1
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Krafčíková MD, Beriashvili D, Bahri S, Bergmeijer M, Howes SC, Gurinov A, Förster FG, Folkers GE, Baldus M. A DNP-Supported Solid-State NMR Approach to Study Nucleic Acids In Situ Reveals Berberine-Stabilized Hoogsteen Structures in Mitochondria. Angew Chem Int Ed Engl 2025; 64:e202424131. [PMID: 40052409 PMCID: PMC12087828 DOI: 10.1002/anie.202424131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 03/04/2025] [Accepted: 03/06/2025] [Indexed: 03/19/2025]
Abstract
Mitochondria are central to cellular bioenergetics, with the unique ability to translate and transcribe a subset of their own proteome. Given the critical importance of energy production, mitochondria seem to utilize higher-order nucleic acid structures to regulate gene expression, much like nuclei. Herein, we introduce a tailored approach to probe the formation of such structures, specifically G-quadruplexes, within intact mitochondria by using sensitivity-enhanced dynamic nuclear polarization-supported solid-state NMR (DNP-ssNMR). We acquired NMR spectra on isolated intact isotopically labeled mitochondria treated with berberine, a known high-affinity G-quadruplex stabilizer. The DNP-ssNMR data revealed spectral changes in nucleic acid sugar correlations, increased signal intensity for guanosine carbons, and enhanced Hoogsteen hydrogen bond formation, providing evidence of in vivo G-quadruplex formation in mitochondria. Together, our workflow enables the study of mitochondrial nucleic acid-ligand interactions at endogenous concentrations within biologically relevant environments by DNP-ssNMR, thus paving the way for future research into mitochondrial diseases and their potential treatments.
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Affiliation(s)
- Michaela Dzurov Krafčíková
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8Utrecht3584CHThe Netherlands
| | - David Beriashvili
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8Utrecht3584CHThe Netherlands
| | - Salima Bahri
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8Utrecht3584CHThe Netherlands
| | - Menno Bergmeijer
- Structural BiochemistryBijvoet Center for Biomolecular ResearchUtrecht UniversityUniversiteitsweg 99Utrecht3584CGThe Netherlands
| | - Stuart C. Howes
- Structural BiochemistryBijvoet Center for Biomolecular ResearchUtrecht UniversityUniversiteitsweg 99Utrecht3584CGThe Netherlands
| | - Andrei Gurinov
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8Utrecht3584CHThe Netherlands
| | - Friedrich G. Förster
- Structural BiochemistryBijvoet Center for Biomolecular ResearchUtrecht UniversityUniversiteitsweg 99Utrecht3584CGThe Netherlands
| | - Gert E. Folkers
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8Utrecht3584CHThe Netherlands
| | - Marc Baldus
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 8Utrecht3584CHThe Netherlands
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2
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Bertuzzi S, Lete MG, Franconetti A, Diercks T, Delgado S, Oyenarte I, Moure MJ, Nuñez‐Franco R, Valverde P, Lenza MP, Sobczak K, Jiménez‐Osés G, Paulson JC, Ardá A, Ereño‐Orbea J, Jiménez‐Barbero J. Exploring Glycan-Lectin Interactions in Natural-Like Environments: A View Using NMR Experiments Inside Cell and on Cell Surface. Chemistry 2025; 31:e202403102. [PMID: 39588609 PMCID: PMC11833217 DOI: 10.1002/chem.202403102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Accepted: 11/25/2024] [Indexed: 11/27/2024]
Abstract
Glycan-mediated molecular recognition events are essential for life. NMR is widely used to monitor glycan binding to lectins in solution using isolated glycans and lectins. In this context, we herein explore diverse NMR methodologies, from both the receptor and ligand perspectives, to monitor glycan-lectin interactions under experimental conditions mimicking the native milieu inside cells and on cell surface. For the NMR experiments inside cells, galectin-7 is employed as model, since most galectins are soluble and carry out their functions in the cellular micro-environment. Using Danio Rerio oocytes, the 1H-15N HMQC NMR spectrum of a folded galectin has been observed inside cell for the first time, using a glycomimetic ligand (TDG) to overcoming the natural tendency of galectins to bind to numerous galactose-containing receptors within cells. Alternatively, most lectins, other than galectins, are displayed on the cell surface, providing a multivalent presentation to bind their glycan partners in cis (at the same cell) or in trans (on other cells). In this case, ligand-based STD-NMR experiments have been successfully applied to account for the interactions of natural glycans and glycomimetics with Siglec-10. These methodologies provide the proof-of-concept to open the door to the NMR analysis of the recognition of glycans in native-like settings.
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Affiliation(s)
- Sara Bertuzzi
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Marta G. Lete
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Antonio Franconetti
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Tammo Diercks
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Sandra Delgado
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Iker Oyenarte
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Maria J. Moure
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Reyes Nuñez‐Franco
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Pablo Valverde
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Maria Pia Lenza
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Klaudia Sobczak
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - Gonzalo Jiménez‐Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
| | - James C. Paulson
- Departments of Molecular Medicine and Immunology & MicrobiologyThe Scripps Research Institute10550 North Torrey Pines RoadLa Jolla, California92037USA
| | - Ana Ardá
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
| | - June Ereño‐Orbea
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
| | - Jesús Jiménez‐Barbero
- Center for Cooperative Research in Biosciences (CIC bioGUNE)Basque Research and Technology Alliance (BRTA)48160Derio, BizkaiaSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
- Department of Organic & Inorganic ChemistryFaculty of Science and TechnologyUniversity of the Basque Country, EHU-UPV48940Leioa, BizkaiaSpain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias28029MadridSpain
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3
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Rosati M, Barbieri L, Hlavac M, Kratzwald S, Lichtenecker RJ, Konrat R, Luchinat E, Banci L. Towards cost-effective side-chain isotope labelling of proteins expressed in human cells. JOURNAL OF BIOMOLECULAR NMR 2024; 78:237-247. [PMID: 39172315 PMCID: PMC11615012 DOI: 10.1007/s10858-024-00447-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Side chain isotope labelling is a powerful tool to study protein structure and interactions by NMR spectroscopy. 1H,13C labelling of side-chain methyl groups in a deuterated background allows studying large molecules, while side-chain aromatic groups are highly sensitive to the interaction with ligands, drugs, and other proteins. In E. coli, side chain labelling is performed by substituting amino acids with isotope-labelled precursors. However, proteins that can only be produced in mammalian cells require expensive isotope-labelled amino acids. Here we provide a simple and cost-effective method to label side chains in mammalian cells, which exploits the reversible reaction catalyzed by endogenous transaminases to convert isotope-labelled α-ketoacid precursors. We show by in-cell and in-lysate NMR spectroscopy that replacing an amino acid in the medium with its cognate precursor is sufficient to achieve selective labelling without scrambling, and how this approach allows monitoring conformational changes such as those arising from ligand binding.
