenez D. A Fluorinated BODIPY-Based Zirconium Metal-Organic Framework for In Vivo Enhanced Photodynamic Therapy. J Am Chem Soc 2024; 146:1644-1656. [PMID: 38174960 PMCID: PMC10797627 DOI: 10.1021/jacs.3c12416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
Photodynamic therapy (PDT), an emergent noninvasive cancer treatment, is largely dependent on the presence of efficient photosensitizers (PSs) and a sufficient oxygen supply. However, the therapeutic efficacy of PSs is greatly compromised by poor solubility, aggregation tendency, and oxygen depletion within solid tumors during PDT in hypoxic microenvironments. Despite the potential of PS-based metal-organic frameworks (MOFs), addressing hypoxia remains challenging. Boron dipyrromethene (BODIPY) chromophores, with excellent photostability, have exhibited great potential in PDT and bioimaging. However, their practical application suffers from limited chemical stability under harsh MOF synthesis conditions. Herein, we report the synthesis of the first example of a Zr-based MOF, namely, 69-L2, exclusively constructed from the BODIPY-derived ligands via a single-crystal to single-crystal post-synthetic exchange, where a direct solvothermal method is not applicable. To increase the PDT performance in hypoxia, we modify 69-L2 with fluorinated phosphate-functionalized methoxy poly(ethylene glycol). The resulting 69-L2@F is an oxygen carrier, enabling tumor oxygenation and simultaneously acting as a PS for reactive oxygen species (ROS) generation under LED irradiation. We demonstrate that 69-L2@F has an enhanced PDT effect in triple-negative breast cancer MDA-MB-231 cells under both normoxia and hypoxia. Following positive results, we evaluated the in vivo activity of 69-L2@F with a hydrogel, enabling local therapy in a triple-negative breast cancer mice model and achieving exceptional antitumor efficacy in only 2 days. We envision BODIPY-based Zr-MOFs to provide a solution for hypoxia relief and maximize efficacy during in vivo PDT, offering new insights into the design of promising MOF-based PSs for hypoxic tumors.
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Affiliation(s)
- Xu Chen
- The
Adsorption & Advanced Materials Laboratory (AML),
Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Bárbara
B. Mendes
- ToxOmics,
NOVA Medical School, Faculdade de Ciências Médicas,
NMS|FCM, Universidade Nova de Lisboa, Lisboa 2775-405, Portugal
| | - Yunhui Zhuang
- The
Adsorption & Advanced Materials Laboratory (AML),
Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - João Conniot
- ToxOmics,
NOVA Medical School, Faculdade de Ciências Médicas,
NMS|FCM, Universidade Nova de Lisboa, Lisboa 2775-405, Portugal
| | - Sergio Mercado Argandona
- The
Adsorption & Advanced Materials Laboratory (AML),
Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Francesca Melle
- The
Adsorption & Advanced Materials Laboratory (AML),
Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Diana P. Sousa
- ToxOmics,
NOVA Medical School, Faculdade de Ciências Médicas,
NMS|FCM, Universidade Nova de Lisboa, Lisboa 2775-405, Portugal
| | - David Perl
- Synchrotron
SOLEIL-UR1, L’Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
| | - Alexandru Chivu
- Department
of Surgical Biotechnology, University College
London, London NW3 2PF, U.K.
| | - Hirak K. Patra
- Department
of Surgical Biotechnology, University College
London, London NW3 2PF, U.K.
| | - William Shepard
- Synchrotron
SOLEIL-UR1, L’Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France
| | - João Conde
- ToxOmics,
NOVA Medical School, Faculdade de Ciências Médicas,
NMS|FCM, Universidade Nova de Lisboa, Lisboa 2775-405, Portugal
| | - David Fairen-Jimenez
- The
Adsorption & Advanced Materials Laboratory (AML),
Department of Chemical Engineering & Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
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Oms O, Maity N, Marrot J, Yu J, Rivière E, Shepard W, Benseghir Y, Talbi K, Dolbecq A, Ha-Thi MH, Galan-Mascaros JR, Mialane P. Structure and Electronic Properties of Large Oligomeric Heterometallic 3d/Ce IV Polyoxometalates. Inorg Chem 2023; 62:18856-18863. [PMID: 37921695 DOI: 10.1021/acs.inorgchem.3c02078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Merging the rich chemistry of Ce(IV) polyoxometalates (POMs) with that of 3d polyanions remains a challenge due to the strong competition between these highly oxophilic lanthanide cations and 3d metallic ions for coordination to lacunary molecular metal oxides. We report herein the characterization of an unprecedented water stable hexameric CeIV/CoII POM (Ce12Co6) made of two {(SiW9)2Ce6} units connected to a {(SiW10)2Co6(PO4)2} core. In addition, the pentameric CeIV/NiII compound Ce6Ni8, where two {PW9Ni3W} and a {PW10Ni2} fragments are grafted on a {(PW9)2Ce6} moiety, has been obtained. Magnetic studies of Ce6Ni8 revealed ferromagnetic interactions between the NiII centers constituting the {Ni3PW10} fragments, in agreement with the geometry of such a trinuclear cluster. Related insoluble barium salts of Ce12Co6 and Ce6Ni8 were also prepared, allowing their solid-state electrochemical investigations and showing in particular that in Ce12Co6, both the cobalt, cerium, and silicotungstate moieties are electroactive. Finally, photophysical studies demonstrate the formation of long-lived reduced POMs photosensitized by [Ru(bpy)3]2+, suggesting that Ce12Co6 and Ce6Ni8 could be used as efficient reservoirs of reduction equivalents for photocatalytic reactions.
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Affiliation(s)
- Olivier Oms
- Institut Lavoisier de Versailles (ILV), UMR 8180, Université Paris-Saclay, Université de Versailles Saint-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France
| | - Nishith Maity
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles (ILV), UMR 8180, Université Paris-Saclay, Université de Versailles Saint-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France
| | - Jiahao Yu
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), ES-43007 Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel. lí Domingo 1, 43007 Tarragona, Spain
| | - Eric Rivière
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, CNRS, Université Paris-Saclay, Bâtiment Henri Moissan, 19 Avenue des Sciences, 91400 Orsay, France
| | - William Shepard
- Dept PROXIMA2 A, Synchrotron Soleil, Saint-Aubin, BP 48, Gif-sur-Yvette 91192, France
| | - Youven Benseghir
- Institut Lavoisier de Versailles (ILV), UMR 8180, Université Paris-Saclay, Université de Versailles Saint-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France
| | - Khadija Talbi
- Institut Lavoisier de Versailles (ILV), UMR 8180, Université Paris-Saclay, Université de Versailles Saint-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France
| | - Anne Dolbecq
- Institut Lavoisier de Versailles (ILV), UMR 8180, Université Paris-Saclay, Université de Versailles Saint-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France
| | - Minh-Huong Ha-Thi
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | | | - Pierre Mialane
- Institut Lavoisier de Versailles (ILV), UMR 8180, Université Paris-Saclay, Université de Versailles Saint-Quentin en Yvelines, 45 Avenue des Etats-Unis, 78035 Versailles Cedex, France
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5
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Tolbatov I, Marrone A, Shepard W, Chiaverini L, Upadhyay Kahaly M, La Mendola D, Marzo T, Ciccone L. Inorganic Drugs as a Tool for Protein Structure Solving and Studies on Conformational Changes. Chemistry 2023; 29:e202202937. [PMID: 36477932 DOI: 10.1002/chem.202202937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Inorganic drugs are capable of tight interactions with proteins through coordination towards aminoacidic residues, and this feature is recognized as a key aspect for their pharmacological action. However, the "protein metalation process" is exploitable for solving the phase problem and structural resolution. In fact, the use of inorganic drugs bearing specific metal centers and ligands capable to drive the binding towards the desired portions of the protein target could represent a very intriguing and fruitful strategy. In this context, a theoretical approach may further contribute to solve protein structures and their refinement. Here, we delineate the main features of a reliable experimental-theoretical integrated approach, based on the use of metallodrugs, for protein structure solving.
