1
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Li M, Xu G, Gong Z, Wu Q, Jiang L, Li C. Simultaneous measurement of multiple fluorine labelling effect on GB1 stability by 19F NMR. Talanta 2025; 292:127959. [PMID: 40112587 DOI: 10.1016/j.talanta.2025.127959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 03/09/2025] [Accepted: 03/15/2025] [Indexed: 03/22/2025]
Abstract
The incorporation of fluorinated amino acids into proteins through natural biosynthesis in E. coli often leads to the production of heterogeneous fluorinated proteins. The stabilities of proteins with different 19F labelling states can vary, but these differences are challenging to measure due to the difficulty in separating the fluorinated protein mixtures that differ by only a few 19F atoms. Here, we simultaneously incorporated both fluoro-phenylalanines (3-fluoro-phenylalanine, 3FF; or 4-fluoro-phenylalanine, 4FF) and 5-fluoro-tryptophan (5FW) into GB1 protein. We are able to measure the stability of GB1 protein with different 19F labelling states without the need for sample separation by taking the advantage of 19F NMR. The results showed that 4FF-5FW-GB1 with varying 19F labelling states exhibited significantly different protein stability, with higher 4FF labeling efficiency correlating with decreased stability. Furthermore, residues F30 and F52 show synergistic effects on GB1 stability. In contrast, the 3FF and 5FW substitution exhibits a slightly stabilizing effect on GB1 stability. The present research provides a convenient 19F NMR method to simultaneously measure fluorine labelling effects on protein stability, favouring precise understanding and analysis of fluorine labelling effects.
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Affiliation(s)
- Manman Li
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, 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, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Guohua Xu
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, 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, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, 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, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Qiong Wu
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, 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, 430071, PR China
| | - Ling Jiang
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, 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, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance Spectroscopy and Imaging, 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, 430071, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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2
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Kang C. 19F NMR in RNA structural biology: exploring structures, dynamics, and small molecule interactions. Eur J Med Chem 2025; 292:117682. [PMID: 40300458 DOI: 10.1016/j.ejmech.2025.117682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2025] [Revised: 04/22/2025] [Accepted: 04/23/2025] [Indexed: 05/01/2025]
Abstract
RNA molecules play essential roles in numerous biological pathways, making them attractive targets for drug discovery. Despite the challenges in developing small molecules targeting RNA, the success in developing compounds that modulate RNA function underscores its therapeutic potential. 19F NMR spectroscopy has emerged as a powerful tool in structural biology and drug discovery, particularly for studying macromolecular structures and ligand interactions. As RNA continues to gain prominence as a drug target, 19F NMR is expected to play a pivotal role in advancing RNA-focused drug discovery. This review describes the diverse applications of 19F NMR in RNA biology, including its use in characterizing RNA structures, probing molecular dynamics, identifying small-molecule binders, and investigating interaction mechanisms of small-molecule ligands. By providing detailed structural and ligand binding insights, 19F NMR will facilitate the discovery of RNA-targeting therapeutics and deepen our understanding of RNA modulatory mechanisms.
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Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A∗STAR), 10 Biopolis Road, #05-01, 138670, Singapore.
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3
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Streit JO, Chan SHS, Daya S, Christodoulou J. Rational design of 19F NMR labelling sites to probe protein structure and interactions. Nat Commun 2025; 16:4300. [PMID: 40341366 PMCID: PMC12062419 DOI: 10.1038/s41467-025-59105-6] [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: 01/14/2025] [Accepted: 04/11/2025] [Indexed: 05/10/2025] Open
Abstract
Proteins are investigated in increasingly more complex biological systems, where 19F NMR is proving highly advantageous due to its high gyromagnetic ratio and background-free spectra. Its application has, however, been hindered by limited chemical shift dispersions and an incomprehensive relationship between chemical shifts and protein structure. Here, we exploit the sensitivity of 19F chemical shifts to ring currents by designing labels with direct contact to a native or engineered aromatic ring. Fifty protein variants predicted by AlphaFold and molecular dynamics simulations show 80-90% success rates and direct correlations of their experimental chemical shifts with the magnitude of the engineered ring current. Our method consequently improves the chemical shift dispersion and through simple 1D experiments enables structural analyses of alternative conformational states, including ribosome-bound folding intermediates, and in-cell measurements of protein-protein interactions and thermodynamics. Our strategy thus provides a simple and sensitive tool to extract residue contact restraints from chemical shifts for previously intractable systems.
