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Mori M, Cocorullo M, Tresoldi A, Cazzaniga G, Gelain A, Stelitano G, Chiarelli LR, Tomaiuolo M, Delre P, Mangiatordi GF, Garofalo M, Cassetta A, Covaceuszach S, Villa S, Meneghetti F. Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus. Eur J Med Chem 2024; 265:116073. [PMID: 38169270 DOI: 10.1016/j.ejmech.2023.116073] [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: 11/16/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Blocking iron uptake and metabolism has been emerging as a promising therapeutic strategy for the development of novel antimicrobial compounds. Like all mycobacteria, M. abscessus (Mab) has evolved several countermeasures to scavenge iron from host carrier proteins, including the production of siderophores, which play a crucial role in these processes. In this study, we solved, for the first time, the crystal structure of Mab-SaS, the first enzyme involved in the biosynthesis of siderophores. Moreover, we screened a small, focused library and identified a compound exhibiting a potent inhibitory effect against Mab-SaS (IC50 ≈ 2 μM). Its binding mode was investigated by means of Induced Fit Docking simulations, performed on the crystal structure presented herein. Furthermore, cytotoxicity data and pharmacokinetic predictions revealed the safety and drug-likeness of this class of compounds. Finally, the crystallographic data were used to optimize the model for future virtual screening campaigns. Taken together, the findings of our study pave the way for the identification of potent Mab-SaS inhibitors, based on both established and unexplored chemotypes.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Mario Cocorullo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Andrea Tresoldi
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giovanni Stelitano
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via A. Ferrata 9, 27100, Pavia, Italy
| | - Martina Tomaiuolo
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy
| | - Pietro Delre
- Institute of Crystallography, National Research Council, Via G. Amendola 122/o, 70126, Bari, Italy
| | - Giuseppe F Mangiatordi
- Institute of Crystallography, National Research Council, Via G. Amendola 122/o, 70126, Bari, Italy
| | - Mariangela Garofalo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo 5, 35131, Padova, Italy
| | - Alberto Cassetta
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy
| | - Sonia Covaceuszach
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, 34149, Trieste, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy
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2
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Paoletti F, Covaceuszach S, Cassetta A, Calabrese AN, Novak U, Konarev P, Grdadolnik J, Lamba D, Golič Grdadolnik S. Distinct conformational changes occur within the intrinsically unstructured pro-domain of pro-Nerve Growth Factor in the presence of ATP and Mg 2. Protein Sci 2023; 32:e4563. [PMID: 36605018 PMCID: PMC9878617 DOI: 10.1002/pro.4563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Nerve growth factor (NGF), the prototypical neurotrophic factor, is involved in the maintenance and growth of specific neuronal populations, whereas its precursor, proNGF, is involved in neuronal apoptosis. Binding of NGF or proNGF to TrkA, p75NTR , and VP10p receptors triggers complex intracellular signaling pathways that can be modulated by endogenous small-molecule ligands. Here, we show by isothermal titration calorimetry and NMR that ATP binds to the intrinsically disordered pro-peptide of proNGF with a micromolar dissociation constant. We demonstrate that Mg2+ , known to play a physiological role in neurons, modulates the ATP/proNGF interaction. An integrative structural biophysics analysis by small angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry unveils that ATP binding induces a conformational rearrangement of the flexible pro-peptide domain of proNGF. This suggests that ATP may act as an allosteric modulator of the overall proNGF conformation, whose likely distinct biological activity may ultimately affect its physiological homeostasis.
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Affiliation(s)
- Francesca Paoletti
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
| | | | - Alberto Cassetta
- Institute of Crystallography—C.N.R.—Trieste OutstationTriesteItaly
| | - Antonio N. Calabrese
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Urban Novak
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
| | - Petr Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”Russian Academy of SciencesMoscowRussia
| | - Jože Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
| | - Doriano Lamba
- Institute of Crystallography—C.N.R.—Trieste OutstationTriesteItaly
- Interuniversity Consortium “Biostructures and Biosystems National Institute”RomeItaly
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory DepartmentNational Institute of ChemistryLjubljanaSlovenia
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3
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Romagnoli L, D’Annibale A, Blundo E, Polimeni A, Cassetta A, Chita G, Panetta R, Ciccioli A, Latini A. Synthesis, Structure, and Characterization of 4,4'-(Anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) Bismuth Iodide (C 30H 22N 2) 3Bi 4I 18, an Air, Water, and Thermally Stable 0D Hybrid Perovskite with High Photoluminescence Efficiency. Cryst Growth Des 2022; 22:7426-7433. [PMID: 36510624 PMCID: PMC9732820 DOI: 10.1021/acs.cgd.2c01005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/10/2022] [Indexed: 06/17/2023]
Abstract
4,4'-(Anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) bismuth iodide (C30H22N2)3Bi4I18 (AEPyBiI) was obtained as a black powder by a very simple route by mixing an acetone solution of BiI3 and an aqueous solution of C30H22N2I2. This novel perovskite is air and water stable and displays a remarkable thermal stability up to nearly 300 °C. The highly conjugated cation C30H22N2 2+ is hydrolytically stable, being nitrogen atoms quaternarized, and this accounts for the insensitivity of the perovskite toward water and atmospheric oxygen under ambient conditions. The cation in aqueous solution is highly fluorescent under UV irradiation (emitting yellow-orange light). AEPyBiI as well is intensely luminescent, its photoluminescence emission being more than 1 order of magnitude greater than that of high-quality InP epilayers. The crystal structure of AEPyBiI was determined using synchrotron radiation single-crystal X-ray diffraction. AEPyBiI was extensively characterized using a wide range of techniques, such as X-ray powder diffraction, diffuse reflectance UV-vis spectroscopy, Fourier transform infrared (FTIR) and Raman spectroscopies, thermogravimetry-differential thermal analysis (TG-DTA), elemental analysis, electrospray ionization mass spectroscopy (ESI-MS), and photoluminescence spectroscopy. AEPyBiI displays a zero-dimensional (0D) perovskite structure in which the inorganic part is constituted by binuclear units consisting of two face-sharing BiI6 octahedra (Bi2I9 3- units). The C30H22N2 2+ cations are stacked along the a-axis direction in a complex motif. Considering its noteworthy light-emitting properties coupled with an easy synthesis and environmental stability, and its composition that does not contain toxic lead or easily oxidable Sn(II), AEPyBiI is a promising candidate for environmentally friendly light-emitting devices.
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Affiliation(s)
- Lorenza Romagnoli
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro
5, 00185Roma, Italy
| | - Andrea D’Annibale
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro
5, 00185Roma, Italy
| | - Elena Blundo
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro
5, 00185Roma, Italy
| | - Antonio Polimeni
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro
5, 00185Roma, Italy
| | - Alberto Cassetta
- Consiglio
Nazionale delle Ricerche, Istituto di Cristallografia,
Sede Secondaria di Trieste, Area Science Park − Basovizza, Strada Statale
14, km 163.5, 34149Trieste, Italy
| | - Giuseppe Chita
- Consiglio
Nazionale delle Ricerche, Istituto di Cristallografia,
Sede Secondaria di Trieste, Area Science Park − Basovizza, Strada Statale
14, km 163.5, 34149Trieste, Italy
| | - Riccardo Panetta
- Ispa
- Istituto Sperimentale Problematiche Ambientali, Via San Nicandro snc, 03042Atina, FR, Italy
| | - Andrea Ciccioli
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro
5, 00185Roma, Italy
| | - Alessandro Latini
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro
5, 00185Roma, Italy
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4
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Paoletti F, Merzel F, Cassetta A, Ogris I, Covaceuszach S, Grdadolnik J, Lamba D, Golič Grdadolnik S. Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions. Comput Struct Biotechnol J 2021; 19:2938-2949. [PMID: 34136093 PMCID: PMC8164016 DOI: 10.1016/j.csbj.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
High-resolution solution NMR structure of rhNGF has been determined. Quinary interactions characterize ATP binding to rhNGF. SPR, ITC and STD-NMR reveal ATP binding to rhNGF with mM affinity. NMR and MD analysis pinpoint to the presence of two binding sites of ATP on rhNGF. Stoichiometry of ATP-Mg2+ or Zn2+-rhNGF mixtures affects KD affinity to TrkA/p75NTR.