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Affiliation(s)
- Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Alessandro Marrone
- Department of Pharmacy, University "G. D'Annunzio" Chieti-Pescara, Via dei Vestini, 31, 66100, Chieti, Italy
| | - William Shepard
- Department PROXIMA2 A, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Lorenzo Chiaverini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | | | - Diego La Mendola
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Tiziano Marzo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Department PROXIMA2 A, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
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6
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Fa Bamba I, Falaise C, Marrot J, Atheba P, Gbassi G, Landy D, Shepard W, Haouas M, Cadot E. Host-Guest Complexation Between Cyclodextrins and Hybrid Hexavanadates: What are the Driving Forces? Chemistry 2021; 27:15516-15527. [PMID: 34523167 DOI: 10.1002/chem.202102684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Indexed: 11/12/2022]
Abstract
Host-guest complexes between native cyclodextrins (α-, β- and γ-CD) and hybrid Lindqvist-type polyoxovanadates (POVs) [V6 O13 ((OCH2 )3 C-R)2 ]2- with R = CH2 CH3 , NO2 , CH2 OH and NH(BOC) (BOC = N-tert-butoxycarbonyl) were studied in aqueous solution. Six crystal structures determined by single-crystal X-ray diffraction analysis revealed the nature of the functional R group strongly influences the host-guest conformation and also the crystal packing. In all systems isolated in the solid-state, the organic groups R are embedded within the cyclodextrin cavities, involving only a few weak supramolecular contacts. The interaction between hybrid POVs and the macrocyclic organic hosts have been deeply studied in solution using ITC, cyclic voltammetry and NMR methods (1D 1 H NMR, and 2D DOSY, and ROESY). This set of complementary techniques provides clear insights about the strength of interactions and the binding host-guest modes occurring in aqueous solution, highlighting a dramatic influence of the functional group R on the supramolecular properties of the hexavanadate polyoxoanions (association constant K1:1 vary from 0 to 2 000 M-1 ) while isolated functional organic groups exhibit only very weak intrinsic affinity with CDs. Electrochemical and calorimetric investigations suggest that the driving force of the host-guest association involving larger CDs (β- and γ-CD) is mainly related to the chaotropic effect. In contrast, the hydrophobic effect supported by weak attractive forces appears as the main contributor for the formation of α-CD-containing host-guest complexes. In any cases, the origin of driving forces is clearly related to the ability of the macrocyclic host to desolvate the exposed moieties of the hybrid POVs.
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Affiliation(s)
- Ibrahima Fa Bamba
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France.,UFR Sciences Pharmaceutiques et Biologiques (UFR SPB), Université Félix Houphouet Boigny (UFHB), Abidjan, Côte d'Ivoire
| | - Clément Falaise
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Patrick Atheba
- UFR Sciences des Structures de la Matière et Technologie (UFR SSMT), Université Félix Houphouet Boigny (UFHB), Abidjan, Côte d'Ivoire
| | - Gildas Gbassi
- UFR Sciences Pharmaceutiques et Biologiques (UFR SPB), Université Félix Houphouet Boigny (UFHB), Abidjan, Côte d'Ivoire
| | - David Landy
- Unité de Chimie Environnementale et Interactions sur le Vivant, ULCO, Dunkerque, UR 4492, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers Saint-Aubain BP 48, 91192 Gif-sur-Yvette, CEDEX, France
| | - Mohamed Haouas
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Emmanuel Cadot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
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Falaise C, Khlifi S, Bauduin P, Schmid P, Shepard W, Ivanov AA, Sokolov MN, Shestopalov MA, Abramov PA, Cordier S, Marrot J, Haouas M, Cadot E. “Host in Host” Supramolecular Core–Shell Type Systems Based on Giant Ring‐Shaped Polyoxometalates. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Clément Falaise
- Institut Lavoisier de Versailles CNRS, UVSQ, Université Paris-Saclay Versailles France
| | - Soumaya Khlifi
- Institut Lavoisier de Versailles CNRS, UVSQ, Université Paris-Saclay Versailles France
| | - Pierre Bauduin
- ICSM, CEA CNRS ENSCM Université Montpellier 34199 Marcoule France
| | - Philipp Schmid
- ICSM, CEA CNRS ENSCM Université Montpellier 34199 Marcoule France
| | - William Shepard
- Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubain BP 48 91192 Gif-sur-Yvette, CEDEX France
| | - Anton A. Ivanov
- Nikolaev Institute of Inorganic Chemistry SB RAS 630090 Novosibirsk Russia
| | - Maxim N. Sokolov
- Nikolaev Institute of Inorganic Chemistry SB RAS 630090 Novosibirsk Russia
| | | | - Pavel A. Abramov
- Nikolaev Institute of Inorganic Chemistry SB RAS 630090 Novosibirsk Russia
- South Ural State University, Prospekt Lenina, 76 454080 Chelyabinsk Russia
| | - Stéphane Cordier
- CNRS Institut des Sciences Chimiques de Rennes ISCR—UMR 6226 Univ Rennes 35000 Rennes France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles CNRS, UVSQ, Université Paris-Saclay Versailles France
| | - Mohamed Haouas
- Institut Lavoisier de Versailles CNRS, UVSQ, Université Paris-Saclay Versailles France
| | - Emmanuel Cadot
- Institut Lavoisier de Versailles CNRS, UVSQ, Université Paris-Saclay Versailles France
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8
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Falaise C, Khlifi S, Bauduin P, Schmid P, Shepard W, Ivanov AA, Sokolov MN, Shestopalov MA, Abramov PA, Cordier S, Marrot J, Haouas M, Cadot E. "Host in Host" Supramolecular Core-Shell Type Systems Based on Giant Ring-Shaped Polyoxometalates. Angew Chem Int Ed Engl 2021; 60:14146-14153. [PMID: 33724635 DOI: 10.1002/anie.202102507] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 11/08/2022]
Abstract
Herein, we show how the chaotropic effect arising from reduced molybdate ions in acidified aqueous solution is able to amplify drastically weak supramolecular interactions. Time-resolved Small Angle X-ray Scattering (SAXS) analysis suggests that molybdenum-blue oligomeric species form huge aggregates in the presence of γ-cyclodextrin (γ-CD) which results in the fast formation of nanoscopic {Mo154 }-based host-guest species, while X-ray diffraction analysis reveals that the ending-point of the scenario results in an unprecedented three-component well-ordered core-shell-like motif. A similar arrangement was found by using preformed hexarhenium chalcogenide-type cluster [Re6 Te8 (CN)6 ]4- as exogenous guest. This seminal work brings better understanding of the self-assembly processes in general and gives new opportunities for practical applications in the design of complex multicomponent materials via the simplicity of the non-covalent chemistry.