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Affiliation(s)
- Julian O Streit
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Saifu Daya
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
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4
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Náplavová A, Kozeleková A, Crha R, Gronenborn AM, Hritz J. Harnessing the power of 19F NMR for characterizing dimerization and ligand binding of 14-3-3 proteins. Int J Biol Macromol 2025; 305:141253. [PMID: 39978522 DOI: 10.1016/j.ijbiomac.2025.141253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 01/30/2025] [Accepted: 02/17/2025] [Indexed: 02/22/2025]
Abstract
The main role of dimeric 14-3-3 proteins is to modulate the activity of several hundred binding partners by interacting with phosphorylated residues of the partner proteins, often located in disordered regions. The inherent flexibility or large size of 14-3-3 complexes hampers their structural characterization by X-ray crystallography, cryo-electron microscopy (EM) and traditional solution nuclear magnetic resonance (NMR) spectroscopy. Here, we employ solution 1D 19F-Trp NMR spectroscopy to characterize substrate binding and dimerization of 14-3-3 proteins, focusing on 14-3-3ζ - an abundant human isoform as an example. Both conserved Trp residues are located in distinct functionally important sites - the dimeric interface and the ligand-binding groove. We substituted them by 5F-Trp, thereby introducing a convenient NMR probe. Fluorination of the two Trp did not impact the stability and interaction properties of 14-3-3ζ in a substantive manner, permitting to carry out 19F NMR experiments to assess 14-3-3's structure and behavior. Importantly, 5F-Trp228 reports on binding of substrates in the amphipathic binding groove of 14-3-3ζ and permitted to distinguish distinct recognition modes. Thus, we established that 19F NMR is a powerful approach to evaluate the binding of partner proteins to 14-3-3 and to characterize the properties of the resulting complexes.
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Affiliation(s)
- Alexandra Náplavová
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czechia
| | - Aneta Kozeleková
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czechia
| | - Radek Crha
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czechia
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czechia; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czechia.
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5
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Zhang Y, Zhu Y, Zhang Y, Shi C, Zhang L, Liang J, Tian C, Shi P. 19F NMR chemical shift encoded peptide screening targeting the potassium channel Kv1.3. Chem Commun (Camb) 2025; 61:6162-6165. [PMID: 40162494 DOI: 10.1039/d5cc00595g] [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: 04/02/2025]
Abstract
19F nuclear magnetic resonance (19F-NMR) is a pivotal technique for protein dynamic studies and drug screening because of its high sensitivity. Herein, we report a 19F-NMR chemical shift-based ligand screening strategy targeting membrane proteins using multiple peptide ligands containing different 19F-incorporating unnatural amino acids. Five different 19F-labelled unnatural amino acids (3FF, 4FF, 5FW, 6FW and 7FW) with distinctive 19F chemical shift values were applied to chemically synthesize multiple toxin peptides, which can potentially bind to and inhibit the conductance function of the autoimmune disease-related potassium channel Kv1.3. The 19F NMR relaxation-filtered one-dimensional spectra of competitively eluted peptides from the Kv1.3-peptide complex directly revealed the high-affinity binding of the peptides, which was verified using patch-clamp electrophysiological analysis. This 19F-NMR chemical shift-based encoded peptide screening method can be directly extended for large-scale peptide library screening targeting membrane proteins.