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Affiliation(s)
- Martina Rosati
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy
| | | | | | - Roman J Lichtenecker
- MAG-LAB GmbH, Vienna, Austria
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Robert Konrat
- MAG-LAB GmbH, Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Enrico Luchinat
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
| | - Lucia Banci
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
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4
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Annecke HTP, Eidelpes R, Feyrer H, Ilgen J, Gürdap CO, Dasgupta R, Petzold K. Optimising in-cell NMR acquisition for nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024; 78:249-264. [PMID: 39162911 PMCID: PMC11614993 DOI: 10.1007/s10858-024-00448-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/08/2024] [Indexed: 08/21/2024]
Abstract
Understanding the structure and function of nucleic acids in their native environment is crucial to structural biology and one focus of in-cell NMR spectroscopy. Many challenges hamper in-cell NMR in human cell lines, e.g. sample decay through cell death and RNA degradation. The resulting low signal intensities and broad line widths limit the use of more complex NMR experiments, reducing the possible structural and dynamic information that can be extracted. Here, we optimize the detection of imino proton signals, indicators of base-pairing and therefore secondary structure, of a double-stranded DNA oligonucleotide in HeLa cells, using selective excitation. We demonstrate the reproducible quantification of in-cell selective longitudinal relaxation times (selT1), which are reduced compared to the in vitro environment, as a result of interactions with the complex cellular environment. By measuring the intracellular selT1, we optimize the existing proton pulse sequences, and shorten measurement time whilst enhancing the signal gained per unit of time. This exemplifies an advantage of selective excitation over conventional methods like jump-return water suppression for in-cell NMR. Furthermore, important experimental controls are discussed, including intracellular quantification, supernatant control measurements, as well as the processing of lowly concentrated in-cell NMR samples. We expect that robust and fast in-cell NMR experiments of nucleic acids will facilitate the study of structure and dynamics and reveal their functional correlation.
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Affiliation(s)
- Henry T P Annecke
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Reiner Eidelpes
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
| | - Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
| | - Julian Ilgen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
| | - Cenk Onur Gürdap
- Department of Women's and Children's Health, Karolinska Institutet, 171 65, Solna, Sweden
- Science for Life Laboratory, 171 65, Solna, Sweden
| | - Rubin Dasgupta
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden.
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden.
- Science for Life Laboratory, 171 65, Solna, Sweden.
- Center of Excellence for the Chemical Mechanisms of Life, Uppsala University, 752 37, Uppsala, Sweden.
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5
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Toscano G, Rosati M, Barbieri L, Maier K, Banci L, Luchinat E, Konrat R, Lichtenecker RJ. The synthesis of specifically isotope labelled fluorotryptophan and its use in mammalian cell-based protein expression for 19F-NMR applications. Chem Commun (Camb) 2024; 60:14188-14191. [PMID: 39512115 DOI: 10.1039/d4cc04789c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
19F nuclei serve as versatile sensors for detecting protein interactions and dynamics in biomolecular NMR spectroscopy. Although various methods have been developed to incorporate fluorine-containing aromatic residues into proteins using E. coli or cell-free expression techniques, similar approaches for protein production in mammalian cell lines remain limited. Here, we present a cost-effective synthetic route to obtain selectively deuterated, carbon-13 labeled fluorotryptophan and demonstrate its use in introducing 19F-13C spin pairs into carbonic anhydrase 2 and superoxide dismutase, following an expression protocol utilizing HEK cells.
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Affiliation(s)
- Giorgia Toscano
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090-Vienna, Austria.
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währingerstraße 42, 1090 Vienna, Austria
| | - Martina Rosati
- CERM Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine CIRMMP, Sesto Fiorentino, Italy
| | - Katharina Maier
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090-Vienna, Austria.
| | - Lucia Banci
- CERM Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine CIRMMP, Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Enrico Luchinat
- CERM Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine CIRMMP, Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030-Vienna, Austria
- Mag-Lab, Karl-Farkas-Gasse 22, 1030 Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090-Vienna, Austria.
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
- Mag-Lab, Karl-Farkas-Gasse 22, 1030 Vienna, Austria
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6
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Rao Y, Berruyer P, Bertarello A, Venkatesh A, Mazzanti M, Emsley L. An Efficient and Stable Polarizing Agent for In-Cell Magic-Angle Spinning Dynamic Nuclear Polarization NMR Spectroscopy. J Phys Chem Lett 2024; 15:11601-11607. [PMID: 39528911 PMCID: PMC11587084 DOI: 10.1021/acs.jpclett.4c02709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Revised: 11/01/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy would be a method of choice to follow biochemical events in cells because it can analyze molecules in complex environments. However, the intrinsically low sensitivity of NMR makes in-cell measurements challenging. Dynamic Nuclear Polarization (DNP) has emerged as a method to circumvent this limitation, but most polarizing agents developed for DNP are unstable in reducing cellular environments. Here, we introduce the use of Gd(III)-based DNP polarizing agents for in-cell NMR spectroscopy. Specifically, we show their persistent stability in cellular formulations, and we investigate the DNP performance of the Gd(III)-based complex [Gd(tpatcn)] in human embryonic kidney cell lysates and intact cells. For cell lysates, DNP enhancements up to -27 are obtained on the cellular signals, reproducible even after storage at room temperature for days. Mixing the [Gd(tpatcn)] solution with intact cells enables the observation of cellular signals with DNP, and DNP enhancement factors of about -40 are achieved.
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Affiliation(s)
- Yu Rao
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Group
of Coordination Chemistry, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Pierrick Berruyer
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrea Bertarello
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Amrit Venkatesh
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marinella Mazzanti
- Group
of Coordination Chemistry, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Lyndon Emsley
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), 1015 Lausanne, Switzerland
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7
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Subedi GP, Roberts ET, Davis AR, Kremer PG, Amster IJ, Barb AW. A comprehensive assessment of selective amino acid 15N-labeling in human embryonic kidney 293 cells for NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2024; 78:125-132. [PMID: 38407675 PMCID: PMC11178438 DOI: 10.1007/s10858-023-00434-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/31/2023] [Indexed: 02/27/2024]
Abstract
A large proportion of human proteins contain post-translational modifications that cannot be synthesized by prokaryotes. Thus, mammalian expression systems are often employed to characterize structure/function relationships using NMR spectroscopy. Here we define the selective isotope labeling of secreted, post-translationally modified proteins using human embryonic kidney (HEK)293 cells. We determined that alpha-[15N]- atoms from 10 amino acids experience minimal metabolic scrambling (C, F, H, K, M, N, R, T, W, Y). Two more interconvert to each other (G, S). Six others experience significant scrambling (A, D, E, I, L, V). We also demonstrate that tuning culture conditions suppressed V and I scrambling. These results define expectations for 15N-labeling in HEK293 cells.