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Affiliation(s)
- Clément Falaise
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Soumaya Khlifi
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Pierre Bauduin
- ICSM, CEA, CNRS, ENSCM, Université Montpellier, 34199, Marcoule, France
| | - Philipp Schmid
- ICSM, CEA, CNRS, ENSCM, Université Montpellier, 34199, Marcoule, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubain BP 48, 91192, Gif-sur-Yvette, CEDEX, France
| | - Anton A Ivanov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 630090, Novosibirsk, Russia
| | - Maxim N Sokolov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 630090, Novosibirsk, Russia
| | | | - Pavel A Abramov
- Nikolaev Institute of Inorganic Chemistry SB RAS, 630090, Novosibirsk, Russia.,South Ural State University, Prospekt Lenina, 76, 454080, Chelyabinsk, Russia
| | - Stéphane Cordier
- CNRS, Institut des Sciences Chimiques de Rennes, ISCR-UMR 6226, Univ Rennes, 35000, Rennes, France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Mohamed Haouas
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
| | - Emmanuel Cadot
- Institut Lavoisier de Versailles, CNRS, UVSQ, Université Paris-Saclay, Versailles, France
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9
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Wang S, Cabrero-Antonino M, Navalón S, Cao CC, Tissot A, Dovgaliuk I, Marrot J, Martineau-Corcos C, Yu L, Wang H, Shepard W, García H, Serre C. A Robust Titanium Isophthalate Metal-Organic Framework for Visible-Light Photocatalytic CO2 Methanation. Chem 2020. [DOI: 10.1016/j.chempr.2020.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Ciccone L, Nencetti S, Tonali N, Fruchart-Gaillard C, Shepard W, Nuti E, Camodeca C, Rossello A, Orlandini E. Monoaryl derivatives as transthyretin fibril formation inhibitors: Design, synthesis, biological evaluation and structural analysis. Bioorg Med Chem 2020; 28:115673. [DOI: 10.1016/j.bmc.2020.115673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
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11
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Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard CC, Wojdyr M, Shepard W, Rigden DJ, Keegan RM. Using Phaser and ensembles to improve the performance of SIMBAD. Acta Crystallogr D Struct Biol 2020; 76:1-8. [PMID: 31909738 PMCID: PMC6939438 DOI: 10.1107/s2059798319015031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/06/2019] [Indexed: 01/07/2023]
Abstract
The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.
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Affiliation(s)
- Adam J Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M H Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, BP 48, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Andrey Lebedev
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles C Ballard
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | | | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, BP 48, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M Keegan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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12
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Bou-Nader C, Barraud P, Pecqueur L, Pérez J, Velours C, Shepard W, Fontecave M, Tisné C, Hamdane D. Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2. Nucleic Acids Res 2019; 47:3117-3126. [PMID: 30605527 PMCID: PMC6451096 DOI: 10.1093/nar/gky1302] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/12/2018] [Accepted: 12/29/2018] [Indexed: 11/17/2022] Open
Abstract
Double stranded RNA-binding domain (dsRBD) is a ubiquitous domain specialized in the recognition of double-stranded RNAs (dsRNAs). Present in many proteins and enzymes involved in various functional roles of RNA metabolism, including RNA splicing, editing, and transport, dsRBD generally binds to RNAs that lack complex structures. However, this belief has recently been challenged by the discovery of a dsRBD serving as a major tRNA binding module for human dihydrouridine synthase 2 (hDus2), a flavoenzyme that catalyzes synthesis of dihydrouridine within the complex elbow structure of tRNA. We here unveil the molecular mechanism by which hDus2 dsRBD recognizes a tRNA ligand. By solving the crystal structure of this dsRBD in complex with a dsRNA together with extensive characterizations of its interaction with tRNA using mutagenesis, NMR and SAXS, we establish that while hDus2 dsRBD retains a conventional dsRNA recognition capability, the presence of an N-terminal extension appended to the canonical domain provides additional residues for binding tRNA in a structure-specific mode of action. Our results support that this extension represents a feature by which the dsRBD specializes in tRNA biology and more broadly highlight the importance of structural appendages to canonical domains in promoting the emergence of functional diversity.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Pierre Barraud
- Institut de biologie physico-chimique (IBPC), CNRS, UMR 8261 CNRS/Université Paris Diderot, 13 rue Pierre et Marie Curie, Paris 75005, France.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | - Christophe Velours
- Macromolecular interaction platform of I2BC, UMR9198, Centre de Recherche de Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Carine Tisné
- Institut de biologie physico-chimique (IBPC), CNRS, UMR 8261 CNRS/Université Paris Diderot, 13 rue Pierre et Marie Curie, Paris 75005, France.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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13
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Wang S, Xhaferaj N, Wahiduzzaman M, Oyekan K, Li X, Wei K, Zheng B, Tissot A, Marrot J, Shepard W, Martineau-Corcos C, Filinchuk Y, Tan K, Maurin G, Serre C. Engineering Structural Dynamics of Zirconium Metal–Organic Frameworks Based on Natural C4 Linkers. J Am Chem Soc 2019; 141:17207-17216. [DOI: 10.1021/jacs.9b07816] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sujing Wang
- UMR 8004 CNRS, Ecole Normale Supérieure, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, Institut des Matériaux Poreux de Paris, 75005 Paris, France
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, 230026 Hefei, China
| | - Nertil Xhaferaj
- UMR 8004 CNRS, Ecole Normale Supérieure, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, Institut des Matériaux Poreux de Paris, 75005 Paris, France
| | - Mohammad Wahiduzzaman
- Institut Charles Gerhardt, Montpellier UMR 5253 CNRS ENSCM UM, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier CEDEX 05, France
| | - Kolade Oyekan
- Department of Materials Science & Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Xiao Li
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, B-1348 Louvain-la-Neuve, Belgium
| | - Kevin Wei
- Department of Materials Science & Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Bin Zheng
- Institut Charles Gerhardt, Montpellier UMR 5253 CNRS ENSCM UM, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier CEDEX 05, France
| | - Antoine Tissot
- UMR 8004 CNRS, Ecole Normale Supérieure, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, Institut des Matériaux Poreux de Paris, 75005 Paris, France
| | - Jérôme Marrot
- Institut Lavoisier de Versailles, UMR 8180 CNRS, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, 78035 Versailles, France
| | - William Shepard
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-Sur-Yvette, France
| | - Charlotte Martineau-Corcos
- Institut Lavoisier de Versailles, UMR 8180 CNRS, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, 78035 Versailles, France
- CEMHTI, UPR 3079, CNRS, 45071 Orléans CEDEX 2, France
| | - Yaroslav Filinchuk
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, B-1348 Louvain-la-Neuve, Belgium
| | - Kui Tan
- Department of Materials Science & Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Guillaume Maurin
- Institut Charles Gerhardt, Montpellier UMR 5253 CNRS ENSCM UM, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier CEDEX 05, France
| | - Christian Serre
- UMR 8004 CNRS, Ecole Normale Supérieure, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, Institut des Matériaux Poreux de Paris, 75005 Paris, France
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14
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De Zitter E, Savko M, Jeangerard D, Tissot A, Marot J, Cadot E, Serre C, Shepard W. Serial-MOF: developing serial crystallography methods for MOF nano-crystals. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319090296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Simpkin A, Simkovic F, Thomas J, Savko M, Lebedev A, Uski V, Wojdyr M, Ballard C, Shepard W, Rigden D, Keegan R. SIMBAD: structure-based search model identification for molecular replacement using the PDB. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319093793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Oscarsson M, Beteva A, Flot D, Gordon E, Guijarro M, Leonard G, McSweeney S, Monaco S, Mueller-Dieckmann C, Nanao M, Nurizzo D, Popov AN, von Stetten D, Svensson O, Rey-Bakaikoa V, Chado I, Chavas LMG, Gadea L, Gourhant P, Isabet T, Legrand P, Savko M, Sirigu S, Shepard W, Thompson A, Mueller U, Nan J, Eguiraun M, Bolmsten F, Nardella A, Milàn-Otero A, Thunnissen M, Hellmig M, Kastner A, Schmuckermaier L, Gerlach M, Feiler C, Weiss MS, Bowler MW, Gobbo A, Papp G, Sinoir J, McCarthy AA, Karpics I, Nikolova M, Bourenkov G, Schneider T, Andreu J, Cuní G, Juanhuix J, Boer R, Fogh R, Keller P, Flensburg C, Paciorek W, Vonrhein C, Bricogne G, de Sanctis D. MXCuBE2: the dawn of MXCuBE Collaboration. J Synchrotron Radiat 2019; 26:393-405. [PMID: 30855248 PMCID: PMC6412183 DOI: 10.1107/s1600577519001267] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/23/2019] [Indexed: 05/22/2023]
Abstract
MXCuBE2 is the second-generation evolution of the MXCuBE beamline control software, initially developed and used at ESRF - the European Synchrotron. MXCuBE2 extends, in an intuitive graphical user interface (GUI), the functionalities and data collection methods available to users while keeping all previously available features and allowing for the straightforward incorporation of ongoing and future developments. MXCuBE2 introduces an extended abstraction layer that allows easy interfacing of any kind of macromolecular crystallography (MX) hardware component, whether this is a diffractometer, sample changer, detector or optical element. MXCuBE2 also works in strong synergy with the ISPyB Laboratory Information Management System, accessing the list of samples available for a particular experimental session and associating, either from instructions contained in ISPyB or from user input via the MXCuBE2 GUI, different data collection types to them. The development of MXCuBE2 forms the core of a fruitful collaboration which brings together several European synchrotrons and a software development factory and, as such, defines a new paradigm for the development of beamline control platforms for the European MX user community.