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Affiliation(s)
- Yong Zhang
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
| | - Yongjie Zhu
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
| | - Yi Zhang
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
| | - Chaowei Shi
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
| | - Longhua Zhang
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
| | - Jun Liang
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
| | - Changlin Tian
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
- School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Sciences, Shanghai Jiao Tong University, Shanghai, China
- Beijing Life Science Academy, Beijing, China
| | - Pan Shi
- Department of Endocrinology, the First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, University of Science and Technology of China, Anhui 230026, P. R. China.
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6
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Hilber S, Attionu SK, Dayie TK, Kreutz C. Advances in Isotope Labeling for Solution Nucleic Acid Nuclear Magnetic Resonance Spectroscopy. Chempluschem 2025:e2400752. [PMID: 40202339 DOI: 10.1002/cplu.202400752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 04/09/2025] [Accepted: 04/09/2025] [Indexed: 04/10/2025]
Abstract
The availability of structural biology methods for nucleic acid still lags behind that of proteins, as evidenced by the smaller number of structures (DNA: 2513, RNA: 1899, nucleic acid-protein complexes: 13 842, protein: 196 887) deposited in the protein database. The skewed ratio of nucleic acid structures, relative to proteins (≈1:50), is inverted with respect to the cellular output of RNA and proteins in higher organisms (≈50:1). While nuclear magnetic resonance (NMR) is an attractive biophysical tool capable of bridging this gap at the molecular level, the conformational flexibility, line broadening, and low chemical shift dispersion of nucleic acids have made the NMR method challenging, especially for structures larger than 35 nucleotides. The incorporation of NMR-active isotopes is a f strategy to combat these problems. Significant strides made to push the size limits of nucleic acid structures solved by NMR using chemoenzymatic 13C- methyl and aromatic 15N- and 19F-13C-labeling are reviewed and challenges and opportunities are evaluated. Combining these isotopic labeling patterns with superior NMR spectroscopic properties, and new DNA/RNA synthesis methods (palindrome-nicking-dependent amplification and segmental labeling and site-specific modifications by template-directed tension), may stimulate advances in NMR studies of large DNA/RNA and their complexes with important biological functions.
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Affiliation(s)
- Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain, 80/82, 6020, Innsbruck, Austria
| | - Solomon Kojo Attionu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20782, USA
| | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20782, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain, 80/82, 6020, Innsbruck, Austria
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7
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El Hage K, Dhayalan B, Chen Y, Phillips NB, Whittaker J, Carr K, Whittaker L, Phillips MH, Ismail‐Beigi F, Meuwly M, Weiss MA. Stabilization of a protein by a single halogen-based aromatic amplifier. Protein Sci 2025; 34:e70064. [PMID: 39969055 PMCID: PMC11837044 DOI: 10.1002/pro.70064] [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: 08/23/2024] [Revised: 01/30/2025] [Accepted: 01/31/2025] [Indexed: 02/20/2025]
Abstract
The utility of halogenation in protein design is investigated by a combination of quantitative atomistic simulations and experiment. Application to insulin is of complementary basic and translational interest. In a singly halogenated aromatic ring, regiospecific inductive effects were predicted to modulate multiple surrounding electrostatic (weakly polar) interactions, thereby amplifying changes in thermodynamic stability. In accordance with the simulations, we demonstrated stabilization of insulin by single halogen atoms at the ortho position of an invariant phenylalanine (2-F-PheB24, 2-Cl-PheB24, and 2-Br-PheB24; ΔΔGu = -0.5 to -1.0 kcal/mol) located at the edge of a protein crevice; corresponding meta and para substitutions had negligible effects. Although receptor-binding affinities were generally decreased (in accordance with packing of the native Phe at the hormone-receptor interface), the ortho-analogs retained biological activity in mammalian cells and in a rat model of diabetes mellitus. Further, the ortho-modified analogs exhibited enhanced resistance to fibrillation above room temperature in two distinct assays of physical stability. Regiospecific halo-aromatic stabilization may thus augment the shelf life of pharmaceutical insulin formulations under real-world conditions. This approach, extending principles of medicinal chemistry, promises to apply to a broad range of therapeutic proteins and vaccines whose biophysical stabilization would enhance accessibility in the developing world.