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Affiliation(s)
- Ganesh P Subedi
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Elijah T Roberts
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Alexander R Davis
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - Paul G Kremer
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA
| | - I Jonathan Amster
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
- Department of Chemistry, University of Georgia, Athens, 30602, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, 120 E. Green St., Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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8
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Razew A, Herail Q, Miyachiro M, Anoyatis-Pelé C, Bougault C, Dessen A, Arthur M, Simorre JP. Monitoring Drug-Protein Interactions in the Bacterial Periplasm by Solution Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2024; 146:9252-9260. [PMID: 38500259 DOI: 10.1021/jacs.4c00604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The rapid spread of antimicrobial resistance across bacterial pathogens poses a serious risk to the efficacy and sustainability of available treatments. This puts pressure on research concerning the development of new drugs. Here, we present an in-cell NMR-based research strategy to monitor the activity of the enzymes located in the periplasmic space delineated by the inner and outer membranes of Gram-negative bacteria. We demonstrate its unprecedented analytical power in monitoring in situ and in real time (i) the hydrolysis of β-lactams by β-lactamases, (ii) the interaction of drugs belonging to the β-lactam family with their essential targets, and (iii) the binding of inhibitors to these enzymes. We show that in-cell NMR provides a powerful analytical tool for investigating new drugs targeting the molecular components of the bacterial periplasm.
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Affiliation(s)
- Alicja Razew
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Quentin Herail
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Mayara Miyachiro
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | | | - Catherine Bougault
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Andrea Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université Paris Cité, Paris, 75006, France
| | - Jean-Pierre Simorre
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, 38044, France
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9
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Costantino A, Pham LBT, Barbieri L, Calderone V, Ben‐Nissan G, Sharon M, Banci L, Luchinat E. Controlling the incorporation of fluorinated amino acids in human cells and its structural impact. Protein Sci 2024; 33:e4910. [PMID: 38358125 PMCID: PMC10868450 DOI: 10.1002/pro.4910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Fluorinated aromatic amino acids (FAAs) are promising tools when studying protein structure and dynamics by NMR spectroscopy. The incorporation FAAs in mammalian expression systems has been introduced only recently. Here, we investigate the effects of FAAs incorporation in proteins expressed in human cells, focusing on the probability of incorporation and its consequences on the 19 F NMR spectra. By combining 19 F NMR, direct MS and x-ray crystallography, we demonstrate that the probability of FAA incorporation is only a function of the FAA concentration in the expression medium and is a pure stochastic phenomenon. In contrast with the MS data, the x-ray structures of carbonic anhydrase II reveal that while the 3D structure is not affected, certain positions lack fluorine, suggesting that crystallization selectively excludes protein molecules featuring subtle conformational modifications. This study offers a predictive model of the FAA incorporation efficiency and provides a framework for controlling protein fluorination in mammalian expression systems.
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Affiliation(s)
- Azzurra Costantino
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Lan B. T. Pham
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Letizia Barbieri
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
| | - Vito Calderone
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Gili Ben‐Nissan
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Michal Sharon
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lucia Banci
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Enrico Luchinat
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
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10
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Katti SS, Igumenova TI. Protein-Cadmium Interactions in Crowded Biomolecular Environments Probed by In-cell and Lysate NMR Spectroscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565546. [PMID: 38405767 PMCID: PMC10888879 DOI: 10.1101/2023.11.03.565546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
One of the mechanisms by which toxic metal ions interfere with cellular functions is ionic mimicry, where they bind to protein sites in lieu of native metals Ca 2+ and Zn 2+ . The influence of crowded intracellular environments on these interactions is not well understood. Here, we demonstrate the application of in-cell and lysate NMR spectroscopy to obtain atomic-level information on how a potent environmental toxin cadmium interacts with its protein targets. The experiments, conducted in intact E. coli cells and their lysates, revealed that Cd 2+ can profoundly affect the quinary interactions of its protein partners, and can replace Zn 2+ in both labile and non-labile protein structural sites without significant perturbation of the membrane binding function. Surprisingly, in crowded molecular environments Cd 2+ can effectively target not only all-sulfur and mixed sulfur/nitrogen but also all-oxygen coordination sites. The sulfur-rich coordination environments show significant promise for bioremedial applications, as demonstrated by the ability of the designed protein scaffold α 3 DIV to sequester intracellular cadmium. Our data suggests that in-cell NMR spectroscopy is a powerful tool for probing interactions of toxic metal ions with their potential protein targets, and for the assessment of potency of sequestering agents.
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11
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Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L. Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells. J Med Chem 2024; 67:1115-1126. [PMID: 38215028 PMCID: PMC10823471 DOI: 10.1021/acs.jmedchem.3c01600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/14/2024]
Abstract
The development of more effective drugs requires knowledge of their bioavailability and binding efficacy directly in the native cellular environment. In-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating ligand-target interactions directly in living cells. However, the target molecule may be NMR-invisible due to interactions with cellular components, while observing the ligand by 1H NMR is impractical due to the cellular background. Such limitations can be overcome by observing fluorinated ligands by 19F in-cell NMR as they bind to the intracellular target. Here we report a novel approach based on real-time in-cell 19F NMR that allows measuring ligand binding affinities in human cells by competition binding, using a fluorinated compound as a reference. The binding of a set of compounds toward Hsp90α was investigated. In principle, this approach could be applied to other pharmacologically relevant targets, thus aiding the design of more effective compounds in the early stages of drug development.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, Cesena 47521, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Letizia Barbieri
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Ben Davis
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Paul A. Brough
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Matteo Pennestri
- Pharmaceutical
Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, U.K.
| | - Lucia Banci
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Centro
di Risonanze Magnetiche—CERM, Università
degli Studi di Firenze, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, Sesto Fiorentino 50019, Italy
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12
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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13
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Pham LB, Costantino A, Barbieri L, Calderone V, Luchinat E, Banci L. Direct Expression of Fluorinated Proteins in Human Cells for 19F In-Cell NMR Spectroscopy. J Am Chem Soc 2023; 145:1389-1399. [PMID: 36604341 PMCID: PMC9853860 DOI: 10.1021/jacs.2c12086] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In-cell NMR spectroscopy is a powerful approach to study protein structure and function in the native cellular environment. It provides precious insights into the folding, maturation, interactions, and ligand binding of important pharmacological targets directly in human cells. However, its widespread application is hampered by the fact that soluble globular proteins often interact with large cellular components, causing severe line broadening in conventional heteronuclear NMR experiments. 19F NMR can overcome this issue, as fluorine atoms incorporated in proteins can be detected by simple background-free 1D NMR spectra. Here, we show that fluorinated amino acids can be easily incorporated in proteins expressed in human cells by employing a medium switch strategy. This straightforward approach allows the incorporation of different fluorinated amino acids in the protein of interest, reaching fluorination efficiencies up to 60%, as confirmed by mass spectrometry and X-ray crystallography. The versatility of the approach is shown by performing 19F in-cell NMR on several proteins, including those that would otherwise be invisible by 1H-15N in-cell NMR. We apply the approach to observe the interaction between an intracellular target, carbonic anhydrase 2, and its inhibitors, and to investigate how the formation of a complex between superoxide dismutase 1 and its chaperone CCS modulates the interaction of the chaperone subunit with the cellular environment.
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Affiliation(s)
- Lan B.