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Affiliation(s)
- Marcus Oscarsson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Antonia Beteva
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David Flot
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Elspeth Gordon
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Matias Guijarro
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Gordon Leonard
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sean McSweeney
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Stephanie Monaco
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Max Nanao
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Didier Nurizzo
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Alexander N. Popov
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - David von Stetten
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olof Svensson
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | | | | | - Laurent Gadea
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | | | - Martin Savko
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | - Serena Sirigu
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette Cedex, France
| | | | | | - Uwe Mueller
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Jie Nan
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden
| | | | | | | | | | - Michael Hellmig
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Alexandra Kastner
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Lukas Schmuckermaier
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Martin Gerlach
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Christian Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Alexandre Gobbo
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gergely Papp
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jeremy Sinoir
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ivars Karpics
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Marina Nikolova
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Gleb Bourenkov
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Thomas Schneider
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22603 Hamburg, Germany
| | - Jordi Andreu
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Guifré Cuní
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Judith Juanhuix
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Roeland Boer
- CELLS-ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain
| | - Rasmus Fogh
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Peter Keller
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Claus Flensburg
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Wlodek Paciorek
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Clemens Vonrhein
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Gerard Bricogne
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AK, UK
| | - Daniele de Sanctis
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
- Correspondence e-mail:
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17
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Ciccone L, Fruchart-Gaillard C, Mourier G, Savko M, Nencetti S, Orlandini E, Servent D, Stura EA, Shepard W. Copper mediated amyloid-β binding to Transthyretin. Sci Rep 2018; 8:13744. [PMID: 30213975 PMCID: PMC6137083 DOI: 10.1038/s41598-018-31808-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/23/2018] [Indexed: 01/27/2023] Open
Abstract
Transthyretin (TTR), a homotetrameric protein that transports thyroxine and retinol both in plasma and in cerebrospinal (CSF) fluid provides a natural protective response against Alzheimer's disease (AD), modulates amyloid-β (Aβ) deposition by direct interaction and co-localizes with Aβ in plaques. TTR levels are lower in the CSF of AD patients. Zn2+, Mn2+ and Fe2+ transform TTR into a protease able to cleave Aβ. To explain these activities, monomer dissociation or conformational changes have been suggested. Here, we report that when TTR crystals are exposed to copper or iron salts, the tetramer undergoes a significant conformational change that alters the dimer-dimer interface and rearranges residues implicated in TTR's ability to neutralize Aβ. We also describe the conformational changes in TTR upon the binding of the various metal ions. Furthermore, using bio-layer interferometry (BLI) with immobilized Aβ(1-28), we observe the binding of TTR only in the presence of copper. Such Cu2+-dependent binding suggests a recognition mechanism whereby Cu2+ modulates both the TTR conformation, induces a complementary Aβ structure and may participate in the interaction. Cu2+-soaked TTR crystals show a conformation different from that induced by Fe2+, and intriguingly, TTR crystals grown in presence of Aβ(1-28) show different positions for the copper sites from those grown its absence.
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Affiliation(s)
- Lidia Ciccone
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Carole Fruchart-Gaillard
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Gilles Mourier
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Susanna Nencetti
- Dipartimento di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Elisabetta Orlandini
- Dipartimento di Scienze della Terra, Universitá di Pisa, Via Santa Maria 53-55, 56100, Pisa, Italy
| | - Denis Servent
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Enrico A Stura
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France.
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18
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Simpkin A, Simkovic F, Thomas J, Savko M, Ballard C, Wojdyr M, Shepard W, Rigden D, Keegan R. Identification of contaminants with SIMBAD: a sequence-independent molecular replacement pipeline. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard C, Wojdyr M, Wu R, Sanishvili R, Xu Y, Lisa MN, Buschiazzo A, Shepard W, Rigden DJ, Keegan RM. SIMBAD: a sequence-independent molecular-replacement pipeline. Acta Crystallogr D Struct Biol 2018; 74:595-605. [PMID: 29968670 PMCID: PMC6038384 DOI: 10.1107/s2059798318005752] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
Abstract
The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here, SIMBAD, a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD, this approach has solved novel cases that have otherwise proved difficult to solve.
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Affiliation(s)
- Adam J. Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Martin Savko
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Andrey Lebedev
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Ville Uski
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Charles Ballard
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Marcin Wojdyr
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- Global Phasing Ltd, Cambridge CB3 0AX, England
| | - Rui Wu
- Feil Family Brain and Mind Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ruslan Sanishvili
- GM/CA@APS, The X-Ray Science Division, The Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yibin Xu
- Division of Structural Biology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Royal Parade, Parkville, VIC 3050, Australia
| | - María-Natalia Lisa
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - William Shepard
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
- STFC, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
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Simpkin AJ, Lebedev A, Uski V, Ballard C, Shepard W, Rigden D, Keegan R. SIMBAD: a sequence-independent molecular replacement pipeline. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317085709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Polsinelli I, Savko M, Rouanet-Mehouas C, Ciccone L, Nencetti S, Orlandini E, Stura EA, Shepard W. Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies. J Synchrotron Radiat 2017; 24:42-52. [PMID: 28009545 DOI: 10.1107/s1600577516018488] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
X-ray radiation in macromolecular crystallography can chemically alter the biological material and deteriorate the integrity of the crystal lattice with concomitant loss of resolution. Typical alterations include decarboxylation of glutamic and aspartic residues, breaking of disulfide bonds and the reduction of metal centres. Helical scans add a small translation to the crystal in the rotation method, so that for every image the crystal is shifted to expose a fresh part. On beamline PROXIMA 2A at Synchrotron SOLEIL, this procedure has been tested with various parameters in an attempt to understand how to mitigate the effects of radiation damage. Here, the strategies used and the crystallographic metrics for various scenarios are reported. Among these, the loss of bromine from bromophenyl moieties appears to be a useful monitor of radiation damage as the carbon-bromine bond is very sensitive to X-ray irradiation. Two cases are focused on where helical scans are shown to be superior in obtaining meaningful data compared with conventional methods. In one case the initial resolution of the crystal is extended over time, and in the second case the anomalous signal is preserved to provide greater effective multiplicity and easier phasing.