The Nerve Growth Factor (NGF) neurotrophin acts in the maintenance and growth of neuronal populations. Despite the detailed knowledge of NGF’s role in neuron physiology, the structural and mechanistic determinants of NGF bioactivity modulated by essential endogenous ligands are still lacking. We present the results of an integrated structural and advanced computational approach to characterize the extracellular ATP-NGF interaction. We mapped by NMR the interacting surface and ATP orientation on NGF and revealed the functional role of this interaction in the binding to TrkA and p75NTR receptors by SPR. The role of divalent ions was explored in conjunction with ATP. Our results pinpoint ATP as a likely transient molecular modulator of NGF signaling, in health and disease states.
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Key Words
- ARIA, Ambiguous Restraints for Iterative Assignment
- ATP modulation
- BDNF, Brain Derived Neurotrophic Factor
- CARA, Computer Aided Resonance Assignment
- CS-E, Chrondroitin Sulfate E
- CSP, Chemical Shift Perturbation
- DSF, Differential Scanning Fluorimetry
- EI-MS, Electron Ionization Mass Spectrometry
- Endogenous ligands
- FGF2, Fibroblast Growth Factor 2
- FT-IR, Fourier Transform Infrared Spectroscopy
- HBD, Heparin Binding Domain
- HSQC, Heteronuclear Single Quantum Coherence
- ITC, Isothermal Titration Calorimetry
- MALDI-TOF MS, Matrix Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry
- MD, Molecular Dynamics
- MS, Mass Spectrometry
- NGF interactions
- NGF, Nerve Growth Factor
- NMR, Nuclear Magnetic Resonance
- NOE, Nuclear Overhouser Effect
- NOESY, Nuclear Overhauser Effect Spectroscopy
- NT, NeuroTrophin
- Neurotrophins
- P20, Polysorbate 20
- PME, Particle Mesh Ewald
- RMSD, Root Mean Square Deviation
- SAR, Structure-Activity Relationship
- SPR, Surface Plasmon Resonance
- STD, Saturation-Transfer Difference
- TrkA, Tyrosine Kinase Receptor A
- TrkA, p75NTR receptors
- p75NTR, p75 NeuroTrophin Receptor
- proNGF, proNGF – NGF precursor
- rh-proNGF, recombinant human proNGF – NGF precursor
- rhNGF, recombinant human NGF
- rmNGF, recombinant mouse NGF
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Affiliation(s)
- Francesca Paoletti
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Franci Merzel
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Alberto Cassetta
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
| | - Iza Ogris
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sonia Covaceuszach
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
| | - Jože Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Doriano Lamba
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy.,Interuniversity Consortium "Biostructures and Biosystems National Institute", Viale delle Medaglie d'Oro 305, I-00136 Roma, Italy
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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5
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Maso L, Trande M, Liberi S, Moro G, Daems E, Linciano S, Sobott F, Covaceuszach S, Cassetta A, Fasolato S, Moretto LM, De Wael K, Cendron L, Angelini A. Unveiling the binding mode of perfluorooctanoic acid to human serum albumin. Protein Sci 2021; 30:830-841. [PMID: 33550662 DOI: 10.1002/pro.4036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 10/13/2020] [Revised: 01/12/2021] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
Perfluorooctanoic acid (PFOA) is a toxic compound that is absorbed and distributed throughout the body by noncovalent binding to serum proteins such as human serum albumin (hSA). Though the interaction between PFOA and hSA has been already assessed using various analytical techniques, a high resolution and detailed analysis of the binding mode is still lacking. We report here the crystal structure of hSA in complex with PFOA and a medium-chain saturated fatty acid (FA). A total of eight distinct binding sites, four occupied by PFOAs and four by FAs, have been identified. In solution binding studies confirmed the 4:1 PFOA-hSA stoichiometry and revealed the presence of one high and three low affinity binding sites. Competition experiments with known hSA-binding drugs allowed locating the high affinity binding site in sub-domain IIIA. The elucidation of the molecular basis of the interaction between PFOA and hSA might provide not only a better assessment of the absorption and elimination mechanisms of these compounds in vivo but also have implications for the development of novel molecular receptors for diagnostic and biotechnological applications.
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Affiliation(s)
- Lorenzo Maso
- Department of Biology, University of Padua, Padova, Italy
| | - Matteo Trande
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Stefano Liberi
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Giulia Moro
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.,Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Elise Daems
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.,Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Antwerp, Belgium.,Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | | | - Alberto Cassetta
- Istituto di Cristallografia - CNR, Trieste Outstation, Trieste, Italy
| | | | - Ligia M Moretto
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Karolien De Wael
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Laura Cendron
- Department of Biology, University of Padua, Padova, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.,European Centre for Living Technology (ECLT), Venice, Italy
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6
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Moro G, Bottari F, Liberi S, Covaceuszach S, Cassetta A, Angelini A, De Wael K, Moretto LM. Covalent immobilization of delipidated human serum albumin on poly(pyrrole-2-carboxylic) acid film for the impedimetric detection of perfluorooctanoic acid. Bioelectrochemistry 2020; 134:107540. [PMID: 32361666 DOI: 10.1016/j.bioelechem.2020.107540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 02/27/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022]
Abstract
The immobilization of biomolecules at screen printed electrodes for biosensing applications is still an open challenge. To enrich the toolbox of bioelectrochemists, graphite screen printed electrodes (G-SPE) were modified with an electropolymerized film of pyrrole-2-carboxilic acid (Py-2-COOH), a pyrrole derivative rich in carboxylic acid functional groups. These functionalities are suitable for the covalent immobilization of biomolecular recognition layers. The electropolymerization was first optimized to obtain stable and conductive polymeric films, comparing two different electrolytes: sodium dodecyl sulphate (SDS) and sodium perchlorate. The G-SPE modified with Py-2-COOH in 0.1 M SDS solution showed the required properties and were further tested. A proof-of-concept study for the development of an impedimetric sensor for perfluorooctanoic acid (PFOA) was carried out using the delipidated human serum albumin (hSA) as bioreceptor. The data interpretation was supported by size exclusion chromatography and small-angle X-ray scattering (SEC-SAXS) analysis of the bioreceptor-target complex and the preliminary results suggest the possibility to further develop this biosensing strategy for toxicological and analytical studies.