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Affiliation(s)
- Krystel El Hage
- Department of ChemistryUniversity of BaselBaselSwitzerland
- Qubit PharmaceuticalsParisFrance
| | - Balamurugan Dhayalan
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Yen‐Shan Chen
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Nelson B. Phillips
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
| | - Jonathan Whittaker
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
| | - Kelley Carr
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
| | - Linda Whittaker
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
| | | | - Faramarz Ismail‐Beigi
- Department of BiochemistryCase Western Reserve UniversityClevelandOhioUSA
- Department of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Markus Meuwly
- Department of ChemistryUniversity of BaselBaselSwitzerland
| | - Michael A. Weiss
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndianaUSA
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8
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Zhu W, Monnie CM, Kitoka K, Gronenborn AM. High-Efficiency Trifluoromethyl-Methionine Incorporation into Cyclophilin A by Cell-Free Synthesis for 19F NMR Studies. Angew Chem Int Ed Engl 2025; 64:e202419709. [PMID: 39571097 PMCID: PMC11813676 DOI: 10.1002/anie.202419709] [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: 10/11/2024] [Indexed: 02/12/2025]
Abstract
Fluorine-19 NMR spectroscopy has emerged as a powerful tool for studying protein structure, dynamics, and interactions. Of particular interest is the exploitation of trifluoromethyl (tfm) groups, given their high sensitivity and superior transverse relaxation properties, compared to single fluorine atoms. However, biosynthetic incorporation of tfm-bearing amino acids remains challenging due to cytotoxicity and incompatibility with natural tRNA synthetases. Here, we report on overcoming this challenge using cell-free synthesis, incorporating trifluoromethyl-methionine (tfmM) into the protein Cyclophilin A (CypA) with remarkably high efficiency, impossible via biosynthetic means. Importantly, we demonstrate that tfmM CypA binds a native substrate, the N-terminal domain of HIV-1 capsid protein (HIV-1 CA-NTD), and retains peptidyl prolyl cis/trans isomerase activity. It also binds the peptide inhibitor Cyclosporine A (CsA) with the same affinity as non-labeled, wild-type CypA. Furthermore, we show that 19F isotope shifts and 19F solvent paramagnetic relaxation enhancements (PREs) provide valuable structural information on surface exposure. Taken together, our study illustrates that tfmM can be readily incorporated into proteins at very high levels by cell-free synthesis without disturbing protein structure and function, significantly expanding the scope of 19F NMR spectroscopy for studying protein structure and dynamics.
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Affiliation(s)
- Wenkai Zhu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA-15261, United States
| | - Christina M Monnie
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA-15261, United States
| | - Kristīne Kitoka
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA-15261, United States
- Laboratory of Structural Biology and Drug Design, Latvian Institute of Organic Synthesis, Riga, LV1006, Latvia
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA-15261, United States
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9
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Elena-Real CA, Urbanek A, Sagar A, Mohanty P, Levy G, Morató A, Fournet A, Allemand F, Sibille N, Mittal J, Sinnaeve D, Bernadó P. Site-Specific Incorporation of Fluorinated Prolines into Proteins and Their Impact on Neighbouring Residues. Chemistry 2025; 31:e202403718. [PMID: 39661394 PMCID: PMC11772113 DOI: 10.1002/chem.202403718] [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: 10/07/2024] [Revised: 12/11/2024] [Accepted: 12/11/2024] [Indexed: 12/12/2024]
Abstract
The incorporation of fluorinated amino acids into proteins provides new opportunities to study biomolecular structure-function relationships in an elegant manner. The available strategies to incorporate the majority of fluorinated amino acids are not site-specific or imply important structural modifications. Here, we present a chemical biology approach for the site-specific incorporation of three commercially available Cγ-modified fluoroprolines that has been validated using a non-pathogenic version of huntingtin exon-1 (HttExon-1). 19F, 1H and 15N NMR chemical shifts measured for multiple variants of HttExon-1 indicated that the trans/cis ratio was strongly dependent on the fluoroproline variant and the sequence context. By isotopically labelling the rest of the protein, we have shown that the extent of spectroscopic perturbations to the neighbouring residues depends on the number of fluorine atoms and the stereochemistry at Cγ, as well as the isomeric form of the fluoroproline. We have rationalized these observations by means of extensive molecular dynamics simulations, indicating that the observed atomic chemical shift perturbations correlate with the distance to fluorine atoms and that the effect remains very local. These results validate the site-specific incorporation of fluoroprolines as an excellent strategy to monitor intra- and intermolecular interactions in disordered proline-rich proteins.