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Affiliation(s)
- Ivan Polsinelli
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Cecile Rouanet-Mehouas
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), F-91191 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Enrico A Stura
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette, France
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Savko M, Fox G, Stura E, Shepard W. Getting the most of the sample with small beams and fast detectors. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316097163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ciccone L, Policar C, Stura EA, Shepard W. Human TTR conformation altered by rhenium tris-carbonyl derivatives. J Struct Biol 2016; 195:353-364. [PMID: 27402536 DOI: 10.1016/j.jsb.2016.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023]
Abstract
Transthyretin (TTR) is a 54 kDa homotetrameric serum protein that transports thyroxine (T4) and retinol. TTR is potentially amyloidogenic due to homotetramer dissociation into monomeric intermediates that self-assemble as amyloid deposits and insoluble fibrils. Most crystallographic structures, including those of amyloidogenic variants show the same tetramer without major variations in the monomer-monomer interface nor in the volume of the interdimeric cavity. Soaking TTR crystals in a solution containing rhenium tris-carbonyl derivatives yields a TTR conformer never observed before. Only one of the two monomers of the crystallographic dimer is significantly altered, and the inner part of the T4 binding cavity is expanded at one end and shrunk at the other. The result redefines the mechanism of allosteric communication between the two sites, suggesting that negative cooperativity is a function of dimer asymmetry, which can be induced through internal or external binding. An aspect that remains unexplained is why the conformational changes are ubiquitous throughout the crystal although the heavy metal content of the derivatized crystals is relatively low. The conformational changes observed, which include Leu(82), may represent a form of TTR better at scavenging β-Amyloid. At a resolution of 1.69Å, with excellent refinement statistics and well defined electron density for all parts of the structure, it is possible to envisage answering important questions that range from protein cooperative behavior to heavy atom induced protein conformational modifications that can result in crystallographic non-isomorphism.
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Affiliation(s)
- Lidia Ciccone
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France
| | - Clotilde Policar
- Ecole Normale Supérieure, Département de chimie, 24, rue Lhomond, 75005 Paris, France; Université Pierre et Marie Curie Paris 6, 4, Place Jussieu, 75005 Paris, France; CNRS, UMR7203, 75005 Paris, France
| | - Enrico A Stura
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France.
| | - William Shepard
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
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Polsinelli I, Nencetti S, Shepard W, Ciccone L, Orlandini E, Stura EA. A new crystal form of human transthyretin obtained with a curcumin derived ligand. J Struct Biol 2016; 194:8-17. [PMID: 26796656 DOI: 10.1016/j.jsb.2016.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 12/18/2022]
Abstract
Transthyretin (TTR), a 54kDa homotetrameric protein that transports thyroxine (T4), has been associated with clinical cases of TTR amyloidosis for its tendency to aggregate to form fibrils. Many ligands with a potential to inhibit fibril formation have been studied by X-ray crystallography in complex with TTR. Unfortunately, the ligand is often found in ambiguous electron density that is difficult to interpret. The ligand validation statistics suggest over-interpretation, even for the most active compounds like diflunisal. The primary technical reason is its position on a crystallographic 2-fold axis in the most common crystal form. Further investigations with the use of polyethylene glycol (PEG) to crystallize TTR complexes have resulted in a new trigonal polymorph with two tetramers in the asymmetric unit. The ligand used to obtain this new polymorph, 4-hydroxychalcone, is related to curcumin. Here we evaluate this crystal form to understand the contribution it may bring to the study of TTR ligands complexes, which are often asymmetric.
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Affiliation(s)
- Ivan Polsinelli
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - William Shepard
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Enrico A Stura
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France.
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Shepard W, Duran D, Couster SL, Blache F, Delmotte A, Fourme R, Fox G, Meijers R, Moreno T, Pierre-Joseph S, Savko M. Recent results and developments on PROXIMA 2A. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s205327331509717x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Miras I, Saul F, Nowakowski M, Weber P, Haouz A, Shepard W, Picardeau M. Structural characterization of a novel subfamily of leucine-rich repeat proteins from the human pathogen Leptospira interrogans. ACTA ACUST UNITED AC 2015; 71:1351-9. [PMID: 26057675 DOI: 10.1107/s139900471500704x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/08/2015] [Indexed: 12/26/2022]
Abstract
Pathogenic Leptospira spp. are the agents of leptospirosis, an emerging zoonotic disease. Analyses of Leptospira genomes have shown that the pathogenic leptospires (but not the saprophytes) possess a large number of genes encoding proteins containing leucine-rich repeat (LRR) domains. In other pathogenic bacteria, proteins with LRR domains have been shown to be involved in mediating host-cell attachment and invasion, but their functions remain unknown in Leptospira. To gain insight into the potential function of leptospiral LRR proteins, the crystal structures of four LRR proteins that represent a novel subfamily with consecutive stretches of a 23-amino-acid LRR repeat motif have been solved. The four proteins analyzed adopt the characteristic α/β-solenoid horseshoe fold. The exposed residues of the inner concave surfaces of the solenoid, which constitute a putative functional binding site, are not conserved. The various leptospiral LRR proteins could therefore recognize distinct structural motifs of different host proteins and thus serve separate and complementary functions in the physiology of these bacteria.
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Affiliation(s)
- Isabelle Miras
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Frederick Saul
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Mireille Nowakowski
- Institut Pasteur, Plate-forme Protéines Recombinantes, CNRS-UMR 3528, Paris, France
| | - Patrick Weber
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, Gif-sur-Yvette, France
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Bellinzoni M, Haouz A, Miras I, Magnet S, André-Leroux G, Mukherjee R, Shepard W, Cole ST, Alzari PM. Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c. J Struct Biol 2014; 188:156-64. [PMID: 25260828 DOI: 10.1016/j.jsb.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/08/2014] [Accepted: 09/16/2014] [Indexed: 11/18/2022]
Abstract
Among the few proteins shown to be secreted by the Tat system in Mycobacterium tuberculosis, Rv2525c is of particular interest, since its gene is conserved in the minimal genome of Mycobacterium leprae. Previous evidence linked this protein to cell wall metabolism and sensitivity to β-lactams. We describe here the crystal structure of Rv2525c that shows a TIM barrel-like fold characteristic of glycoside hydrolases of the GH25 family, which includes prokaryotic and phage-encoded peptidoglycan hydrolases. Structural comparison with other members of this family combined with substrate docking suggest that, although the 'neighbouring group' catalytic mechanism proposed for this family still appears as the most plausible, the identity of residues involved in catalysis in GH25 hydrolases might need to be revised.
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Affiliation(s)
- Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Ahmed Haouz
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Isabelle Miras
- Institut Pasteur, Plateforme de Cristallographie (CNRS-UMR3528), 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Sophie Magnet
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France; Unité Mathématique, Informatique et Génome (MIG), INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | - Raju Mukherjee
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - William Shepard
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette Cedex, France
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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Duran D, Le Couster S, Fox G, Fourme R, Meijers R, Samama JP, Savko M, Shepard W. PROXIMA 2A: A New Micro-focus Beamline for Macromolecular Crystallography. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314083272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
PROXIMA 2A is a new micro-focus and energy tunable beamline dedicated to biological macromolecular crystallography at Synchrotron SOLEIL. The beamline officially opened in March 2013, and its first year of user operation has yielded excellent results. The X-ray source is a powerful in-vacuum U24 undulator coupled to a cryo-cooled Si[111] channel-cut monochromator and a pair of focussing bimorph mirrors in Kirpatrick-Baez configuration. This combination delivers a photon flux of over 10**12 ph/s into a focal spot of 10 μm × 5 μm (H×V FWHM), which is tunable over 6 – 15 keV. The supports of the optical elements have been designed to minimise the effects of vibrations and thermal dilations on the X-ray beam position, which is stable to within 5 microns over a day. The experimental station consists of a high performance micro-diffractometer, a cryostream, an area detector (ADSC Q315r), and an X-ray fluorescence detector. The X-ray energies for MAD experiments are directly calibrated on the sample. A robot equipped with a large 9 uni-puck dewar (CATS Irelec) is available to users for the automated transfer and screening of cryo-cooled samples. The users launch their experiments via an MXCuBE interface [1], which permits the centering of the sample, collecting of diffraction images, recording of X-ray spectra and the transfer of samples. The X-ray diffraction data are of an excellent quality, and the users readily exploit the micro-focused X-rays to select the best zones of their crystals. The first year of results from users has yielded a variety of success stories including novel protein structures resolved from crystals as small as 5 microns, as well as those solved by SAD & MAD methods. The future perspectives include automated helical and grid scans, in situ plate screening and multi-crystal merging techniques.
