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Qianzhu H, Abdelkader EH, Otting G, Huber T. Genetic Encoding of Fluoro-l-tryptophans for Site-Specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. J Am Chem Soc 2024; 146:13641-13650. [PMID: 38687675 DOI: 10.1021/jacs.4c03743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Toscano G, Holzinger J, Nagl B, Kontaxis G, Kählig H, Konrat R, Lichtenecker RJ. Decorating phenylalanine side-chains with triple labeled 13C/ 19F/ 2H isotope patterns. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00440-z. [PMID: 38509441 DOI: 10.1007/s10858-024-00440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
We present an economic and straightforward method to introduce 13C-19F spin systems into the deuterated aromatic side chains of phenylalanine as reporters for various protein NMR applications. The method is based on the synthesis of [4-13C, 2,3,5,6-2H4] 4-fluorophenylalanine from the commercially available isotope sources [2-13C] acetone and deuterium oxide. This compound is readily metabolized by standard Escherichia coli overexpression in a glyphosate-containing minimal medium, which results in high incorporation rates in the corresponding target proteins.
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Affiliation(s)
- Giorgia Toscano
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090, Vienna, Austria
| | - Julian Holzinger
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Benjamin Nagl
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Hanspeter Kählig
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Roman J Lichtenecker
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
- MAG-LAB, Karl-Farkas-Gasse 22, 1030, Vienna, Austria.
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Vitali V, Torricella F, Massai L, Messori L, Banci L. Enlarging the scenario of site directed 19F labeling for NMR spectroscopy of biomolecules. Sci Rep 2023; 13:22017. [PMID: 38086881 PMCID: PMC10716153 DOI: 10.1038/s41598-023-49247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The possibility of using selectively incorporated 19F nuclei for NMR spectroscopic studies has retrieved increasing interest in recent years. The high gyromagnetic ratio of 19F and its absence in native biomolecular systems make this nucleus an interesting alternative to standard 1H NMR spectroscopy. Here we show how we can attach a label, carrying a 19F atom, to protein tyrosines, through the use of a specific three component Mannich-type reaction. To validate the efficacy and the specificity of the approach, we tested it on two selected systems with the aid of ESI MS measurements.
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Affiliation(s)
- Valentina Vitali
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Francesco Torricella
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Lara Massai
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy.
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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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Maleckis A, Abdelkader EH, Herath ID, Otting G. Synthesis of fluorinated leucines, valines and alanines for use in protein NMR. Org Biomol Chem 2022; 20:2424-2432. [PMID: 35262139 DOI: 10.1039/d2ob00145d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Efficient syntheses of fluorinated leucines, valines and alanines are described. The synthetic routes provide expedient access to various 13C/15N/D isotopologues requiring solely readily available and inexpensive isotope containing reagents such as NaBD4, carbon-13C dioxide and sodium azide-1-15N. The lightly fluorinated leucines and valines were found to be good substrates for cell-free protein expression and even 3-fluoroalanine, which is highly toxic to bacteria in vivo, could be incorporated into proteins this way. 19F-NMR spectra of the protein GB1 produced with these amino acids showed large chemical shift dispersions. Particularly high incorporation yields and clean 19F-NMR spectra were obtained for GB1 produced with valine residues, which had been synthesized with a single fluorine substituting a hydrogen stereospecifically in one of the methyl groups.
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Affiliation(s)
- Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Iresha D Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Orton H, Herath I, Maleckis A, Jabar S, Szabo M, Graham B, Breen C, Topping L, Butler S, Otting G. Localising individual atoms of tryptophan side chains in the metallo- β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:1-13. [PMID: 37905175 PMCID: PMC10583275 DOI: 10.5194/mr-3-1-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/21/2021] [Indexed: 11/01/2023]
Abstract
The metallo-β -lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-13 C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy (Δ χ ) tensors were determined by measuring pseudocontact shifts (PCSs) of backbone amide protons. The Δ χ tensors were subsequently used to identify the atomic coordinates of the tryptophan side chains in the protein. The PCSs were sufficient to determine the location of Trp28, which is in the active site loop targeted by our experiments, with high accuracy. Its average atomic coordinates showed barely significant changes in response to the inhibitor captopril. It was found that localisation spaces could be defined with better accuracy by including only the PCSs of a single paramagnetic lanthanoid ion for each tag and tagging site. The effect was attributed to the shallow angle with which PCS isosurfaces tend to intersect if generated by tags and tagging sites that are identical except for the paramagnetic lanthanoid ion.
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Affiliation(s)
- Henry W. Orton
- ARC Centre of Excellence for Innovations in Peptide & Protein
Science, Research School of Chemistry, Australian National University,
Canberra, ACT 2601, Australia
| | - Iresha D. Herath
- Research School of Chemistry, The Australian National University,
Sullivans Creek Road, Canberra ACT 2601, Australia
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga,
Latvia
| | - Shereen Jabar
- Research School of Chemistry, The Australian National University,
Sullivans Creek Road, Canberra ACT 2601, Australia
| | - Monika Szabo
- Monash Institute of Pharmaceutical Sciences, Monash University,
Parkville, VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University,
Parkville, VIC 3052, Australia
| | - Colum Breen
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Lydia Topping
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Stephen J. Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein
Science, Research School of Chemistry, Australian National University,
Canberra, ACT 2601, Australia
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