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Affiliation(s)
- Carlos A. Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Annika Urbanek
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M, College Station, TX 77843
| | - Geraldine Levy
- Univ. Lille, INSERM, Institut Pasteur de Lille, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases. 59000 Lille, France
- CNRS EMR9002 – Integrative Structural Biology, 59000 Lille, France
| | - Anna Morató
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M, College Station, TX 77843
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Davy Sinnaeve
- Univ. Lille, INSERM, Institut Pasteur de Lille, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases. 59000 Lille, France
- CNRS EMR9002 – Integrative Structural Biology, 59000 Lille, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS 29 rue de Navacelles, 34090 Montpellier (France)
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10
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Kehl A, Sielaff L, Remmel L, Rämisch ML, Bennati M, Meyer A. Frequency and time domain 19F ENDOR spectroscopy: role of nuclear dipolar couplings to determine distance distributions. Phys Chem Chem Phys 2025; 27:1415-1425. [PMID: 39696963 PMCID: PMC11656155 DOI: 10.1039/d4cp04443f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Accepted: 12/11/2024] [Indexed: 12/20/2024]
Abstract
19F electron-nuclear double resonance (ENDOR) spectroscopy is emerging as a method of choice to determine molecular distances in biomolecules in the angstrom to nanometer range. However, line broadening mechanisms in 19F ENDOR spectra can obscure the detected spin-dipolar coupling that encodes the distance information, thus limiting the resolution and accessible distance range. So far, the origin of these mechanisms has not been understood. Here, we employ a combined approach of rational molecular design, frequency and time domain ENDOR methods as well as quantum mechanical spin dynamics simulations to analyze these mechanisms. We present the first application of Fourier transform ENDOR to remove power broadening and measure T2n of the 19F nucleus. We identify nuclear dipolar couplings between the fluorine and protons up to 14 kHz as a major source of spectral broadening. When removing these interactions by H/D exchange, an unprecedented spectral width of 9 kHz was observed suggesting that, generally, the accessible distance range can be extended. In a spin labeled RNA duplex we were able to predict the spectral ENDOR line width, which in turn enabled us to extract a distance distribution. This study represents a first step towards a quantitative determination of distance distributions in biomolecules from 19F ENDOR.
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Affiliation(s)
- Annemarie Kehl
- Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany.
| | - Lucca Sielaff
- Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany.
- Georg-August-Universität Göttingen, Institute of Physical Chemistry, Tammannstr. 6, Göttingen, Germany
| | - Laura Remmel
- Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany.
| | - Maya L Rämisch
- Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany.
- Georg-August-Universität Göttingen, Institute of Physical Chemistry, Tammannstr. 6, Göttingen, Germany
| | - Marina Bennati
- Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany.
- Georg-August-Universität Göttingen, Institute of Physical Chemistry, Tammannstr. 6, Göttingen, Germany
| | - Andreas Meyer
- Research Group ESR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany.