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Duran D, Couster SL, Desjardins K, Delmotte A, Fox G, Meijers R, Moreno T, Savko M, Shepard W. PROXIMA 2A – A New Fully Tunable Micro-focus Beamline for Macromolecular Crystallography. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/425/1/012005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Botros HG, Legrand P, Pagan C, Bondet V, Weber P, Ben-Abdallah M, Lemière N, Huguet G, Bellalou J, Maronde E, Beguin P, Haouz A, Shepard W, Bourgeron T. Crystal structure and functional mapping of human ASMT, the last enzyme of the melatonin synthesis pathway. J Pineal Res 2013; 54:46-57. [PMID: 22775292 DOI: 10.1111/j.1600-079x.2012.01020.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Melatonin is a synchronizer of many physiological processes. Abnormal melatonin signaling is associated with human disorders related to sleep, metabolism, and neurodevelopment. Here, we present the X-ray crystal structure of human N-acetyl serotonin methyltransferase (ASMT), the last enzyme of the melatonin biosynthesis pathway. The polypeptide chain of ASMT consists of a C-terminal domain, which is typical of other SAM-dependent O-methyltransferases, and an N-terminal domain, which intertwines several helices with another monomer to form the physiologically active dimer. Using radioenzymology, we analyzed 20 nonsynonymous variants identified through the 1000 genomes project and in patients with neuropsychiatric disorders. We found that the majority of these mutations reduced or abolished ASMT activity including one relatively frequent polymorphism in the Han Chinese population (N17K, rs17149149). Overall, we estimate that the allelic frequency of ASMT deleterious mutations ranges from 0.66% in Europe to 2.97% in Asia. Mapping of the variants on to the 3-dimensional structure clarifies why some are harmful and provides a structural basis for understanding melatonin deficiency in humans.
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Affiliation(s)
- Hany Goubran Botros
- Institut Pasteur, Human Genetics and Cognitive Functions Unit, Paris, France CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur, Paris, France University Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, Gif-sur-Yvette, France Institut Pasteur, Plate forme 5, 25 rue Dr. Roux, Paris, France Institut Pasteur, Plate forme 6, CNRS-UMR3528, 25 rue Dr. Roux, Paris, France Institute for Anatomy III, Goethe University, Frankfurt, Germany
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Mechaly AE, Haouz A, Miras I, Barilone N, Weber P, Shepard W, Alzari PM, Bellinzoni M. Conformational changes upon ligand binding in the essential class II fumarase Rv1098c fromMycobacterium tuberculosis. FEBS Lett 2012; 586:1606-11. [DOI: 10.1016/j.febslet.2012.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/31/2012] [Accepted: 04/19/2012] [Indexed: 12/17/2022]
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Shepard W, Soutourina O, Courtois E, England P, Haouz A, Martin-Verstraete I. Insights into the Rrf2 repressor family--the structure of CymR, the global cysteine regulator of Bacillus subtilis. FEBS J 2011; 278:2689-701. [PMID: 21624051 DOI: 10.1111/j.1742-4658.2011.08195.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The global regulator CymR represses the transcription of a large set of genes involved in cystine uptake and cysteine biosynthesis in Bacillus subtilis and Staphylococcus aureus. This repressor belongs to the widespread and poorly characterized Rrf2 family of regulators. The crystal structure of CymR from B. subtilis reveals a biologically active dimer, where each monomer folds into two tightly packed domains: a DNA-binding domain, which houses a winged helix-turn-helix (wHTH) motif; and a long dimerization domain, which places the wHTH motifs at the extremes. This architecture explains how these small regulators can span 23-27-bp DNA targets. The wHTH motif of CymR resembles those of the GntR superfamily of regulators, such as FadR and HutC. Superimposing the FadR wHTH motifs bound to their DNA fragments onto the wHTH motifs of the CymR dimer structure suggests that the DNA target and/or the protein must undergo some conformational changes upon binding. The CymR structure also hints at a possible location of the Fe-S centre associated with several Rrf2-type regulators.
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Affiliation(s)
- William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, Gif-sur-Yvette, France
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Graña M, Bellinzoni M, Miras I, Fiez-Vandal C, Haouz A, Shepard W, Buschiazzo A, Alzari PM. Structure of Mycobacterium tuberculosis Rv2714, a representative of a duplicated gene family in Actinobacteria. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:972-7. [PMID: 19851001 DOI: 10.1107/s1744309109035027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 09/01/2009] [Indexed: 11/10/2022]
Abstract
The gene Rv2714 from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is a representative member of a gene family that is largely confined to the order Actinomycetales of Actinobacteria. Sequence analysis indicates the presence of two paralogous genes in most mycobacterial genomes and suggests that gene duplication was an ancient event in bacterial evolution. The crystal structure of Rv2714 has been determined at 2.6 A resolution, revealing a trimer in which the topology of the protomer core is similar to that observed in a functionally diverse set of enzymes, including purine nucleoside phosphorylases, some carboxypeptidases, bacterial peptidyl-tRNA hydrolases and even the plastidic form of an intron splicing factor. However, some structural elements, such as a beta-hairpin insertion involved in protein oligomerization and a C-terminal alpha-helical domain that serves as a lid to the putative substrate-binding (or ligand-binding) site, are only found in Rv2714 bacterial homologues and represent specific signatures of this protein family.
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Affiliation(s)
- Martin Graña
- Institut Pasteur, Unité de Biochimie Structurale, URA CNRS 2185, 25 Rue du Dr Roux, 75724 Paris, France
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36
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Graña M, Haouz A, Buschiazzo A, Miras I, Wehenkel A, Bondet V, Shepard W, Schaeffer F, Cole ST, Alzari PM. The crystal structure of M. leprae ML2640c defines a large family of putative S-adenosylmethionine-dependent methyltransferases in mycobacteria. Protein Sci 2007; 16:1896-904. [PMID: 17660248 PMCID: PMC2206960 DOI: 10.1110/ps.072982707] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mycobacterium leprae protein ML2640c belongs to a large family of conserved hypothetical proteins predominantly found in mycobacteria, some of them predicted as putative S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTase). As part of a Structural Genomics initiative on conserved hypothetical proteins in pathogenic mycobacteria, we have determined the structure of ML2640c in two distinct crystal forms. As expected, ML2640c has a typical MTase core domain and binds the methyl donor substrate AdoMet in a manner consistent with other known members of this structural family. The putative acceptor substrate-binding site of ML2640c is a large internal cavity, mostly lined by aromatic and aliphatic side-chain residues, suggesting that a lipid-like molecule might be targeted for catalysis. A flap segment (residues 222-256), which isolates the binding site from the bulk solvent and is highly mobile in the crystal structures, could serve as a gateway to allow substrate entry and product release. The multiple sequence alignment of ML2640c-like proteins revealed that the central alpha/beta core and the AdoMet-binding site are very well conserved within the family. However, the amino acid positions defining the binding site for the acceptor substrate display a higher variability, suggestive of distinct acceptor substrate specificities. The ML2640c crystal structures offer the first structural glimpses at this important family of mycobacterial proteins and lend strong support to their functional assignment as AdoMet-dependent methyltransferases.