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Affiliation(s)
- Giulia Moro
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy; AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
| | - Fabio Bottari
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Stefano Liberi
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Sonia Covaceuszach
- Istituto di Cristallografia - CNR, Trieste Outstation, Italy SS 14 km 163.5, Basovizza, Trieste, Italy
| | - Alberto Cassetta
- Istituto di Cristallografia - CNR, Trieste Outstation, Italy SS 14 km 163.5, Basovizza, Trieste, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Karolien De Wael
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ligia Maria Moretto
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
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7
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Latini A, Quaranta S, Menchini F, Lisi N, Di Girolamo D, Tarquini O, Colapietro M, Barba L, Demitri N, Cassetta A. A novel water-resistant and thermally stable black lead halide perovskite, phenyl viologen lead iodide C 22H 18N 2(PbI 3) 2. Dalton Trans 2020; 49:2616-2627. [PMID: 32039432 DOI: 10.1039/c9dt04148f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A novel black organoammonium iodoplumbate semiconductor, namely phenyl viologen lead iodide C22H18N2(PbI3)2 (PhVPI), was successfully synthesized and characterized. This material showed physical and chemical properties suitable for photovoltaic applications. Indeed, low direct allowed band gap energy (Eg = 1.32 eV) and high thermal stability (up to at least 300 °C) compared to methylammonium lead iodide CH3NH3PbI3 (MAPI, Eg = 1.5 eV) render PhVPI potentially attractive for solar cell fabrication. The compound was extensively characterized by means of X-ray diffraction (performed on both powder and single crystals), UV-Vis diffuse reflectance spectroscopy (UV-Vis DRS), UV-photoelectron spectroscopy (UPS), FT-IR spectroscopy, TG-DTA, and CHNS analysis. Reactivity towards water was monitored through X-ray powder diffraction carried out after prolonged immersion of the material in water at room temperature. Unlike its methyl ammonium counterpart, PhVPI proved to be unaffected by water exposure. The lack of reactivity towards water is to be attributed to the quaternary nature of the nitrogen atoms of the phenyl viologen units that prevents the formation of acid-base equilibria when in contact with water. On the other hand, PhVPI's thermal stability was evaluated by temperature-controlled powder XRD measurements following an hour-long isothermal treatment at 250 and 300 °C. In both cases no signs of decomposition could be detected. However, the compound melted incongruently at 332 °C producing, upon cooling, a mostly amorphous material. PhVPI was found to be slightly soluble in DMF (∼5 mM) and highly soluble in DMSO. Nevertheless, its solubility in DMF can be dramatically increased by adding an equimolar amount of DMSO. Therefore, phenyl viologen lead iodide can be amenable for the fabrication of solar devices by spin coating as actually done for MAPI-based cells. The crystal structure, determined by means of single crystal X-ray diffraction using synchrotron radiation, turned out to be triclinic and consequently differs from the prototypal perovskite structure. In fact, it comprises infinite double chains of corner-sharing PbI6 octahedra along the a-axis direction with phenyl viologen cations positioned between the columns. Finally, the present determination of PhVPI's electronic band structure achieved through UPS and UV-Vis DRS is instrumental in using the material for solar cells.
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Affiliation(s)
- Alessandro Latini
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy.
| | - Simone Quaranta
- Dipartimento di Ingegneria dell'Informazione, Elettronica e Telecomunicazioni, Sapienza Università di Roma, Via Eudossiana, 18, 00184 Roma, Italy
| | - Francesca Menchini
- ENEA - Energy Technologies Department, Via Anguillarese, 301, 00123 Roma, Italy
| | - Nicola Lisi
- ENEA - Energy Technologies Department, Via Anguillarese, 301, 00123 Roma, Italy
| | - Diego Di Girolamo
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy.
| | - Ombretta Tarquini
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia, Via Salaria km 29, 300, 00015 Monterotondo Scalo, Roma, Italy
| | - Marcello Colapietro
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia, Via Salaria km 29, 300, 00015 Monterotondo Scalo, Roma, Italy
| | - Luisa Barba
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia, Sede Secondaria di Trieste, Area Science Park - Basovizza, Strada Statale 14, km 163.5, 34149 Trieste, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste, Area Science Park - Basovizza, Strada Statale 14, km 163.5, 34149 Trieste, Italy
| | - Alberto Cassetta
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia, Sede Secondaria di Trieste, Area Science Park - Basovizza, Strada Statale 14, km 163.5, 34149 Trieste, Italy
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8
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D'Annibale A, Panetta R, Tarquini O, Colapietro M, Quaranta S, Cassetta A, Barba L, Chita G, Latini A. Synthesis, physico-chemical characterization and structure of the elusive hydroxylammonium lead iodide perovskite NH3OHPbI3. Dalton Trans 2019; 48:5397-5407. [DOI: 10.1039/c9dt00690g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The elusive hydroxylammonium lead iodide NH3OHPbI3 has been successfully synthesized and characterized for the first time.
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Affiliation(s)
- Andrea D'Annibale
- Dipartimento di Chimica
- Università degli Studi di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Riccardo Panetta
- Dipartimento di Chimica
- Università degli Studi di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Ombretta Tarquini
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia
- Roma
- Italy
| | | | - Simone Quaranta
- Dipartimento di Ingegneria dell'Informazione
- Elettronica e Telecomunicazioni
- Università degli Studi di Roma “La Sapienza”
- 00184 Roma
- Italy
| | - Alberto Cassetta
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia
- Sede Secondaria di Trieste
- 34149 Trieste
- Italy
| | - Luisa Barba
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia
- Sede Secondaria di Trieste
- 34149 Trieste
- Italy
| | - Giuseppe Chita
- Consiglio Nazionale delle Ricerche - Istituto di Cristallografia
- Sede Secondaria di Trieste
- 34149 Trieste
- Italy
| | - Alessandro Latini
- Dipartimento di Chimica
- Università degli Studi di Roma “La Sapienza”
- 00185 Roma
- Italy
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9
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White KI, Bugris V, McCarthy AA, Ravelli RBG, Csankó K, Cassetta A, Brockhauser S. Calibration of rotation axes for multi-axis goniometers in macromolecular crystallography. J Appl Crystallogr 2018; 51:1421-1427. [PMID: 30279641 PMCID: PMC6157707 DOI: 10.1107/s1600576718010956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/31/2018] [Indexed: 11/10/2022] Open
Abstract
An easy to perform rotation calibration procedure has been developed for miniKappa and/or other multi-axis goniometers used in macromolecular crystallography to enhance the precision of experiments involving crystal reorientations. The installation of multi-axis goniometers such as the ESRF/EMBL miniKappa goniometer system has allowed the increased use of sample reorientation in macromolecular crystallography. Old and newly appearing data collection methods require precision and accuracy in crystal reorientation. The proper use of such multi-axis systems has necessitated the development of rapid and easy to perform methods for establishing and evaluating device calibration. A new diffraction-based method meeting these criteria has been developed for the calibration of the motors responsible for rotational motion. This method takes advantage of crystal symmetry by comparing the orientations of a sample rotated about a given axis and checking that the magnitude of the real rotation fits the calculated angle between these two orientations. Hence, the accuracy and precision of rotational motion can be assessed. This rotation calibration procedure has been performed on several beamlines at the ESRF and other synchrotrons. Some resulting data are presented here for reference.