T. Pham
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Azzurra Costantino
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Vito Calderone
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019Sesto Fiorentino, Italy
| | - Enrico Luchinat
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, 47521Cesena, Italy,
| | - Lucia Banci
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019Sesto Fiorentino, Italy,
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14
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Camponeschi F, Banci L. Metal trafficking in the cell: Combining atomic resolution with cellular dimension. FEBS Lett 2023; 597:122-133. [PMID: 36285633 DOI: 10.1002/1873-3468.14524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 01/14/2023]
Abstract
Metals are widely present in biological systems as simple ions or complex cofactors, and are involved in a variety of processes essential for life. Their transport inside cells and insertion into the binding sites of the proteins that need metals to function occur through complex and selective pathways involving dedicated multiprotein machineries specifically and transiently interacting with each other, often sharing the coordination of metal ions and/or cofactors. The understanding of these machineries requires integrated approaches, ranging from bioinformatics to experimental investigations, possibly in the cellular context. In this review, we report two case studies where the use of integrated in vitro and in cellulo approaches is necessary to clarify at atomic resolution essential aspects of metal trafficking in cells.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy.,Department of Chemistry, University of Florence, Italy
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15
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Gerez JA, Prymaczok NC, Kadavath H, Ghosh D, Bütikofer M, Fleischmann Y, Güntert P, Riek R. Protein structure determination in human cells by in-cell NMR and a reporter system to optimize protein delivery or transexpression. Commun Biol 2022; 5:1322. [PMID: 36460747 PMCID: PMC9718737 DOI: 10.1038/s42003-022-04251-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Most experimental methods for structural biology proceed in vitro and therefore the contribution of the intracellular environment on protein structure and dynamics is absent. Studying proteins at atomic resolution in living mammalian cells has been elusive due to the lack of methodologies. In-cell nuclear magnetic resonance spectroscopy (in-cell NMR) is an emerging technique with the power to do so. Here, we improved current methods of in-cell NMR by the development of a reporter system that allows monitoring the delivery of exogenous proteins into mammalian cells, a process that we called here "transexpression". The reporter system was used to develop an efficient protocol for in-cell NMR which enables spectral acquisition with higher quality for both disordered and folded proteins. With this method, the 3D atomic resolution structure of the model protein GB1 in human cells was determined with a backbone root-mean-square deviation (RMSD) of 1.1 Å.
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Affiliation(s)
- Juan A Gerez
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
| | | | | | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | | | | | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, 192-0397, Tokyo, Japan
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, 8093, Zürich, Switzerland.
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16
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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: 23] [Impact Index Per Article: 7.7] [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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17
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Zhu W, Guseman AJ, Bhinderwala F, Lu M, Su XC, Gronenborn AM. Visualizing Proteins in Mammalian Cells by 19 F NMR Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202201097. [PMID: 35278268 PMCID: PMC9156538 DOI: 10.1002/anie.202201097] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Indexed: 12/20/2022]
Abstract
In-cell NMR spectroscopy is a powerful tool to investigate protein behavior in physiologically relevant environments. Although proven valuable for disordered proteins, we show that in commonly used 1 H-15 N HSQC spectra of globular proteins, interactions with cellular components often broaden resonances beyond detection. This contrasts 19 F spectra in mammalian cells, in which signals are readily observed. Using several proteins, we demonstrate that surface charges and interaction with cellular binding partners modulate linewidths and resonance frequencies. Importantly, we establish that 19 F paramagnetic relaxation enhancements using stable, rigid Ln(III) chelate pendants, attached via non-reducible thioether bonds, provide an effective means to obtain accurate distances for assessing protein conformations in the cellular milieu.
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Affiliation(s)
- Wenkai Zhu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Alex J Guseman
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Fatema Bhinderwala
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Manman Lu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 300071, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, 300071, Tianjin, China
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
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18
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Luchinat E, Cremonini M, Banci L. Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. Chem Rev 2022; 122:9267-9306. [PMID: 35061391 PMCID: PMC9136931 DOI: 10.1021/acs.chemrev.1c00790] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 12/12/2022]
Abstract
A detailed knowledge of the complex processes that make cells and organisms alive is fundamental in order to understand diseases and to develop novel drugs and therapeutic treatments. To this aim, biological macromolecules should ideally be characterized at atomic resolution directly within the cellular environment. Among the existing structural techniques, solution NMR stands out as the only one able to investigate at high resolution the structure and dynamic behavior of macromolecules directly in living cells. With the advent of more sensitive NMR hardware and new biotechnological tools, modern in-cell NMR approaches have been established since the early 2000s. At the coming of age of in-cell NMR, we provide a detailed overview of its developments and applications in the 20 years that followed its inception. We review the existing approaches for cell sample preparation and isotopic labeling, the application of in-cell NMR to important biological questions, and the development of NMR bioreactor devices, which greatly increase the lifetime of the cells allowing real-time monitoring of intracellular metabolites and proteins. Finally, we share our thoughts on the future perspectives of the in-cell NMR methodology.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum−Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019 Sesto Fiorentino, Italy
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19
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Bertarello A, Berruyer P, Artelsmair M, Elmore CS, Heydarkhan-Hagvall S, Schade M, Chiarparin E, Schantz S, Emsley L. In-Cell Quantification of Drugs by Magic-Angle Spinning Dynamic Nuclear Polarization NMR. J Am Chem Soc 2022; 144:6734-6741. [PMID: 35385274 PMCID: PMC9026252 DOI: 10.1021/jacs.1c12442] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The determination of intracellular drug concentrations can provide a better understanding of the drug function and efficacy. Ideally, this should be performed nondestructively, with no modification of either the drug or the target, and with the capability to detect low amounts of the molecule of interest, in many cases in the μM to nM range (pmol to fmol per million cells). Unfortunately, it is currently challenging to have an experimental technique that provides direct quantitative measurements of intracellular drug concentrations that simultaneously satisfies these requirements. Here, we show that magic-angle spinning dynamic nuclear polarization (MAS DNP) can be used to fulfill these requirements. We apply a quantitative 15N MAS DNP approach in combination with 15N labeling to quantify the intracellular amount of the drug [15N]CHIR-98014, an activator of the Wingless and Int-1 signaling pathway, determining intracellular drug amounts in the range of tens to hundreds of picomoles per million cells. This is, to our knowledge, the first time that MAS DNP has been used to successfully estimate intracellular drug amounts.
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Affiliation(s)
- Andrea Bertarello
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Pierrick Berruyer
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Markus Artelsmair
- Early Chemical Development, Pharmaceutical Science, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Charles S Elmore
- Early Chemical Development, Pharmaceutical Science, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Sepideh Heydarkhan-Hagvall
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceutical R&D AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Markus Schade
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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20
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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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
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21
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Kontogianni VG, Gerothanassis IP. Analytical and Structural Tools of Lipid Hydroperoxides: Present State and Future Perspectives. Molecules 2022; 27:2139. [PMID: 35408537 PMCID: PMC9000705 DOI: 10.3390/molecules27072139] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022] Open
Abstract
Mono- and polyunsaturated lipids are particularly susceptible to peroxidation, which results in the formation of lipid hydroperoxides (LOOHs) as primary nonradical-reaction products. LOOHs may undergo degradation to various products that have been implicated in vital biological reactions, and thus in the pathogenesis of various diseases. The structure elucidation and qualitative and quantitative analysis of lipid hydroperoxides are therefore of great importance. The objectives of the present review are to provide a critical analysis of various methods that have been widely applied, and more specifically on volumetric methods, applications of UV-visible, infrared, Raman/surface-enhanced Raman, fluorescence and chemiluminescence spectroscopies, chromatographic methods, hyphenated MS techniques, NMR and chromatographic methods, NMR spectroscopy in mixture analysis, structural investigations based on quantum chemical calculations of NMR parameters, applications in living cells, and metabolomics. Emphasis will be given to analytical and structural methods that can contribute significantly to the molecular basis of the chemical process involved in the formation of lipid hydroperoxides without the need for the isolation of the individual components. Furthermore, future developments in the field will be discussed.