- Georg-August-Universität Göttingen, Institute of Physical Chemistry, Tammannstr. 6, Göttingen, Germany
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11
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Bhinderwala F, Gronenborn AM. Exploiting 19F NMR in a Multiplexed Assay for Small GTPase Activity. J Am Chem Soc 2025; 147:1028-1033. [PMID: 39693054 PMCID: PMC11719398 DOI: 10.1021/jacs.4c14294] [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: 10/11/2024] [Revised: 12/04/2024] [Accepted: 12/05/2024] [Indexed: 12/19/2024]
Abstract
Small GTPases (smG) are a 150-member family of proteins, comprising five subfamilies: Ras, Rho, Arf, Rab, and Ran-GTPases. These proteins function as molecular switches, toggling between two distinct nucleotide-bound states. Using traditional multidimensional heteronuclear NMR, even for single smGs, numerous experiments, high protein concentrations, expensive isotope labeling, and long analysis times are necessary. 19F NMR of fluorinated proteins or ligands can overcome these drawbacks. Using indole position-specific 19F labeling of the proteins, the activities of several smGs were measured in a multiplexed fashion. We investigated 4-, 5-, 6-, and 7-fluoro tryptophan containing smGs to study nucleotide binding. Distinct resonances for GDP- or GTP-bound states of three different 19F-labeled smGs, RhoA, K-Ras, and Rac1, were observed, and the kinetics of exchange and hydrolysis were measured. This multiplexed system will permit screening of nucleotide-specific ligands of smGs under true physiological conditions.
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Affiliation(s)
- Fatema Bhinderwala
- Department of Structural
Biology, University of Pittsburgh School
of Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department of Structural
Biology, University of Pittsburgh School
of Medicine, Pittsburgh, Pennsylvania 15260, United States
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12
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Sabba F, Kassar C, Zeng T, Mallick SP, Downing L, McNamara P. PFAS in landfill leachate: Practical considerations for treatment and characterization. JOURNAL OF HAZARDOUS MATERIALS 2025; 481:136685. [PMID: 39674787 DOI: 10.1016/j.jhazmat.2024.136685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 11/22/2024] [Accepted: 11/25/2024] [Indexed: 12/16/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are widely used in consumer products and are particularly high in landfill leachate. The practice of sending leachate to wastewater treatment plants (WWTPs) is an issue for utilities that have biosolids land application limits based on PFAS concentrations. Moreover, landfills may face their own effluent limit guidelines for PFAS. The purpose of this review is to understand the most appropriate treatment technology combinations for mitigating PFAS in landfill leachate. The first objective is to understand the unique chemical characteristics of landfill leachate. The second objective is to establish the role and importance of known and emerging analytical techniques for PFAS characterization in leachate, including quantification of precursor compounds. Next, an overview of technologies that concentrate PFAS and technologies that destroy PFAS is provided, including fundamental background content and key operating parameters. Finally, practical considerations for PFAS treatment technologies are reviewed, and recommendations for PFAS treatment trains are described. Both pros and cons of treatment trains are noted. In summary, the complex matrix of leachate requires a separation treatment step first, such as foam fractionation, for example, to concentrate the PFAS into a lower-volume stream. Then, a degradation treatment step can be applied to the concentrated PFAS stream.
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Affiliation(s)
- Fabrizio Sabba
- Black & Veatch, 11401 Lamar Ave, Overland Park, KS 66211, United States; Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244, United States.