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Affiliation(s)
- K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Campus Drive, Stanford, CA 94305, USA.,European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Valeria Bugris
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári körút 62, Szeged, Csongrad 6726, Hungary
| | - Andrew A McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France
| | - Raimond B G Ravelli
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France.,M4I Division of Nanoscopy, Maastricht University, PO Box 616, MD Maastricht, 6200, The Netherlands
| | - Krisztián Csankó
- Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári körút 62, Szeged, Csongrad 6726, Hungary
| | - Alberto Cassetta
- XRD1 Beamline - Elettra, CNR - Istituto di Cristallografia - Unità di Trieste, S.S. 14 Km 163,5, Trieste, Basovizza I-34012, Italy
| | - Sandor Brockhauser
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, Grenoble, 38042, France.,Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári körút 62, Szeged, Csongrad 6726, Hungary.,European X-ray Free-Electron Laser Facility GmbH (XFEL.EU), Holzkoppel 4, Hamburg, Schenefeld 22869, Germany
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10
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Signorino G, Covaceuszach S, Bozzi M, Hübner W, Mönkemöller V, Konarev PV, Cassetta A, Brancaccio A, Sciandra F. Cover Image, Volume 39, Issue 2. Hum Mutat 2018. [DOI: 10.1002/humu.23391] [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: 11/09/2022]
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11
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Signorino G, Covaceuszach S, Bozzi M, Hübner W, Mönkemöller V, Konarev PV, Cassetta A, Brancaccio A, Sciandra F. A dystroglycan mutation (p.Cys667Phe) associated to muscle-eye-brain disease with multicystic leucodystrophy results in ER-retention of the mutant protein. Hum Mutat 2017; 39:266-280. [PMID: 29134705 DOI: 10.1002/humu.23370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 08/07/2017] [Revised: 10/13/2017] [Accepted: 11/06/2017] [Indexed: 01/11/2023]
Abstract
Dystroglycan (DG) is a cell adhesion complex composed by two subunits, the highly glycosylated α-DG and the transmembrane β-DG. In skeletal muscle, DG is involved in dystroglycanopathies, a group of heterogeneous muscular dystrophies characterized by a reduced glycosylation of α-DG. The genes mutated in secondary dystroglycanopathies are involved in the synthesis of O-mannosyl glycans and in the O-mannosylation pathway of α-DG. Mutations in the DG gene (DAG1), causing primary dystroglycanopathies, destabilize the α-DG core protein influencing its binding to modifying enzymes. Recently, a homozygous mutation (p.Cys699Phe) hitting the β-DG ectodomain has been identified in a patient affected by muscle-eye-brain disease with multicystic leucodystrophy, suggesting that other mechanisms than hypoglycosylation of α-DG could be implicated in dystroglycanopathies. Herein, we have characterized the DG murine mutant counterpart by transfection in cellular systems and high-resolution microscopy. We observed that the mutation alters the DG processing leading to retention of its uncleaved precursor in the endoplasmic reticulum. Accordingly, small-angle X-ray scattering data, corroborated by biochemical and biophysical experiments, revealed that the mutation provokes an alteration in the β-DG ectodomain overall folding, resulting in disulfide-associated oligomerization. Our data provide the first evidence of a novel intracellular mechanism, featuring an anomalous endoplasmic reticulum-retention, underlying dystroglycanopathy.
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Affiliation(s)
- Giulia Signorino
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
| | | | - Manuela Bozzi
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy.,Istituto di Chimica del Riconoscimento Molecolare - CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Wolfgang Hübner
- Biomolecular Photonics, University of Bielefeld, Bielefeld, Germany
| | | | - Petr V Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninsky prospect 59, Moscow, Russia
| | - Alberto Cassetta
- Istituto di Cristallografia - CNR, Trieste Outstation, Trieste, Italy
| | - Andrea Brancaccio
- Istituto di Chimica del Riconoscimento Molecolare - CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy.,School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Francesca Sciandra
- Istituto di Chimica del Riconoscimento Molecolare - CNR c/o Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
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12
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Covaceuszach S, Bozzi M, Bigotti MG, Sciandra F, Konarev PV, Brancaccio A, Cassetta A. The effect of the pathological V72I, D109N and T190M missense mutations on the molecular structure of α-dystroglycan. PLoS One 2017; 12:e0186110. [PMID: 29036200 PMCID: PMC5643065 DOI: 10.1371/journal.pone.0186110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
Dystroglycan (DG) is a highly glycosylated protein complex that links the cytoskeleton with the extracellular matrix, mediating fundamental physiological functions such as mechanical stability of tissues, matrix organization and cell polarity. A crucial role in the glycosylation of the DG α subunit is played by its own N-terminal region that is required by the glycosyltransferase LARGE. Alteration in this O-glycosylation deeply impairs the high affinity binding to other extracellular matrix proteins such as laminins. Recently, three missense mutations in the gene encoding DG, mapped in the α-DG N-terminal region, were found to be responsible for hypoglycosylated states, causing congenital diseases of different severity referred as primary dystroglycanopaties.To gain insight on the molecular basis of these disorders, we investigated the crystallographic and solution structures of these pathological point mutants, namely V72I, D109N and T190M. Small Angle X-ray Scattering analysis reveals that these mutations affect the structures in solution, altering the distribution between compact and more elongated conformations. These results, supported by biochemical and biophysical assays, point to an altered structural flexibility of the mutant α-DG N-terminal region that may have repercussions on its interaction with LARGE and/or other DG-modifying enzymes, eventually reducing their catalytic efficiency.
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Affiliation(s)
| | - Manuela Bozzi
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
- Istituto di Chimica del Riconoscimento Molecolare—CNR c/o Università Cattolica del Sacro Cuore, Roma, Italy
| | | | - Francesca Sciandra
- Istituto di Chimica del Riconoscimento Molecolare—CNR c/o Università Cattolica del Sacro Cuore, Roma, Italy
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Andrea Brancaccio
- Istituto di Chimica del Riconoscimento Molecolare—CNR c/o Università Cattolica del Sacro Cuore, Roma, Italy
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Alberto Cassetta
- Istituto di Cristallografia–CNR, Trieste Outstation, Trieste, Italy
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13
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Covaceuszach S, Bozzi M, Bigotti MG, Sciandra F, Konarev PV, Brancaccio A, Cassetta A. Structural flexibility of human α-dystroglycan. FEBS Open Bio 2017; 7:1064-1077. [PMID: 28781947 PMCID: PMC5537065 DOI: 10.1002/2211-5463.12259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 01/13/2023] Open
Abstract
Dystroglycan (DG), composed of α and β subunits, belongs to the dystrophin-associated glycoprotein complex. α-DG is an extracellular matrix protein that undergoes a complex post-translational glycosylation process. The bifunctional glycosyltransferase like-acetylglucosaminyltransferase (LARGE) plays a crucial role in the maturation of α-DG, enabling its binding to laminin. We have already structurally analyzed the N-terminal region of murine α-DG (α-DG-Nt) and of a pathological single point mutant that may affect recognition of LARGE, although the structural features of the potential interaction between LARGE and DG remain elusive. We now report on the crystal structure of the wild-type human α-DG-Nt that has allowed us to assess the reliability of our murine crystallographic structure as a α-DG-Nt general model. Moreover, we address for the first time both structures in solution. Interestingly, small-angle X-ray scattering (SAXS) reveals the existence of two main protein conformations ensembles. The predominant species is reminiscent of the crystal structure, while the less populated one assumes a more extended fold. A comparative analysis of the human and murine α-DG-Nt solution structures reveals that the two proteins share a common interdomain flexibility and population distribution of the two conformers. This is confirmed by the very similar stability displayed by the two orthologs as assessed by biochemical and biophysical experiments. These results highlight the need to take into account the molecular plasticity of α-DG-Nt in solution, as it can play an important role in the functional interactions with other binding partners.