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Affiliation(s)
- Vassiliki G. Kontogianni
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
| | - Ioannis P. Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
- International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi 75270, Pakistan
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22
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Gronenborn AM, Zhu W, Guseman AJ, Bhinderwala F, Lu M, Su XC. Visualizing Proteins in Mammalian Cells by 19F NMR spectroscopy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Angela M Gronenborn
- University of Pittsburgh, School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Wenkai Zhu
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Alex J Guseman
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Fatema Bhinderwala
- University of Pittsburgh School of Medicine Department of Structural Biology UNITED STATES
| | - Manman Lu
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Xun-Cheng Su
- Nankai University College of Chemistry State Key Laboratory of Elemento-Organic Chemistry 300071 Tianjin CHINA
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23
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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24
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Luchinat E, Barbieri L, Cremonini M, Pennestri M, Nocentini A, Supuran CT, Banci L. Determination of intracellular protein-ligand binding affinity by competition binding in-cell NMR. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1270-1281. [PMID: 34605430 PMCID: PMC8489230 DOI: 10.1107/s2059798321009037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
Structure-based drug development suffers from high attrition rates due to the poor activity of lead compounds in cellular and animal models caused by low cell penetrance, off-target binding or changes in the conformation of the target protein in the cellular environment. The latter two effects cause a change in the apparent binding affinity of the compound, which is indirectly assessed by cellular activity assays. To date, direct measurement of the intracellular binding affinity remains a challenging task. In this work, in-cell NMR spectroscopy was applied to measure intracellular dissociation constants in the nanomolar range by means of protein-observed competition binding experiments. Competition binding curves relative to a reference compound could be retrieved either from a series of independent cell samples or from a single real-time NMR bioreactor run. The method was validated using a set of sulfonamide-based inhibitors of human carbonic anhydrase II with known activity in the subnanomolar to submicromolar range. The intracellular affinities were similar to those obtained in vitro, indicating that these compounds selectively bind to the intracellular target. In principle, the approach can be applied to any soluble intracellular target that gives rise to measurable chemical shift changes upon ligand binding.
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Affiliation(s)
- Enrico Luchinat
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Pennestri
- Pharmaceutical Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, United Kingdom
| | - Alessio Nocentini
- Dipartimento Neurofarba, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- CERM - Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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25
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Itai Bloch
- Biotechnology Department MIGAL-Galilee Research Institute Kiryat-Shmona 11016 Israel
| | - Maayan Gal
- Department of Oral Biology The Goldschleger School of Dental Medicine Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Nir London
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michal Sharon
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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26
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein-Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021; 60:19637-19642. [PMID: 34101963 PMCID: PMC8457057 DOI: 10.1002/anie.202104947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/23/2021] [Indexed: 12/22/2022]
Abstract
Understanding protein–ligand interactions in a cellular context is an important goal in molecular biology and biochemistry, and particularly for drug development. Investigators must demonstrate that drugs penetrate cells and specifically bind their targets. Towards that end, we present a native mass spectrometry (MS)‐based method for analyzing drug uptake and target engagement in eukaryotic cells. This method is based on our previously introduced direct‐MS method for rapid analysis of proteins directly from crude samples. Here, direct‐MS enables label‐free studies of protein–drug binding in human cells and is used to determine binding affinities of lead compounds in crude samples. We anticipate that this method will enable the application of native MS to a range of problems where cellular context is important, including protein–protein interactions, drug uptake and binding, and characterization of therapeutic proteins.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Itai Bloch
- Biotechnology Department, MIGAL-Galilee Research Institute, Kiryat-Shmona, 11016, Israel
| | - Maayan Gal
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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27
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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28
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Farina B, Andrea C, Del Gatto A, Comegna D, Di Gaetano S, Capasso D, Paladino A, Acconcia C, Teresa Gentile M, Saviano M, Fattorusso R, Zaccaro L, Russo L. A novel approach for studying receptor-ligand interactions on living cells surface by using NUS/T1ρ-NMR methodologies combined with computational techniques: The RGDechi15D-α vβ 5 integrin complex. Comput Struct Biotechnol J 2021; 19:3303-3318. [PMID: 34188779 PMCID: PMC8207173 DOI: 10.1016/j.csbj.2021.05.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
Structural investigations of receptor-ligand interactions on living cells surface by high-resolution Nuclear Magnetic Resonance (NMR) are problematic due to their short lifetime, which often prevents the acquisition of experiments longer than few hours. To overcome these limitations, we developed an on-cell NMR-based approach for exploring the molecular determinants driving the receptor-ligand recognition mechanism under native conditions. Our method relies on the combination of high-resolution structural and dynamics NMR data with Molecular Dynamics simulations and Molecular Docking studies. The key point of our strategy is the use of Non Uniform Sampling (NUS) and T1ρ-NMR techniques to collect atomic-resolution structural and dynamics information on the receptor-ligand interactions with living cells, that can be used as conformational constraints in computational studies. In fact, the application of these two NMR methodologies allows to record spectra with high S/N ratio and resolution within the lifetime of cells. In particular, 2D NUS [1H–1H] trNOESY spectra are used to explore the ligand conformational changes induced by receptor binding; whereas T1ρ-based experiments are applied to characterize the ligand binding epitope by defining two parameters: T1ρ Attenuation factor and T1ρ Binding Effect. This approach has been tested to characterize the molecular determinants regulating the recognition mechanism of αvβ5-integrin by a selective cyclic binder peptide named RGDechi15D. Our data demonstrate that the developed strategy represents an alternative in-cell NMR tool for studying, at atomic resolution, receptor-ligand recognition mechanism on living cells surface. Additionally, our application may be extremely useful for screening of the interaction profiling of drugs with their therapeutic targets in their native cellular environment.
