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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Abstract
The use of magnetic resonance imaging (MRI) and spectroscopy (MRS) in the clinical setting enables the acquisition of valuable anatomical information in a rapid, non-invasive fashion. However, MRI applications for identifying disease-related biomarkers are limited due to low sensitivity at clinical magnetic field strengths. The development of hyperpolarized (hp) 129Xe MRI/MRS techniques as complements to traditional 1H-based imaging has been a burgeoning area of research over the past two decades. Pioneering experiments have shown that hp 129Xe can be encapsulated within host molecules to generate ultrasensitive biosensors. In particular, xenon has high affinity for cryptophanes, which are small organic cages that can be functionalized with affinity tags, fluorophores, solubilizing groups, and other moieties to identify biomedically relevant analytes. Cryptophane sensors designed for proteins, metal ions, nucleic acids, pH, and temperature have achieved nanomolar-to-femtomolar limits of detection via a combination of 129Xe hyperpolarization and chemical exchange saturation transfer (CEST) techniques. This review aims to summarize the development of cryptophane biosensors for 129Xe MRI applications, while highlighting innovative biosensor designs and the consequent enhancements in detection sensitivity, which will be invaluable in expanding the scope of 129Xe MRI. This review aims to summarize the development of cryptophane biosensors for 129Xe MRI applications, while highlighting innovative biosensor designs and the consequent enhancements in detection sensitivity, which will be invaluable in expanding the scope of 129Xe MRI.![]()
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Affiliation(s)
- Serge D Zemerov
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323, USA
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323, USA
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Chighine K, Léonce E, Boutin C, Desvaux H, Berthault P. 129Xe ultra-fast Z spectroscopy enables micromolar detection of biosensors on a 1 T benchtop spectrometer. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:409-420. [PMID: 37904767 PMCID: PMC10539730 DOI: 10.5194/mr-2-409-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/31/2021] [Indexed: 11/01/2023]
Abstract
The availability of a benchtop nuclear magnetic resonance (NMR) spectrometer, of low cost and easily transportable, can allow detection of low quantities of biosensors, provided that hyperpolarized species are used. Here we show that the micromolar threshold can easily be reached by employing laser-polarized xenon and cage molecules reversibly hosting it. Indirect detection of caged xenon is made via chemical exchange, using ultra-fast Z spectroscopy based on spatio-temporal encoding. On this non-dedicated low-field spectrometer, several ideas are proposed to improve the signal.
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Affiliation(s)
- Kévin Chighine
- Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Estelle Léonce
- Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Céline Boutin
- Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Hervé Desvaux
- Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Patrick Berthault
- Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
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Jayapaul J, Schröder L. Molecular Sensing with Host Systems for Hyperpolarized 129Xe. Molecules 2020; 25:E4627. [PMID: 33050669 PMCID: PMC7587211 DOI: 10.3390/molecules25204627] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.
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Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
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Baydoun O, De Rycke N, Léonce E, Boutin C, Berthault P, Jeanneau E, Brotin T. Synthesis of Cryptophane-223-Type Derivatives with Dual Functionalization. J Org Chem 2019; 84:9127-9137. [DOI: 10.1021/acs.joc.9b01093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Orsola Baydoun
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Nicolas De Rycke
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Estelle Léonce
- NIMBE, CEA, CNRS, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Céline Boutin
- NIMBE, CEA, CNRS, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Patrick Berthault
- NIMBE, CEA, CNRS, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Erwann Jeanneau
- Centre de Diffractométrie Henri Longchambon, Université Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Thierry Brotin
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
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Mari E, Bousmah Y, Boutin C, Léonce E, Milanole G, Brotin T, Berthault P, Erard M. Bimodal Detection of Proteins by 129 Xe NMR and Fluorescence Spectroscopy. Chembiochem 2019; 20:1450-1457. [PMID: 30650230 DOI: 10.1002/cbic.201800802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 11/10/2022]
Abstract
A full understanding of biological phenomena involves sensitive and noninvasive detection. Herein, we report the optimization of a probe for intracellular proteins that combines the advantages of fluorescence and hyperpolarized 129 Xe NMR spectroscopy detection. The fluorescence detection part is composed of six residues containing a tetracysteine tag (-CCXXCC-) genetically incorporated into the protein of interest and of a small organic molecule, CrAsH. CrAsH becomes fluorescent if it binds to the tetracysteine tag. The part of the biosensor that enables detection by means of 129 Xe NMR spectroscopy, which is linked to the CrAsH moiety by a spacer, is based on a cryptophane core that is fully suited to reversibly host xenon. Three different peptides, containing the tetracysteine tag and four organic biosensors of different stereochemistry, are benchmarked to propose the best couple that is fully suited for the in vitro detection of proteins.
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Affiliation(s)
- Emilie Mari
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
- Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, Batiment 349, 91405, Orsay, France
| | - Yasmina Bousmah
- Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, Batiment 349, 91405, Orsay, France
| | - Céline Boutin
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Estelle Léonce
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Gaelle Milanole
- SCBM, Université Paris-Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Thierry Brotin
- Université Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Université Lyon 1, Laboratoire de Chimie, 46 allée d'Italie, 69364, Lyon, France
| | - Patrick Berthault
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Marie Erard
- Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, Batiment 349, 91405, Orsay, France
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Brotin T, Jeanneau E, Berthault P, Léonce E, Pitrat D, Mulatier JC. Synthesis of Cryptophane-B: Crystal Structure and Study of Its Complex with Xenon. J Org Chem 2018; 83:14465-14471. [DOI: 10.1021/acs.joc.8b02246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Thierry Brotin
- Laboratoire de Chimie, Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Université Lyon 1, 46 allée d’Italie, Lyon F69364, France
| | - Erwann Jeanneau
- Centre de Diffractométrie Henri Longchambon, Université Lyon 1, 5 rue de la Doua, Villeurbanne 69100, France
| | - Patrick Berthault
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, Gif-sur-Yvette 91191, France
| | - Estelle Léonce
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, Gif-sur-Yvette 91191, France
| | - Delphine Pitrat
- Laboratoire de Chimie, Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Université Lyon 1, 46 allée d’Italie, Lyon F69364, France
| | - Jean-Christophe Mulatier
- Laboratoire de Chimie, Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Université Lyon 1, 46 allée d’Italie, Lyon F69364, France
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Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Enantioselective Complexation of Chiral Oxirane Derivatives by an Enantiopure Cryptophane in Water. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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