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Affiliation(s)
| | - Manuela Bozzi
- Istituto di Biochimica e Biochimica ClinicaUniversità Cattolica del Sacro CuoreRomaItaly
- Istituto di Chimica del Riconoscimento MolecolareCNR c/o Università Cattolica del Sacro CuoreRomaItaly
| | | | - Francesca Sciandra
- Istituto di Chimica del Riconoscimento MolecolareCNR c/o Università Cattolica del Sacro CuoreRomaItaly
| | - Petr Valeryevich Konarev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre“Crystallography and Photonics” of Russian Academy of SciencesMoscowRussia
- National Research Centre “Kurchatov Institute”MoscowRussia
| | - Andrea Brancaccio
- Istituto di Chimica del Riconoscimento MolecolareCNR c/o Università Cattolica del Sacro CuoreRomaItaly
- School of BiochemistryUniversity of BristolUK
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14
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Cassetta A, Stojan J, Krastanova I, Kristan K, Brunskole Švegelj M, Lamba D, Lanišnik Rižner T. Structural basis for inhibition of 17β-hydroxysteroid dehydrogenases by phytoestrogens: The case of fungal 17β-HSDcl. J Steroid Biochem Mol Biol 2017; 171:80-93. [PMID: 28259640 DOI: 10.1016/j.jsbmb.2017.02.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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] [Received: 12/12/2016] [Revised: 02/10/2017] [Accepted: 02/28/2017] [Indexed: 01/03/2023]
Abstract
Phytoestrogens are plant-derived compounds that functionally and structurally mimic mammalian estrogens. Phytoestrogens have broad inhibitory activities toward several steroidogenic enzymes, such as the 17β-hydroxysteroid dehydrogenases (17β-HSDs), which modulate the biological potency of androgens and estrogens in mammals. However, to date, no crystallographic data are available to explain phytoestrogens binding to mammalian 17β-HSDs. NADP(H)-dependent 17β-HSD from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) has been the subject of extensive biochemical, kinetic and quantitative structure-activity relationship studies that have shown that the flavonols are the most potent inhibitors. In the present study, we investigated the structure-activity relationships of the ternary complexes between the holo form of 17β-HSDcl and the flavonols kaempferol and 3,7-dihydroxyflavone, in comparison with the isoflavones genistein and biochanin A. Crystallographic data are accompanied by kinetic analysis of the inhibition mechanisms for six flavonols (3-hydroxyflavone, 3,7-dihydroxyflavone, kaempferol, quercetin, fisetin, myricetin), one flavanone (naringenin), one flavone (luteolin), and two isoflavones (genistein, biochanin A). The kinetics analysis shows that the degree of hydroxylation of ring B significantly influences the overall inhibitory efficacy of the flavonols. A distinct binding mode defines the interactions between 17β-HSDcl and the flavones and isoflavones. Moreover, the complex with biochanin A reveals an unusual binding mode that appears to account for its greater inhibition of 17β-HSDcl with respect to genistein. Overall, these data provide a blueprint for identification of the distinct molecular determinants that underpin 17β-HSD inhibition by phytoestrogens.
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Affiliation(s)
- Alberto Cassetta
- Istituto di Cristallografia, UOS Trieste, Consiglio Nazionale delle Ricerche, S. S. 14-Km 163.5, I-34149, Trieste, Italy.
| | - Jure Stojan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia.
| | - Ivet Krastanova
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S. C. p. A., S. S. 14-Km 163.5, I-34149, Trieste, Italy
| | - Katja Kristan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Mojca Brunskole Švegelj
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Doriano Lamba
- Istituto di Cristallografia, UOS Trieste, Consiglio Nazionale delle Ricerche, S. S. 14-Km 163.5, I-34149, Trieste, Italy
| | - Tea Lanišnik Rižner
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
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15
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Covaceuszach S, Konarev PV, Cassetta A, Paoletti F, Svergun DI, Lamba D, Cattaneo A. The conundrum of the high-affinity NGF binding site formation unveiled? Biophys J 2015; 108:687-97. [PMID: 25650935 PMCID: PMC4317559 DOI: 10.1016/j.bpj.2014.11.3485] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 11/15/2022] Open
Abstract
The homodimer NGF (nerve growth factor) exerts its neuronal activity upon binding to either or both distinct transmembrane receptors TrkA and p75(NTR). Functionally relevant interactions between NGF and these receptors have been proposed, on the basis of binding and signaling experiments. Namely, a ternary TrkA/NGF/p75(NTR) complex is assumed to be crucial for the formation of the so-called high-affinity NGF binding sites. However, the existence, on the cell surface, of direct extracellular interactions is still a matter of controversy. Here, supported by a small-angle x-ray scattering solution study of human NGF, we propose that it is the oligomerization state of the secreted NGF that may drive the formation of the ternary heterocomplex. Our data demonstrate the occurrence in solution of a concentration-dependent distribution of dimers and dimer of dimers. A head-to-head molecular assembly configuration of the NGF dimer of dimers has been validated. Overall, these findings prompted us to suggest a new, to our knowledge, model for the transient ternary heterocomplex, i.e., a TrkA/NGF/p75(NTR) ligand/receptors molecular assembly with a (2:4:2) stoichiometry. This model would neatly solve the problem posed by the unconventional orientation of p75(NTR) with respect to TrkA, as being found in the crystal structures of the TrkA/NGF and p75(NTR)/NGF complexes.
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Affiliation(s)
- Sonia Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - Petr V Konarev
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany; Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
| | - Alberto Cassetta
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Trieste, Italy.
| | - Antonino Cattaneo
- European Brain Research Institute, Roma, Italy; Scuola Normale Superiore, Pisa, Italy.
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16
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Covaceuszach S, Cassetta A, Konarev PV, Gonfloni S, Rudolph R, Svergun DI, Lamba D, Cattaneo A. Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody. J Mol Biol 2008; 381:881-96. [PMID: 18635195 DOI: 10.1016/j.jmb.2008.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/30/2008] [Accepted: 06/04/2008] [Indexed: 11/29/2022]
Abstract
The anti-nerve growth factor (NGF) monoclonal antibody alphaD11 is a potent antagonist that neutralizes the biological functions of its antigen in vivo. NGF antagonism is expected to be a highly effective and safe therapeutic approach in many pain states. A comprehensive functional and structural analysis of alphaD11 monoclonal antibody was carried out, showing its ability to neutralize NGF binding to either tropomyosine receptor kinase A (TrkA) or p75 receptors. The 3-D structure of the alphaD11 Fab fragment was solved at 1.7 A resolution. A computational docking model of the alphaD11 Fab-NGF complex, based on epitope mapping using a pool of 44 NGF mutants and experimentally validated by small-angle X-ray scattering, provided the structural basis for identifying the residues involved in alphaD11 Fab binding. The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor.
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17
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Portalone G, Cassetta A, Colapietro M, Plattner SH. (3 R,5 S)-5(3)-Carboxy-3,4,5,6-tetrahydro-2 H-1,4-thiazin-4-ium-3(5)-carboxylate. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o636. [PMID: 21201967 PMCID: PMC2960813 DOI: 10.1107/s1600536808005151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 02/22/2008] [Indexed: 11/10/2022]
Abstract
The molecule of the zwitterionic title compound, C6H9NO4S, which lies on a mirror plane, shows a puckered chair conformation of the six-membered ring with the S and N atoms out of the mean plane of the other four C atoms by 0.929 (2) and 0.647 (2) Å, respectively. The ionized carboxyl group is equatorially oriented. The hydrogen-bonding network includes very short O—H⋯O [2.470 (2) Å] and N—H⋯S [3.471 (2) and 3.416 (2) Å] intermolecular contacts.