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Affiliation(s)
- Martin Graña
- Unité de Biochimie Structurale (CNRS-URA 2185), Institut Pasteur, 75724 Paris, France
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Bellinzoni M, Wehenkel A, Shepard W, Alzari PM. Insights into the Catalytic Mechanism of PPM Ser/Thr Phosphatases from the Atomic Resolution Structures of a Mycobacterial Enzyme. Structure 2007; 15:863-72. [PMID: 17637345 DOI: 10.1016/j.str.2007.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 06/07/2007] [Accepted: 06/10/2007] [Indexed: 01/11/2023]
Abstract
Serine/threonine-specific phosphatases (PPs) represent, after protein tyrosine phosphatases, the second major class of enzymes that catalyze the dephosphorylation of proteins. They are classed in two large families, known as PPP and PPM, on the basis of sequence similarities, metal ion dependence, and inhibitor sensitivity. Despite their wide species distribution and broad physiological roles, the catalytic mechanism of PPM phosphatases has been primarily inferred from studies of a single enzyme, human PP2Calpha. Here, we report the biochemical characterization and the atomic resolution structures of a soluble PPM phosphatase from the saprophyte Mycobacterium smegmatis in complex with different ligands. The structures provide putative snapshots along the catalytic cycle, which support an associative reaction mechanism that differs in some important aspects from the currently accepted model and reinforces the hypothesis of convergent evolution in PPs.
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Affiliation(s)
- Marco Bellinzoni
- Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, 75724 Paris Cedex 15, France
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Shepard W, Haouz A, Graña M, Buschiazzo A, Betton JM, Cole ST, Alzari PM. The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria. J Bacteriol 2006; 189:1899-904. [PMID: 17172346 PMCID: PMC1855704 DOI: 10.1128/jb.01435-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene Rv0813c from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is conserved within the order Actinomycetales but absent elsewhere. The crystal structure of Rv0813c reveals a new family of proteins that resemble the fatty acid-binding proteins (FABPs) found in eukaryotes. Rv0813c adopts the 10-stranded beta-barrel fold typical of FABPs but lacks the double-helix insert that covers the entry to the binding site in the eukaryotic proteins. The barrel encloses a deep cavity, at the bottom of which a small cyclic ligand was found to bind to the hydroxyl group of Tyr192. This residue is part of a conserved Arg-X-Tyr motif much like the triad that binds the carboxylate group of fatty acids in FABPs. Most of the residues forming the internal surface of the cavity are conserved in homologous protein sequences found in CG-rich prokaryotes, strongly suggesting that Rv0813c is a member of a new family of bacterial FABP-like proteins that may have roles in the recognition, transport, and/or storage of small molecules in the bacterial cytosol.
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Affiliation(s)
- William Shepard
- Unité de Biochimie Structurale, CNRS URA 2185, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
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Beteva A, Cipriani F, Cusack S, Delageniere S, Gabadinho J, Gordon EJ, Guijarro M, Hall DR, Larsen S, Launer L, Lavault CB, Leonard GA, Mairs T, McCarthy A, McCarthy J, Meyer J, Mitchell E, Monaco S, Nurizzo D, Pernot P, Pieritz R, Ravelli RGB, Rey V, Shepard W, Spruce D, Stuart DI, Svensson O, Theveneau P, Thibault X, Turkenburg J, Walsh M, McSweeney SM. High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline. Acta Crystallogr D Biol Crystallogr 2006; 62:1162-9. [PMID: 17001093 DOI: 10.1107/s0907444906032859] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 08/16/2006] [Indexed: 11/10/2022]
Abstract
An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF (European Synchrotron Radiation Facility) as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline. The system allows remote interaction with beamline-control systems and automatic sample mounting, alignment, characterization, data collection and processing. Reports of all actions taken are available for inspection via database modules and web services.
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Affiliation(s)
- A Beteva
- ESRF, 6 Rue Jules Horowitz, Grenoble, France
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Bellinzoni M, Haouz A, Graña M, Munier-Lehmann H, Shepard W, Alzari PM. The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer. Protein Sci 2006; 15:1489-93. [PMID: 16672241 PMCID: PMC2242552 DOI: 10.1110/ps.062163406] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The crystal structure of Mycobacterium tuberculosis adenylate kinase (MtAK) in complex with two ADP molecules and Mg2+ has been determined at 1.9 A resolution. Comparison with the solution structure of the enzyme, obtained in the absence of substrates, shows significant conformational changes of the LID and NMP-binding domains upon substrate binding. The ternary complex represents the state of the enzyme at the start of the backward reaction (ATP synthesis). The structure is consistent with a direct nucleophilic attack of a terminal oxygen from the acceptor ADP molecule on the beta-phosphate from the donor substrate, and both the geometry and the distribution of positive charge in the active site support the hypothesis of an associative mechanism for phosphoryl transfer.
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Affiliation(s)
- Marco Bellinzoni
- Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, F-75724 Paris, France
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Buschiazzo A, Goytia M, Schaeffer F, Degrave W, Shepard W, Grégoire C, Chamond N, Cosson A, Berneman A, Coatnoan N, Alzari PM, Minoprio P. Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase. Proc Natl Acad Sci U S A 2006; 103:1705-10. [PMID: 16446443 PMCID: PMC1413642 DOI: 10.1073/pnas.0509010103] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amino acid racemases catalyze the stereoinversion of the chiral C alpha to produce the d-enantiomers that participate in biological processes, such as cell wall construction in prokaryotes. Within this large protein family, bacterial proline racemases have been extensively studied as a model of enzymes acting with a pyridoxal-phosphate-independent mechanism. Here we report the crystal structure of the proline racemase from the human parasite Trypanosoma cruzi (TcPRACA), a secreted enzyme that triggers host B cell polyclonal activation, which prevents specific humoral immune responses and is crucial for parasite evasion and fate. The enzyme is a homodimer, with each monomer folded in two symmetric alpha/beta subunits separated by a deep crevice. The structure of TcPRACA in complex with a transition-state analog, pyrrole-2-carboxylic acid, reveals the presence of one reaction center per monomer, with two Cys residues optimally located to perform acid/base catalysis through a carbanion stabilization mechanism. Mutation of the catalytic Cys residues abolishes the enzymatic activity but preserves the mitogenic properties of the protein. In contrast, inhibitor binding promotes the closure of the interdomain crevice and completely abrogates B cell proliferation, suggesting that the mitogenic properties of TcPRACA depend on the exposure of transient epitopes in the ligand-free enzyme.
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Affiliation(s)
| | - Maira Goytia
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - Francis Schaeffer
- *Unité de Biochimie Structurale, Unité de Recherche Associeé 2185, and
| | - Wim Degrave
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - William Shepard
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, F-38043 Grenoble, France
| | - Christophe Grégoire
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - Nathalie Chamond
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - Alain Cosson
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - Armand Berneman
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - Nicolas Coatnoan
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
| | - Pedro M. Alzari
- *Unité de Biochimie Structurale, Unité de Recherche Associeé 2185, and
- **To whom correspondence may be addressed. E-mail:
or
| | - Paola Minoprio
- Unité d’Immunophysio-pathologie Infectieuse, Unité de Recherche Associeé 1961, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France; and
- **To whom correspondence may be addressed. E-mail:
or
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Flot D, Gordon EJ, Hall DR, Leonard GA, McCarthy A, McCarthy J, McSweeney S, Mitchell E, Nurizzo D, Ravelli RGB, Shepard W. The care and nurture of undulator data sets. Acta Crystallogr D Biol Crystallogr 2005; 62:65-71. [PMID: 16369095 DOI: 10.1107/s0907444905032646] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Accepted: 10/11/2005] [Indexed: 11/11/2022]
Abstract
Undulator radiation is the X-ray source of choice for modern macromolecular crystallography beamlines. Here, the basic properties of undulator sources are described and it is indicated why they make such good X-ray sources for macromolecular crystallography. Collection of excellent data from these beamlines is not always straightforward; therefore, a number of rules are postulated for undulator data collection and guidelines are offered which will help to ensure a satisfactory experiment.