| | - Christian Kassar
- Black & Veatch, 11401 Lamar Ave, Overland Park, KS 66211, United States
| | - Teng Zeng
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244, United States
| | - Synthia P Mallick
- Black & Veatch, 11401 Lamar Ave, Overland Park, KS 66211, United States
| | - Leon Downing
- Black & Veatch, 11401 Lamar Ave, Overland Park, KS 66211, United States
| | - Patrick McNamara
- Black & Veatch, 11401 Lamar Ave, Overland Park, KS 66211, United States; Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, United States
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13
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Daminato A, Loland CJ, Cabrita EJ. Monitoring conformational changes in the human neurotransmitter transporter homologue LeuT with 19F-NMR spectroscopy. J Neurochem 2025; 169:e16278. [PMID: 39680492 DOI: 10.1111/jnc.16278] [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: 04/30/2024] [Revised: 11/18/2024] [Accepted: 11/19/2024] [Indexed: 12/18/2024]
Abstract
Neurotransmitter:sodium symporters (NSS) reuptake neurotransmitter molecules from the synaptic space through Na+-coupled transport. They are thought to work via the alternating access mechanism, exploring multiple configurations dictated by the binding of substrates and ions. Much of the current knowledge about these transporters has been derived from examining the structure of the Leucine Transporter (LeuT), a bacterial counterpart to human NSSs. Multiple crystal structures of LeuT provided valuable information regarding the steps involved in this mechanism. Dynamical data connecting the crystal structure to the transport cycle are critical to understanding how ligands are translated through the membrane. In the present study, we applied 19F-based nuclear magnetic resonance (NMR) spectroscopy to 19F labelled LeuT to monitor how substrates and ions binding affect the conformations of the transporter. By selecting mutations and ligands known to affect the conformational equilibrium of LeuT, we identified and assigned four NMR resonances to specific conformational states of LeuT. We observe that Na+ ions produce closure of the extracellular vestibule to a state similarly induced by Na+ and substrates. Conversely, K+ ions seem to shift the conformational equilibrium toward inward-facing intermediates, arguably by competing with Na+. The present study assembles a framework for NMR-based dynamical studies of NSS transporters and demonstrates its feasibility for tackling large membrane LeuT-fold transporters.
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Affiliation(s)
- Alberto Daminato
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eurico J Cabrita
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
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14
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Li Q, Kang C. Perspectives on Applications of 19F-NMR in Fragment-Based Drug Discovery. Molecules 2024; 29:5748. [PMID: 39683906 DOI: 10.3390/molecules29235748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 11/22/2024] [Accepted: 12/03/2024] [Indexed: 12/18/2024] Open
Abstract
Fragment-based drug discovery is a powerful approach in drug discovery, applicable to a wide range of targets. This method enables the discovery of potent compounds that can modulate target functions, starting from fragment compounds that bind weakly to the targets. While biochemical, biophysical, and cell-based assays are commonly used to identify fragments, 19F-NMR spectroscopy has emerged as a powerful tool for exploring interactions between biomolecules and ligands. Because fluorine atoms are not naturally present in biological systems, 19F-NMR serves as a sensitive method for fragment screening against diverse targets. Herein, we reviewed the applications of 19F-NMR in fragment screening, highlighting its effectiveness in identifying fragments that bind weakly to various targets such as proteins and RNA. The accumulated evidence suggests that 19F-NMR will continue to be a crucial tool in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore 138670, Singapore
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15
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Liu X, Guo P, Yu Q, Gao SQ, Yuan H, Tan X, Lin YW. Site-specific incorporation of 19F-nulcei at protein C-terminus to probe allosteric conformational transitions of metalloproteins. Commun Biol 2024; 7:1613. [PMID: 39627324 PMCID: PMC11615248 DOI: 10.1038/s42003-024-07331-x] [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: 08/21/2024] [Accepted: 11/27/2024] [Indexed: 12/06/2024] Open
Abstract
Allosteric conformational change is an important paradigm in the regulation of protein function, which is typically triggered by the binding of small cofactors, metal ions or protein partners. Here, we found those conformational transitions can be effectively monitored by 19F NMR, facilitated by a site-specific 19F incorporation strategy at the protein C-terminus using asparaginyl endopeptidase (AEP). Three case studies show that C-terminal 19F-nuclei can reveal protein dynamics not only adjacent but also distal to C-terminus, including those occurring in a hemoprotein neuroglobin (Ngb), calmodulin (CaM), and a cobalt metalloregulator (CoaR) responding to both cobalt and tetrapyrrole. In Ngb, the heme orientation disorder is affected by missense mutations that perturb backbone rigidity or surface charges close to the heme axial ligands. In CaM, the C-terminal 19F-nuclei is an ideal probe for detecting the binding states of Ca2+, peptides and inhibitors. Furthermore, multiple 19F-moieties were incorporated into the two domains of CoaR, revealing the intrinsically disordered C-terminal metal binding tail might be an allosteric conformational switch to maintain cobalt homeostasis and balance corrinoid biosynthesis. This study demonstrates that the AEP-based 19F-modification strategy can be applied to various targets to study allosteric regulation, especially for those biological processes modulated by the protein C-terminus.