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18
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Cassetta A, Büdefeld T, Rizner TL, Kristan K, Stojan J, Lamba D. Crystallization, X-ray diffraction analysis and phasing of 17beta-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1032-4. [PMID: 16511227 PMCID: PMC1978160 DOI: 10.1107/s1744309105034949] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [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: 09/07/2005] [Accepted: 10/26/2005] [Indexed: 11/11/2022]
Abstract
17beta-Hydroxysteroid dehydrogenase from the filamentous fungus Cochliobolus lunatus (17beta-HSDcl) is an NADP(H)-dependent enzyme that preferentially catalyses the oxidoreduction of oestrogens and androgens. The enzyme belongs to the short-chain dehydrogenase/reductase superfamily and is the only fungal hydroxysteroid dehydrogenase known to date. 17beta-HSDcl has recently been characterized and cloned and has been the subject of several functional studies. Although several hypotheses on the physiological role of 17beta-HSDcl in fungal metabolism have been formulated, its function is still unclear. An X-ray crystallographic study has been undertaken and the optimal conditions for crystallization of 17beta-HSDcl (apo form) were established, resulting in well shaped crystals that diffracted to 1.7 A resolution. The space group was identified as I4(1)22, with unit-cell parameters a = b = 67.14, c = 266.77 A. Phasing was successfully performed by Patterson search techniques. A catalytic inactive mutant Tyr167Phe was also engineered, expressed, purified and crystallized for functional and structural studies.
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Affiliation(s)
- Alberto Cassetta
- Institute of Crystallography, CNR, Trieste Outstation, Area Science Park-Basovizza, S.S.14, I-34012 Trieste, Italy.
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Di Profio G, Perrone G, Curcio E, Cassetta A, Lamba D, Drioli E. Preparation of Enzyme Crystals with Tunable Morphology in Membrane Crystallizers. Ind Eng Chem Res 2005. [DOI: 10.1021/ie0508233] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [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)
- Gianluca Di Profio
- Institute on Membrane Technology (ITM-CNR), c/o University of Calabria, Via P. Bucci, CUBO 17/C, I-87030 Arcavacata di Rende (CS), Italy, University of Calabria, Department of Chemical Engineering and Materials, Via P. Bucci, CUBO 45/A, I-87030 Arcavacata di Rende (CS), Italy, and Institute of Crystallography (IC-CNR), Trieste Oustation, Area Science Park Basovizza, S.S. 14, Km. 163.5, I-34012 Trieste, Italy
| | - Gisella Perrone
- Institute on Membrane Technology (ITM-CNR), c/o University of Calabria, Via P. Bucci, CUBO 17/C, I-87030 Arcavacata di Rende (CS), Italy, University of Calabria, Department of Chemical Engineering and Materials, Via P. Bucci, CUBO 45/A, I-87030 Arcavacata di Rende (CS), Italy, and Institute of Crystallography (IC-CNR), Trieste Oustation, Area Science Park Basovizza, S.S. 14, Km. 163.5, I-34012 Trieste, Italy
| | - Efrem Curcio
- Institute on Membrane Technology (ITM-CNR), c/o University of Calabria, Via P. Bucci, CUBO 17/C, I-87030 Arcavacata di Rende (CS), Italy, University of Calabria, Department of Chemical Engineering and Materials, Via P. Bucci, CUBO 45/A, I-87030 Arcavacata di Rende (CS), Italy, and Institute of Crystallography (IC-CNR), Trieste Oustation, Area Science Park Basovizza, S.S. 14, Km. 163.5, I-34012 Trieste, Italy
| | - Alberto Cassetta
- Institute on Membrane Technology (ITM-CNR), c/o University of Calabria, Via P. Bucci, CUBO 17/C, I-87030 Arcavacata di Rende (CS), Italy, University of Calabria, Department of Chemical Engineering and Materials, Via P. Bucci, CUBO 45/A, I-87030 Arcavacata di Rende (CS), Italy, and Institute of Crystallography (IC-CNR), Trieste Oustation, Area Science Park Basovizza, S.S. 14, Km. 163.5, I-34012 Trieste, Italy
| | - Doriano Lamba
- Institute on Membrane Technology (ITM-CNR), c/o University of Calabria, Via P. Bucci, CUBO 17/C, I-87030 Arcavacata di Rende (CS), Italy, University of Calabria, Department of Chemical Engineering and Materials, Via P. Bucci, CUBO 45/A, I-87030 Arcavacata di Rende (CS), Italy, and Institute of Crystallography (IC-CNR), Trieste Oustation, Area Science Park Basovizza, S.S. 14, Km. 163.5, I-34012 Trieste, Italy
| | - Enrico Drioli
- Institute on Membrane Technology (ITM-CNR), c/o University of Calabria, Via P. Bucci, CUBO 17/C, I-87030 Arcavacata di Rende (CS), Italy, University of Calabria, Department of Chemical Engineering and Materials, Via P. Bucci, CUBO 45/A, I-87030 Arcavacata di Rende (CS), Italy, and Institute of Crystallography (IC-CNR), Trieste Oustation, Area Science Park Basovizza, S.S. 14, Km. 163.5, I-34012 Trieste, Italy
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Covaceuszach S, Cassetta A, Cattaneo A, Lamba D. Unraveling the binding mode of the neutralizing neuroantibody αD11 to NGF. Acta Crystallogr A 2005. [DOI: 10.1107/s010876730509001x] [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: 11/10/2022] Open
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21
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Krastanova I, Cassetta A, Lamba D. Structural and functional studies of carbohydrate esterase family 7 enzymes. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305091154] [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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22
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Artali R, Marchini N, Meneghetti F, Cavazzini D, Cassetta A, Sassone C. Structure of S35C flavodoxin mutant fromDesulfovibrio vulgarisin the semiquinone state. Acta Crystallogr D Biol Crystallogr 2005; 61:481-4. [PMID: 15805604 DOI: 10.1107/s0907444905001502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Accepted: 01/14/2005] [Indexed: 11/10/2022]
Abstract
The crystallographic structure of an engineered flavodoxin mutant from Desulfovibrio vulgaris has been analysed. Site-directed mutagenesis was used to substitute serine 35 with a cysteine to provide a possible covalent linkage. The crystal structure of the semiquinone form of this mutant is similar to the corresponding oxidation state of the wild-type flavodoxin. Analysis of the structural changes reveals the interaction between N(5)H of the flavin and the carbonyl O atom of Gly61 to be critical for modulation of the electrochemical properties of the protein.
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Affiliation(s)
- R Artali
- Institute of Pharmaceutical Chemistry, University of Milano, Italy.
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Covaceuszach S, Cassetta A, Cattaneo A, Lamba D. Purification, crystallization, X-ray diffraction analysis and phasing of a Fab fragment of monoclonal neuroantibody αD11 against nerve growth factor. Acta Crystallogr D Biol Crystallogr 2004; 60:1323-7. [PMID: 15213405 DOI: 10.1107/s0907444904011485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2004] [Accepted: 05/11/2004] [Indexed: 11/10/2022]
Abstract
The rat monoclonal neuroantibody alphaD11 is a potent antagonist that prevents the binding of nerve growth factor (NGF) to its tyrosine kinase A receptor (TrkA) in a variety of systems, most notably in two in vivo systems linked to crucial pathological states, such as Alzheimer's disease and HIV infection. To provide further insights into the mechanism of action of this potentially therapeutic monoclonal antibody, structural studies of the antigen-binding fragment (Fab) of alphaD11 were performed. alphaD11 IgG2a immunoglobulin was obtained from hybridomas by in vitro tissue culture. The alphaD11 Fab crystallizes in two crystal forms. Form I belongs to space group P1, with unit-cell parameters a = 42.7, b = 50.6, c = 102.7 A, alpha = 82.0, beta = 89.1, gamma = 86.0 degrees. With two molecules in the asymmetric unit, V(M) is 2.3 A(3) Da(-1) and the solvent content is 46%. A complete data set has been collected at 2.7 A resolution on beamline XRD-1 (ELETTRA, Trieste, Italy). Form II belongs to space group C2, with unit-cell parameters a = 114.8, b = 69.4, c = 64.10 A, beta = 117.0 degrees. With one molecule in the asymmetric unit, V(M) is 2.4 A(3) Da(-1) and the solvent content is 48%. A complete data set has been collected at 1.7 A resolution on beamline ID14-1 (ESRF, Grenoble, France). Phasing was successfully performed by Patterson search techniques and refinement of the structures is currently under way. Crystal forms I and II display a close-packing pattern.