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Affiliation(s)
- Biancamaria Farina
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Advanced Accelerator Applications, a Novartis Company, via Vivaldi 43, 81100 Caserta, Italy
| | - Corvino Andrea
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Daniela Comegna
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Domenica Capasso
- Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.,Center for Life Sciences and Technologies (CESTEV) University of Naples Federico II, Via Tommaso De Amicis 95, 80145 Naples, Italy
| | - Antonella Paladino
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis, Benevento 82100, Italy
| | - Clementina Acconcia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Teresa Gentile
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
| | - Michele Saviano
- Institute of Crystallography-CNR, Via Amendola 122/O, 70126 Bari, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
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29
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Luchinat E, Barbieri L, Cremonini M, Banci L. Protein in-cell NMR spectroscopy at 1.2 GHz. JOURNAL OF BIOMOLECULAR NMR 2021; 75:97-107. [PMID: 33580357 PMCID: PMC8018933 DOI: 10.1007/s10858-021-00358-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
In-cell NMR spectroscopy provides precious structural and functional information on biological macromolecules in their native cellular environment at atomic resolution. However, the intrinsic low sensitivity of NMR imposes a big limitation in the applicability of the methodology. In this respect, the recently developed commercial 1.2 GHz NMR spectrometer is expected to introduce significant benefits. However, cell samples may suffer from detrimental effects at ultrahigh fields, that must be carefully evaluated. Here we show the first in-cell NMR spectra recorded at 1.2 GHz on human cells, and we compare resolution and sensitivity against those obtained at 900 and 950 MHz. To evaluate the effects of different spin relaxation rates, SOFAST-HMQC and BEST-TROSY spectra were recorded on intracellular α-synuclein and carbonic anhydrase. Major improvements are observed at 1.2 GHz when analyzing unfolded proteins, such as α-synuclein, while the TROSY scheme improves the resolution for both globular and unfolded proteins.
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Affiliation(s)
- Enrico Luchinat
- Università degli Studi di Firenze, Via Luigi sacconi 6, 50019, Sesto Fiorentino, Italy.
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase - CSGI, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Letizia Barbieri
- Università degli Studi di Firenze, Via Luigi sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Università degli Studi di Firenze, Via Luigi sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Lucia Banci
- Università degli Studi di Firenze, Via Luigi sacconi 6, 50019, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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30
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Narasimhan S, Pinto C, Lucini Paioni A, van der Zwan J, Folkers GE, Baldus M. Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy. Nat Protoc 2021; 16:893-918. [PMID: 33442051 DOI: 10.1038/s41596-020-00439-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
For a long time, solid-state nuclear magnetic resonance (ssNMR) has been employed to study complex biomolecular systems at the detailed chemical, structural, or dynamic level. Recent progress in high-resolution and high-sensitivity ssNMR, in combination with innovative sample preparation and labeling schemes, offers novel opportunities to study proteins in their native setting irrespective of the molecular tumbling rate. This protocol describes biochemical preparation schemes to obtain cellular samples of both soluble as well as insoluble or membrane-associated proteins in bacteria. To this end, the protocol is suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations. In the first stage of the procedure, an appropriate strain of Escherichia coli (DE3) is transformed with a plasmid of interest harboring the protein of interest under the control of an inducible T7 promoter. Next, the cells are adapted to grow in minimal (M9) medium. Before the growth enters stationary phase, protein expression is induced, and shortly thereafter, the native E. coli RNA polymerase is inhibited using rifampicin for targeted labeling of the protein of interest. The cells are harvested after expression and prepared for ssNMR rotor filling. In addition to conventional 13C/15N-detected ssNMR, we also outline how these preparations can be readily subjected to multidimensional ssNMR experiments using dynamic nuclear polarization (DNP) or proton (1H) detection schemes. We estimate that the entire preparative procedure until NMR experiments can be started takes 3-5 days.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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31
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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32
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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33
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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34
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Unione L, Ardá A, Jiménez-Barbero J, Millet O. NMR of glycoproteins: profiling, structure, conformation and interactions. Curr Opin Struct Biol 2020; 68:9-17. [PMID: 33129067 DOI: 10.1016/j.sbi.2020.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
In glycoproteins, carbohydrates are responsible for the selective interaction and tight regulation of cellular processes, constituting the main information transducer interface in protein-glycoprotein interactions. Increasing experimental and computational evidence suggest that such interactions often induce allosteric changes in the host protein, underlining the importance of studying intact glycoproteins. Technical issues have precluded such studies for years but, nowadays, a promising era is emerging where NMR spectroscopy, among other techniques, allows the characterization of the composition, structure and segmental dynamics of glycoproteins. In this review, we discuss such advances and highlight some selected examples. This novel technology unravels multiple new functional mechanisms, subtly hidden within the sugar code.
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Affiliation(s)
- Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, Building 800, 48162 Derio, Bizkaia, Spain.
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35
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Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L. Intracellular Binding/Unbinding Kinetics of Approved Drugs to Carbonic Anhydrase II Observed by in-Cell NMR. ACS Chem Biol 2020; 15:2792-2800. [PMID: 32955851 PMCID: PMC7735671 DOI: 10.1021/acschembio.0c00590] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Candidate
drugs rationally designed in vitro often
fail due to low efficacy in vivo caused by low tissue
availability or because of unwanted side effects. To overcome the
limitations of in vitro rational drug design, the
binding of candidate drugs to their target needs to be evaluated in
the cellular context. Here, we applied in-cell NMR to investigate
the binding of a set of approved drugs to the isoform II of carbonic
anhydrase (CA) in living human cells. Some compounds were originally
developed toward other targets and were later found to inhibit CAs.
We observed strikingly different dose- and time-dependent binding,
wherein some drugs exhibited a more complex behavior than others.
Specifically, some compounds were shown to gradually unbind from intracellular
CA II, even in the presence of free compound in the external medium,
therefore preventing the quantitative formation of a stable protein–ligand
complex. Such observations could be correlated to the known off-target
binding activity of these compounds, suggesting that this approach
could provide information on the pharmacokinetic profiles of lead
candidates at the early stages of multitarget drug design.
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Affiliation(s)
- Enrico Luchinat
- CERM − Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio per lo Sviluppo dei Sistemi a Grande Interfase − CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM − Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, Sesto Fiorentino, Italy
| | - Matteo Cremonini
- CERM − Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Claudiu T. Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- CERM − Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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36
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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37
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Boeszoermenyi A, Ogórek B, Jain A, Arthanari H, Wagner G. The precious fluorine on the ring: fluorine NMR for biological systems. JOURNAL OF BIOMOLECULAR NMR 2020; 74:365-379. [PMID: 32651751 PMCID: PMC7539674 DOI: 10.1007/s10858-020-00331-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/29/2020] [Indexed: 05/08/2023]
Abstract
The fluorine-19 nucleus was recognized early to harbor exceptional properties for NMR spectroscopy. With 100% natural abundance, a high gyromagnetic ratio (83% sensitivity compared to 1H), a chemical shift that is extremely sensitive to its surroundings and near total absence in biological systems, it was destined to become a favored NMR probe, decorating small and large molecules. However, after early excitement, where uptake of fluorinated aromatic amino acids was explored in a series of animal studies, 19F-NMR lost popularity, especially in large molecular weight systems, due to chemical shift anisotropy (CSA) induced line broadening at high magnetic fields. Recently, two orthogonal approaches, (i) CF3 labeling and (ii) aromatic 19F-13C labeling leveraging the TROSY (Transverse Relaxation Optimized Spectroscopy) effect have been successfully applied to study large biomolecular systems. In this perspective, we will discuss the fascinating early work with fluorinated aromatic amino acids, which reveals the enormous potential of these non-natural amino acids in biological NMR and the potential of 19F-NMR to characterize protein and nucleic acid structure, function and dynamics in the light of recent developments. Finally, we explore how fluorine NMR might be exploited to implement small molecule or fragment screens that resemble physiological conditions and discuss the opportunity to follow the fate of small molecules in living cells.