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Affiliation(s)
- D Flot
- EMBL, 6 Rue Jules Horowitz, 38042 Grenoble, France
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43
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Buschiazzo A, Schaeffer F, Shepard W, Alzari P. Crystal structure and catalytic mechanism of proline racemase. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305092019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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44
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Guerin M, Buschiazzo A, Gonzalez SL, Gwenaelle A, Ugalde J, Shepard W, Ugalde R, Alzari P. Structural basis of glycogen synthesis. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305088720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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45
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Shepard W, Haouz A, Buschiazzo A, Betton JM, Cole ST, Alzari P. Crystal structure of Rv0813c reveals a new family of putative FABPs. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305098958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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46
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Arzt S, Beteva A, Cipriani F, Delageniere S, Felisaz F, Förstner G, Gordon E, Launer L, Lavault B, Leonard G, Mairs T, McCarthy A, McCarthy J, McSweeney S, Meyer J, Mitchell E, Monaco S, Nurizzo D, Ravelli R, Rey V, Shepard W, Spruce D, Svensson O, Theveneau P. Automation of macromolecular crystallography beamlines. Prog Biophys Mol Biol 2005; 89:124-52. [PMID: 15910915 DOI: 10.1016/j.pbiomolbio.2004.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The production of three-dimensional crystallographic structural information of macromolecules can now be thought of as a pipeline which is being streamlined at every stage from protein cloning, expression and purification, through crystallisation to data collection and structure solution. Synchrotron X-ray beamlines are a key section of this pipeline as it is at these that the X-ray diffraction data that ultimately leads to the elucidation of macromolecular structures are collected. The burgeoning number of macromolecular crystallography (MX) beamlines available worldwide may be enhanced significantly with the automation of both their operation and of the experiments carried out on them. This paper reviews the current situation and provides a glimpse of how a MX beamline may look in the not too distant future.
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Affiliation(s)
- Steffi Arzt
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, Zip 38000, BP 220, F-38043 Grenoble Cedex, France
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47
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Guimarães BG, Souchon H, Honoré N, Saint-Joanis B, Brosch R, Shepard W, Cole ST, Alzari PM. Structure and Mechanism of the Alkyl Hydroperoxidase AhpC, a Key Elementof the Mycobacterium tuberculosis Defense System against OxidativeStress. J Biol Chem 2005; 280:25735-42. [PMID: 15886207 DOI: 10.1074/jbc.m503076200] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peroxiredoxin AhpC from Mycobacterium tuberculosis (MtAhpC) is the foremost element of a NADH-dependent peroxidase and peroxynitrite reductase system, where it directly reduces peroxides and peroxynitrite and is in turn reduced by AhpD and other proteins. Overexpression of MtAhpC in isoniazid-resistant strains of M. tuberculosis harboring mutations in the catalase/peroxidase katG gene provides antioxidant protection and may substitute for the lost enzyme activities. We report here the crystal structure of oxidized MtAhpC trapped in an intermediate oligomeric state of its catalytic cycle. The overall structure folds into a ring-shaped hexamer of dimers instead of the usual pentamer of dimers observed in other reduced peroxiredoxins. Although the general structure of the functional dimer is similar to that of other 2-Cys peroxiredoxins, the alpha-helix containing the peroxidatic cysteine Cys61 undergoes a unique rigid-body movement to allow the formation of the disulfide bridge with the resolving cysteine Cys174. This conformational rearrangement creates a large internal cavity enclosing the active site, which might be exploited for the design of inhibitors that could block the catalytic cycle. Structural and mutagenesis evidence points to a model for the electron transfer pathway in MtAhpC that accounts for the unusual involvement of three cysteine residues in catalysis and suggests a mechanism by which MtAhpC can specifically interact with different redox partners.
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Affiliation(s)
- Beatriz G Guimarães
- Unité de Biochimie Structurale, CNRS URA 2185, 25 rue du Docteur Roux and Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris
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48
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Buschiazzo A, Ugalde JE, Guerin ME, Shepard W, Ugalde RA, Alzari PM. Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation. EMBO J 2004; 23:3196-205. [PMID: 15272305 PMCID: PMC514502 DOI: 10.1038/sj.emboj.7600324] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2004] [Accepted: 06/21/2004] [Indexed: 11/10/2022] Open
Abstract
Glycogen and starch are the major readily accessible energy storage compounds in nearly all living organisms. Glycogen is a very large branched glucose homopolymer containing about 90% alpha-1,4-glucosidic linkages and 10% alpha-1,6 linkages. Its synthesis and degradation constitute central pathways in the metabolism of living cells regulating a global carbon/energy buffer compartment. Glycogen biosynthesis involves the action of several enzymes among which glycogen synthase catalyzes the synthesis of the alpha-1,4-glucose backbone. We now report the first crystal structure of glycogen synthase in the presence and absence of adenosine diphosphate. The overall fold and the active site architecture of the protein are remarkably similar to those of glycogen phosphorylase, indicating a common catalytic mechanism and comparable substrate-binding properties. In contrast to glycogen phosphorylase, glycogen synthase has a much wider catalytic cleft, which is predicted to undergo an important interdomain 'closure' movement during the catalytic cycle. The structures also provide useful hints to shed light on the allosteric regulation mechanisms of yeast/mammalian glycogen synthases.
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Affiliation(s)
| | - Juan E Ugalde
- Instituto de Investigaciones Biotecnológicas, Universidad de General San Martín and CONICET, CC 30, San Martín, Argentina
| | - Marcelo E Guerin
- Unité de Biochimie Structurale, URA 2185 CNRS, Institut Pasteur, Paris, France
| | | | - Rodolfo A Ugalde
- Instituto de Investigaciones Biotecnológicas, Universidad de General San Martín and CONICET, CC 30, San Martín, Argentina
| | - Pedro M Alzari
- Unité de Biochimie Structurale, URA 2185 CNRS, Institut Pasteur, Paris, France
- Unité de Biochimie Structurale, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris cedex 15, France. Tel.: +33 1 45 68 8607; Fax: +33 1 45 68 8604; E-mail:
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49
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Jeppesen MG, Ortiz P, Shepard W, Kinzy TG, Nyborg J, Andersen GR. The crystal structure of the glutathione S-transferase-like domain of elongation factor 1Bgamma from Saccharomyces cerevisiae. J Biol Chem 2003; 278:47190-8. [PMID: 12972429 DOI: 10.1074/jbc.m306630200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the N-terminal 219 residues (domain 1) of the conserved eukaryotic translation elongation factor 1Bgamma (eEF1Bgamma), encoded by the TEF3 gene in Saccharomyces cerevisiae, has been determined at 3.0 A resolution by the single wavelength anomalous dispersion technique. The structure is overall very similar to the glutathione S-transferase proteins and contains a pocket with architecture highly homologous to what is observed in glutathione S-transferase enzymes. The TEF3-encoded form of eEF1Bgamma has no obvious catalytic residue. However, the second form of eEF1Bgamma encoded by the TEF4 gene contains serine 11, which may act catalytically. Based on the x-ray structure and gel filtration studies, we suggest that the yeast eEF1 complex is organized as an [eEF1A.eEF1Balpha.eEF1Bgamma]2 complex. A 23-residue sequence in the middle of eEF1Bgamma is essential for the stable dimerization of eEF1Bgamma and the quaternary structure of the eEF1 complex.
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Affiliation(s)
- Mads Gravers Jeppesen
- Department of Molecular Biology, University of Arhus, Gustav Wieds vej 10 C, 8000 Arhus C, Denmark
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50
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Coste F, Shepard W, Zelwer C. Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6 Å resolution against experimental MAD phases. Addendum. Acta Crystallogr D Biol Cryst 2002. [DOI: 10.1107/s0907444902005759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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