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24
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Haedener A, Nieh YP, Cassetta A, Raftery J, Niemann AC, Carr PD, Wulff M, Ursby T, Moy JP, Thompson AW, Helliwell JR. Time-resolved structural studies of hydroxymethylbilane synthase (HMBS). Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302094655] [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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25
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Arcadi A, Cacchi S, Cassetta A, Fabrizi G, Parisi LM. Indole[1,2-c]quinazolines by Palladium-Catalyzed Cyclization of Bis(o-trifluoroacetamidophenyl) acetylene with Aryl and Vinyl Halides or Triflates. Synlett 2001. [DOI: 10.1055/s-2001-17458] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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26
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Hädener A, Matzinger PK, Battersby AR, McSweeney S, Thompson AW, Hammersley AP, Harrop SJ, Cassetta A, Deacon A, Hunter WN, Nieh YP, Raftery J, Hunter N, Helliwell JR. Determination of the structure of seleno-methionine-labelled hydroxymethylbilane synthase in its active form by multi-wavelength anomalous dispersion. Acta Crystallogr D Biol Crystallogr 1999; 55:631-43. [PMID: 10089459 DOI: 10.1107/s0907444998014711] [Citation(s) in RCA: 14] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The enzyme hydroxymethylbilane synthase (HMBS, E.C. 4.3.1.8) catalyzes the conversion of porphobilinogen into hydroxymethylbilane, a key intermediate for the biosynthesis of heme, chlorophylls, vitamin B12 and related macrocycles. The enzyme is found in all organisms, except viruses. The crystal structure of the selenomethionine-labelled enzyme ([SeMet]HMBS) from Escherichia coli has been solved by the multi-wavelength anomalous dispersion (MAD) experimental method using the Daresbury SRS station 9.5. In addition, [SeMet]HMBS has been studied by MAD at the Grenoble ESRF MAD beamline BM14 (BL19) and this work is described especially with respect to the use of the ESRF CCD detector. The structure at ambient temperature has been refined, the R factor being 16.8% at 2. 4 A resolution. The dipyrromethane cofactor of the enzyme is preserved in its reduced form in the crystal and its geometrical shape is in full agreement with the crystal structures of authentic dipyrromethanes. Proximal to the reactive C atom of the reduced cofactor, spherical density is seen consistent with there being a water molecule ideally placed to take part in the final step of the enzyme reaction cycle. Intriguingly, the loop with residues 47-58 is not ordered in the structure of this form of the enzyme, which carries no substrate. Direct experimental study of the active enzyme is now feasible using time-resolved Laue diffraction and freeze-trapping, building on the structural work described here as the foundation.
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Affiliation(s)
- A Hädener
- Department of Chemistry, University of Basle, Switzerland.
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27
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Sabatino P, Fermani S, Ripamonti A, Cassetta A, Scagliarini S, Trost P. Crystallization and preliminary X-ray study of chloroplast glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr D Biol Crystallogr 1999; 55:566-7. [PMID: 10089381 DOI: 10.1107/s090744499801302x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase from spinach chloroplasts has been crystallized by vapour diffusion in the pH range 7-8.5 in (NH4)2SO4 and Tris-HCl buffer or potassium phosphate buffer at room temperature. Crystals of the A4 isoform, grown at pH 8.5 in Tris-HCl buffer, diffract to 3.0 A (at 100 K) using synchrotron radiation. The crystals belong to the orthorhombic C222 space group, with unit-cell dimensions a = 145.9, b = 185.9 and c = 106.3 A, and probably contain one tetramer per asymmetric unit. Structure determination by molecular replacement is in progress.
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Affiliation(s)
- P Sabatino
- Dipartimento di Chimica 'G. Ciamician', Università di Bologna, via Selmi 2, 40126 Bologna, Italy.
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28
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Pettinari C, Pellei M, Cavicchio G, Crucianelli M, Panzeri W, Colapietro M, Cassetta A. Synthesis and Structural Investigations of Novel Palladium(II) and Rhodium(I) Complexes Containing Chiral Ligands with a Stereogenic Sulfur Donor, Such As β-Amino Sulfoxides and C2-Symmetric Bis-Sulfoxides1. Organometallics 1999. [DOI: 10.1021/om9808460] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claudio Pettinari
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
| | - Maura Pellei
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
| | - Giancarlo Cavicchio
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
| | - Marcello Crucianelli
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
| | - Walter Panzeri
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
| | - Marcello Colapietro
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
| | - Alberto Cassetta
- Dipartimento di Scienze Chimiche, Università degli Studi, via S. Agostino 1, I-62032 Camerino, Macerata, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, via Vetoio, I-67100 L'Aquila, Italy, CNR-CSSON, Dipartimento di Chimica del Politecnico, via Mancinelli 7, I-20131 Milano, Italy, Dipartimento di Chimica, Università di Roma “La Sapienza”, p. le Aldo Moro 5, I-00185 Roma, Italy, and Istituto di Strutturistica Chimica “G. Giacomello”, Consiglio Nazionale delle
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Pettinari C, Accorroni F, Cingolani A, Marchetti F, Cassetta A, Barba L. (1-Phenyl-3-methyl-4-acetylpyrazolon-5-ato)rhodium(I) complexes, synthesis, structural and spectroscopical characterization: Reactivity of diolefin- and dicarbonyl-rhodium complexes toward N-, P- and O-donors. J Organomet Chem 1998. [DOI: 10.1016/s0022-328x(98)00692-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Helliwell JR, Nieh YP, Raftery J, Cassetta A, Habash J, Carr PD, Ursby T, Wulff M, Thompson AW, Niemann AC, and Alfons Hädener M. Time-resolved structures of hydroxymethylbilane synthase (Lys59Gln mutant) as it is loaded with substrate in the crystal determined by Laue diffraction. ACTA ACUST UNITED AC 1998. [DOI: 10.1039/a802217h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Snell EH, Cassetta A, Helliwell JR, Boggon TJ, Chayen NE, Weckert E, Hölzer K, Schroer K, Gordon EJ, Zagalsky PF. Partial Improvement of Crystal Quality for Microgravity-Grown Apocrustacyanin C1. Acta Crystallogr D Biol Crystallogr 1997; 53:231-9. [PMID: 15299925 DOI: 10.1107/s0907444996013996] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The protein apocrustacyanin C(1) has been crystallized by vapour diffusion in both microgravity (the NASA space shuttle USML-2 mission) and on the ground. Rocking width measurements were made on the crystals at the ESRF Swiss-Norwegian beamline using a high-resolution psi-circle diffractometer from the University of Karlsruhe. Crystal perfection was then evaluated, from comparison of the reflection rocking curves from a total of five crystals (three grown in microgravity and two earth controls), and by plotting mosaicity versus reflection signal/noise. Comparison was then made with previous measurements of almost 'perfect' lysozyme crystals grown aboard IML-2 and Spacehab-I and reported by Snell et al. [Snell, Weisgerber, Helliwell, Weckert, Hölzer & Schroer (1995). Acta Cryst. D51, 1099-1102]. Overall, the best diffraction-quality apocrustacyanin C(1) crystal was microgravity grown, but one earth-grown crystal was as good as one of the other microgravity-grown crystals. The remaining two crystals (one from microgravity and one from earth) were poorer than the other three and of fairly equal quality. Crystal movement during growth in microgravity, resulting from the use of vapour-diffusion geometry, may be the cause of not realising the 'theoretical' limit of perfect protein crystal quality.