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Affiliation(s)
- Andras Boeszoermenyi
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Barbara Ogórek
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and, Harvard Medical School, Boston, MA, 02115, USA
| | - Akshay Jain
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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38
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Luchinat E, Barbieri L, Campbell TF, Banci L. Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution. Anal Chem 2020; 92:9997-10006. [PMID: 32551584 PMCID: PMC7735651 DOI: 10.1021/acs.analchem.0c01677] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
In-cell NMR can investigate
protein conformational changes at atomic
resolution, such as those changes induced by drug binding or chemical
modifications, directly in living human cells, and therefore has great
potential in the context of drug development as it can provide an
early assessment of drug potency. NMR bioreactors can greatly improve
the cell sample stability over time and, more importantly, allow for
recording in-cell NMR data in real time to monitor the evolution of
intracellular processes, thus providing unique insights into the kinetics
of drug-target interactions. However, current implementations are
limited by low cell viability at >24 h times, the reduced sensitivity
compared to “static” experiments and the lack of protocols
for automated and quantitative analysis of large amounts of data.
Here, we report an improved bioreactor design which maintains human
cells alive and metabolically active for up to 72 h, and a semiautomated
workflow for quantitative analysis of real-time in-cell NMR data relying
on Multivariate Curve Resolution. We apply this setup to monitor protein–ligand
interactions and protein oxidation in real time. High-quality concentration
profiles can be obtained from noisy 1D and 2D NMR data with high temporal
resolution, allowing further analysis by fitting with kinetic models.
This unique approach can therefore be applied to investigate complex
kinetic behaviors of macromolecules in a cellular setting, and could
be extended in principle to any real-time NMR application in live
cells.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Center for Colloids and Surface Science - CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence Italy
| | - Letizia Barbieri
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Interuniversity Consortium for Magnetic Resonance of Metalloproteins - CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
| | - Timothy F Campbell
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
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39
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Mateos B, Sealey‐Cardona M, Balazs K, Konrat J, Staffler G, Konrat R. NMR Characterization of Surface Receptor Protein Interactions in Live Cells Using Methylcellulose Hydrogels. Angew Chem Int Ed Engl 2020; 59:3886-3890. [PMID: 31721390 PMCID: PMC7065066 DOI: 10.1002/anie.201913585] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/11/2019] [Indexed: 01/29/2023]
Abstract
Interactions of transmembrane receptors with their extracellular ligands are essential for cellular communication and signaling and are therefore a major focus in drug discovery programs. The transition from in vitro to live cell interaction studies, however, is typically a bottleneck in many drug discovery projects due to the challenge of obtaining atomic-resolution information under near-physiological conditions. Although NMR spectroscopy is ideally suited to overcome this limitation, several experimental impairments are still present. Herein, we propose the use of methylcellulose hydrogels to study extracellular proteins and their interactions with plasma membrane receptors. This approach reduces cell sedimentation, prevents the internalization of membrane receptors, and increases cell survival, while retaining the free tumbling of extracellular proteins.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
| | - Marco Sealey‐Cardona
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
- Present address: Calyxha Biotechnologies GmbHKarl-Farkas-Gasse 221030ViennaAustria
| | | | - Judith Konrat
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
| | | | - Robert Konrat
- Department of Structural and Computational BiologyMax Perutz LabsVienna Biocenter Campus 51030ViennaAustria
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40
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Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L. Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Enrico Luchinat
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”Università degli Studi di Firenze Viale Morgagni 50 50134 Florence Italy
| | - Letizia Barbieri
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Consorzio Interuniversitario Risonanze Magnetiche di, Metalloproteine Via Luigi Sacconi 6 Sesto Fiorentino Italy
| | - Matteo Cremonini
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
| | - Alessio Nocentini
- Dipartimento NeurofarbaSezione di Scienze FarmaceuticheUniversità degli Studi di Firenze Via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Claudiu T. Supuran
- Dipartimento NeurofarbaSezione di Scienze FarmaceuticheUniversità degli Studi di Firenze Via Ugo Schiff 6 50019 Sesto Fiorentino Italy
- Dipartimento di ChimicaUniversità degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Banci
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di ChimicaUniversità degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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41
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Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L. Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency. Angew Chem Int Ed Engl 2020; 59:6535-6539. [PMID: 32022355 PMCID: PMC7187179 DOI: 10.1002/anie.201913436] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Structure-based drug development is often hampered by the lack of in vivo activity of promising compounds screened in vitro, due to low membrane permeability or poor intracellular binding selectivity. Herein, we show that ligand screening can be performed in living human cells by "intracellular protein-observed" NMR spectroscopy, without requiring enzymatic activity measurements or other cellular assays. Quantitative binding information is obtained by fast, inexpensive 1 H NMR experiments, providing intracellular dose- and time-dependent ligand binding curves, from which kinetic and thermodynamic parameters linked to cell permeability and binding affinity and selectivity are obtained. The approach was applied to carbonic anhydrase and, in principle, can be extended to any NMR-observable intracellular target. The results obtained are directly related to the potency of candidate drugs, that is, the required dose. The application of this approach at an early stage of the drug design pipeline could greatly increase the low success rate of modern drug development.
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Affiliation(s)
- Enrico Luchinat
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.,Dipartimento di Scienze Biomediche Sperimentali e Cliniche "Mario Serio", Università degli Studi di Firenze, Viale Morgagni 50, 50134, Florence, Italy
| | - Letizia Barbieri
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di, Metalloproteine, Via Luigi Sacconi 6, Sesto Fiorentino, Italy
| | - Matteo Cremonini
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy.,Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Banci
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.,Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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42
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Mateos B, Sealey‐Cardona M, Balazs K, Konrat J, Staffler G, Konrat R. NMR Characterization of Surface Receptor Protein Interactions in Live Cells Using Methylcellulose Hydrogels. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
| | - Marco Sealey‐Cardona
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
- Present address: Calyxha Biotechnologies GmbH Karl-Farkas-Gasse 22 1030 Vienna Austria
| | - Katja Balazs
- AFFiRiS AG Karl-Farkas-Gasse 22 1030 Vienna Austria
| | - Judith Konrat
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
| | | | - Robert Konrat
- Department of Structural and Computational Biology Max Perutz Labs Vienna Biocenter Campus 5 1030 Vienna Austria
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43
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Abstract
At the foundation of many cellular processes as well as a large number of diseases is the (mis)folding of important intrinsically disordered proteins (IDPs). Despite tremendous scientific efforts, the factors driving their structural changes within the cellular context remain poorly understood. In-cell NMR spectroscopy enables investigation of IDPs directly in the living eukaryotic cell enabling investigation of its intermolecular interactions and ensuing modifications at an unprecedented atomic resolution. In the following protocol, we describe how to prepare in-cell NMR samples of IDPs within eukaryotic cells and how to measure these in-cell NMR samples of an IDP in its natural environment, the living mammalian cell. Furthermore, we outline a procedure to assess the intracellular recombinant protein concentration of the studied IDP based on in-cell NMR methods. We use α-synuclein as a model protein, but the presented approach is highly modular and therefore should be easily adapted and altered to the desired needs for the studies of different IDPs.