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Affiliation(s)
- E H Snell
- Chemistry Department, University of Manchester, England
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Snell EH, Cassetta A, Helliwell JR, Boggon TJ, Chayen NE, Weckert E, Holzer K, Schroer K, Gordon EJ, Zagalsky PF. Partial improvement of crystal quality for microgravity-grown apocrustacyanin C1. Acta Crystallogr D Biol Crystallogr 1997; 53:231-9. [PMID: 11540431] [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] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The protein apocrustacyanin C1 has been crystallized by vapour diffusion in both microgravity (the NASA space shuttle USML-2 mission) and on the ground. Rocking width measurements were made on the crystals at the ESRF Swiss-Norwegian beamline using a high-resolution psi-circle diffractometer from the University of Karlsruhe. Crystal perfection was then evaluated, from comparison of the reflection rocking curves from a total of five crystals (three grown in microgravity and two earth controls), and by plotting mosaicity versus reflection signal/noise. Comparison was then made with previous measurements of almost 'perfect' lysozyme crystals grown aboard IML-2 and Spacehab-1 and reported by Snell et al. [Snell, Weisgerber, Helliwell, Weckert, Holzer & Schroer (1995). Acta Cryst. D51, 1099-1102]. Overall, the best diffraction-quality apocrustacyanin C1 crystal was microgravity grown, but one earth-grown crystal was as good as one of the other microgravity-grown crystals. The remaining two crystals (one from microgravity and one from earth) were poorer than the other three and of fairly equal quality. Crystal movement during growth in microgravity, resulting from the use of vapour-diffusion geometry, may be the cause of not realising the 'theoretical' limit of perfect protein crystal quality.
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Affiliation(s)
- E H Snell
- Chemistry Department, University of Manchester, England
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33
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Habash J, Raftery J, Weisgerber S, Cassetta A, Lehmann MS, Hghj P, Wilkinson C, Campbell JW, Helliwell JR. Neutron Laue diffraction study of concanavalin A The proton of Asp28. ACTA ACUST UNITED AC 1997. [DOI: 10.1039/a704143h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Carr PD, Robinson A, Ollis DL, Hädener A, Niemann AC, Helliwell JR, Habash J, Cassetta A, Ursby T, Bourgois D, Schotte F, Wulff M. Time-resolved Laue studies from dienelactone hydrolase and porphobilinogen deaminase. Acta Crystallogr A 1996. [DOI: 10.1107/s010876739609705x] [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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35
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Spagna R, Barba L, Camalli M, Cassetta A, Catricala' M, Marciante C, Pifferi A, Colapietro M, Portalone G. The four-circle diffractometer at ELETTRA. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396098364] [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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36
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Snell EH, Helliwell JR, Cassetta A, Boggon TJ, Chayen NE, Weckert E, Holzer K, Schroer K, Stojanoff V, Siddons DP. Protein crystal perfection and the crystal growth process. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396078920] [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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37
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Chayen NE, Boggon TJ, Cassetta A, Deacon A, Gleichmann T, Habash J, Harrop SJ, Helliwell JR, Nieh YP, Peterson MR, Raftery J, Snell EH, Hädener A, Niemann AC, Siddons DP, Stojanoff V, Thompson AW, Ursby T, Wulff M. Trends and challenges in experimental macromolecular crystallography. Q Rev Biophys 1996; 29:227-78. [PMID: 8968112 DOI: 10.1017/s0033583500005837] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.8] [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: 02/03/2023]
Abstract
Macromolecular X-ray crystallography underpins the vigorous field of structural molecular biology having yielded many protein, nucleic acid and virus structures in fine detail. The understanding of the recognition by these macromolecules, as receptors, of their cognate ligands involves the detailed study of the structural chemistry of their molecular interactions. Also these structural details underpin the rational design of novel inhibitors in modern drug discovery in the pharmaceutical industry. Moreover, from such structures the functional details can be inferred, such as the biological chemistry of enzyme reactivity. There is then a vast number and range of types of biological macromolecules that potentially could be studied. The completion of the protein primary sequencing of the yeast genome, and the human genome sequencing project comprising some 105proteins that is underway, raises expectations for equivalent three dimensional structural databases.
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Affiliation(s)
- N E Chayen
- Biophysics Section, Blackett Laboratory, Imperial College of Science, Technology and Medicine, London, UK.
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38
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Marchetti F, Pettinari C, Cingolani A, Lobbia GG, Cassetta A, Barba L. Triorganotin(IV) derivatives of several 4-acyl-5-pyrazolonato ligands: synthesis, spectroscopic characterization and behavior in solution Crystal structure of aquotrimethyl(4-p-methoxybenzoyl-1-phenyl-3-methyl-pyrazolon-5-ato)tin(IV). J Organomet Chem 1996. [DOI: 10.1016/0022-328x(96)06170-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Helliwell M, Helliwell JR, Cassetta A, Hanson JC, Ericsson T, Krick A, Kaučič V, Frampton C. Anomalous dispersion analyses of the Ni-atom site in an aluminophosphate test crystal including the use of tuned synchrotron radiation. Acta Crystallogr B Struct Sci 1996. [DOI: 10.1107/s0108768195015096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Data were collected close to the Ni K edge, using synchrotron radiation at the National Synchrotron Light Source, and using a Mo Kα rotating anode, from a crystal of a nickel-containing aluminophosphate, NiAl3P4O18C4H21N4 (NiAPO). These data sets, along with an existing Cu Kα rotating anode data set, allowed the calculation of several f′ difference-Fourier maps exploiting the difference in f′ for Ni between the various wavelengths. These differences are expected to be 7.8, 4.5 and 3.3 e for Mo Kα data to SR (synchrotron radiation), Cu Kα to SR and Mo Kα to Cu Kα, respectively. The phases were calculated either excluding the Ni atom or with Al at the Ni-atom site. The f′ difference-Fourier maps revealed peaks at the Ni-atom site, whose height and distance from the refined Ni-atom position depended on the f' difference and the phase set used. The largest peak was located at a distance of only 0.025 Å from the refined Ni-atom site and was obtained from the f′ difference map calculated with the coefficients |F
Mo Kα − F
SR| , using phases calculated with Al at the Ni-atom site. In all cases, it was found that these phases gave optimal results without introducing bias into the maps. The results confirm and expand upon earlier results [Helliwell, Gallois, Kariuki, Kaučič & Helliwell (1993), Acta Cryst. B49, 420–428]. The techniques described are generally applicable to other systems containing anomalous scatterers in chemical crystallography.
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Pettinari C, Marchetti F, Pellei M, Cingolani A, Barba L, Cassetta A. Tin(IV) and organotin(IV) complexes containing mono or bidentate N-donor ligands II. 14-Phenylimidazole derivatives. Crystal and molecular structure of [bis(4-phenylimidazole) trimethyltin(IV) ] chloride. J Organomet Chem 1996. [DOI: 10.1016/0022-328x(95)06054-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Portalone G, Cassetta A, Pagani Zecchini G, Torrini I. (3R,5R)-Tetrahydro-2H-1,4-thiazine-3,5-dicarboxylic acid monohydrate. Acta Crystallogr C 1993. [DOI: 10.1107/s0108270192011181] [Citation(s) in RCA: 4] [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: 11/10/2022] Open
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