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44
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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45
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Unione L, Lenza M, Ardá A, Urquiza P, Laín A, Falcón-Pérez JM, Jiménez-Barbero J, Millet O. Glycoprofile Analysis of an Intact Glycoprotein As Inferred by NMR Spectroscopy. ACS CENTRAL SCIENCE 2019; 5:1554-1561. [PMID: 31572782 PMCID: PMC6764210 DOI: 10.1021/acscentsci.9b00540] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 05/10/2023]
Abstract
Protein N-glycosylation stands out for its intrinsic and functionally related heterogeneity. Despite its biomedical interest, Glycoprofile analysis still remains a major scientific challenge. Here, we present an NMR-based strategy to delineate the N-glycan composition in intact glycoproteins and under physiological conditions. The employed methodology allowed dissecting the glycan pattern of the IgE high-affinity receptor (FcεRIα) expressed in human HEK 293 cells, identifying the presence and relative abundance of specific glycan epitopes. Chemical shifts and differences in the signal line-broadening between the native and the unfolded states were integrated to build a structural model of FcεRIα that was able to identify intramolecular interactions between high-mannose N-glycans and the protein surface. In turn, complex type N-glycans reflect a large solvent accessibility, suggesting a functional role as interaction sites for receptors. The interaction between intact FcεRIα and the lectin hGal3, also studied here, confirms this hypothesis and opens new avenues for the detection of specific N-glycan epitopes and for the studies of glycoprotein-receptor interactions mediated by N-glycans.
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Affiliation(s)
- Luca Unione
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
| | - Maria
Pia Lenza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Pedro Urquiza
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Ana Laín
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
| | - Juan Manuel Falcón-Pérez
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- Basque
Foundation for Science IKERBASQUE, 48009 Bilbao, Spain
- Dept.
Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- E-mail:
| | - Oscar Millet
- CIC
bioGUNE, Bizkaia Technology Park, Bld 800, 48170 Derio, Spain
- E-mail:
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46
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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47
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Han R, Yang Y, Wang S. Longitudinal Relaxation Optimization Enhances 1 H-Detected HSQC in Solid-State NMR Spectroscopy on Challenging Biological Systems. Chemistry 2019; 25:4115-4122. [PMID: 30632195 DOI: 10.1002/chem.201805327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 11/10/2022]
Abstract
Solid-state (SS) NMR spectroscopy is a powerful technique for studying challenging biological systems, but it often suffers from low sensitivity. A longitudinal relaxation optimization scheme to enhance the signal sensitivity of HSQC experiments in SSNMR spectroscopy is reported. Under the proposed scheme, the 1 H spins of 1 H-X (15 N or 13 C) are selected for signal acquisition, whereas other vast 1 H spins are flipped back to the axis of the static magnetic field to accelerate the spin recovery of the observed 1 H spins, resulting in enhanced sensitivity. Three biological systems are used to evaluate this strategy, including a seven-transmembrane protein, an RNA, and a whole-cell sample. For all three samples, the proposed scheme largely shortens the effective 1 H longitudinal relaxation time and results in a 1.3-2.5-fold gain in sensitivity. The selected systems are representative of challenging biological systems for observation by means of SSNMR spectroscopy; thus indicating the general applicability of this method, which is particularly important for biological samples with a short lifetime or with limited sample quantities.
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Affiliation(s)
- Rong Han
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, No. 5th, Yiheyuan Rd., Beijing, 100871, P.R. China
| | - Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, No. 5th, Yiheyuan Rd., Beijing, 100871, P.R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, No. 5th, Yiheyuan Rd., Beijing, 100871, P.R. China.,Beijing National Laboratory for Molecular Sciences, Beijing, P.R. China
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48
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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49
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Polykretis P, Cencetti F, Donati C, Luchinat E, Banci L. Cadmium effects on superoxide dismutase 1 in human cells revealed by NMR. Redox Biol 2019; 21:101102. [PMID: 30654299 PMCID: PMC6348768 DOI: 10.1016/j.redox.2019.101102] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 11/24/2022] Open
Abstract
Cadmium is a toxic pollutant that in recent decades has become more widespread in the environment due to anthropogenic activities, significantly increasing the risk of exposure. Concurrently, a continually growing body of research has begun to enumerate the harmful effects that this heavy metal has on human health. Consequently, additional research is required to better understand the mechanism and effects of cadmium at the molecular level. The main mechanism of cadmium toxicity is based on the indirect induction of severe oxidative stress, through several processes that unbalance the anti-oxidant cellular defence system, including the displacement of metals such as zinc from its native binding sites. Such mechanism was thought to alter the in vivo enzymatic activity of SOD1, one of the main antioxidant proteins of many tissues, including the central nervous system. SOD1 misfolding and aggregation is correlated with cytotoxicity in neurodegenerative diseases such as amyotrophic lateral sclerosis. We assessed the effect of cadmium on SOD1 folding and maturation pathway directly in human cells through in-cell NMR. Cadmium does not directly bind intracellular SOD1, instead causes the formation of its intramolecular disulfide bond in the zinc-bound form. Metallothionein overexpression is strongly induced by cadmium, reaching NMR-detectable levels. The intracellular availability of zinc modulates both SOD1 oxidation and metallothionein overexpression, strengthening the notion that zinc-loaded metallothioneins help maintaining the redox balance under cadmium-induced acute stress.
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Affiliation(s)
- Panagis Polykretis
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesca Cencetti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Chiara Donati
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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50
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Cerofolini L, Giuntini S, Barbieri L, Pennestri M, Codina A, Fragai M, Banci L, Luchinat E, Ravera E. Real-Time Insights into Biological Events: In-Cell Processes and Protein-Ligand Interactions. Biophys J 2019; 116:239-247. [PMID: 30580921 PMCID: PMC6350048 DOI: 10.1016/j.bpj.2018.11.3132] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/30/2018] [Accepted: 11/27/2018] [Indexed: 11/15/2022] Open
Abstract
FlowNMR has the aim of continuously monitoring processes that occur in conditions that are not compatible with being carried out within a closed tube. However, it is sample intensive and not suitable for samples, such as proteins or living cells, that are often available in limited volumes and possibly low concentrations. We here propose a dialysis-based modification of a commercial flowNMR setup that allows for recycling the medium while confining the sample (proteins and cells) within the active volume of the tube. This approach is demonstrated in the specific cases of in-cell NMR and protein-based ligand studies.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Barbieri
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy
| | | | - Anna Codina
- Bruker UK Limited, Banner Lane, Coventry, United Kingdom
| | - Marco Fragai
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Experimental and Clinical Biomedical Sciences, Mario Serio, University of Florence, Florence, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Sesto Fiorentino, Italy; Department of Chemistry, Ugo Schiff, University of Florence, Sesto Fiorentino, Italy.
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