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Affiliation(s)
- Xichun Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China.
| | - Pengfei Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Qiufan Yu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Shu-Qin Gao
- Key Lab of Protein Structure and Function of Universities in Hunan Province, Hengyang Medical School, University of South China, Hengyang, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China.
- Key Lab of Protein Structure and Function of Universities in Hunan Province, Hengyang Medical School, University of South China, Hengyang, China.
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16
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Toyama Y, Shimada I. Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2'- 19F probe in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024; 78:215-235. [PMID: 38918317 DOI: 10.1007/s10858-024-00446-7] [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: 01/12/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as 15N and 13C, which are abundant in biomolecules, fluorine-19 (19F) has recently garnered attention and is being widely used as a site-specific spin probe. While 19F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby 1H spins. In this study, we focused on the ribose 2'-19F spin probe in nucleic acids and investigated the effects of 1H-19F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the 1H-19F dipolar coupling can significantly affect the interpretation of 19F chemical exchange saturation transfer (CEST) experiments when 1H decoupling is applied, while the 1H-19F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various 19F spin systems where 1H-19F interactions are operative, further expanding the utility of 19F relaxation-based NMR experiments.
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Affiliation(s)
- Yuki Toyama
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, 739-8528, Japan.
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17
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Ledwitch K, Künze G, Okwei E, Sala D, Meiler J. Non-canonical amino acids for site-directed spin labeling of membrane proteins. Curr Opin Struct Biol 2024; 89:102936. [PMID: 39454307 DOI: 10.1016/j.sbi.2024.102936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 09/03/2024] [Accepted: 09/11/2024] [Indexed: 10/28/2024]
Abstract
Membrane proteins remain challenging targets for conventional structural biology techniques because they need to reside within complex hydrophobic lipid environments to maintain proper structure and function. Magnetic resonance combined with site-directed spin labeling is an alternative method that provides atomic-level structural and dynamical information from effects introduced by an electron- or nuclear-based spin label. With the advent of bioorthogonal click chemistries and genetically engineered non-canonical amino acids (ncAAs), options for linking spin probes to biomolecules have substantially broadened outside the conventional cysteine-based labeling scheme. Here, we highlight current strategies to spin-label membrane proteins through ncAAs for nuclear and electron paramagnetic resonance applications. Such advances are critical for developing bioorthogonal spin labeling schemes to achieve in-cell labeling and in-cell measurements of membrane protein conformational dynamics.
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Affiliation(s)
- Kaitlyn Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA.
| | - Georg Künze
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Elleansar Okwei
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Davide Sala
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA; Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
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18
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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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19
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Fernández A, Gairí M, González MT, Pons M. A Fast Method to Monitor Tyrosine Kinase Inhibitor Mechanisms. J Med Chem 2024; 67:20571-20579. [PMID: 39513680 PMCID: PMC11613495 DOI: 10.1021/acs.jmedchem.4c02042] [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: 08/28/2024] [Revised: 10/14/2024] [Accepted: 10/21/2024] [Indexed: 11/15/2024]
Abstract
Methionine residues within the kinase domain of Src serve as unique NMR probes capable of distinguishing between distinct conformational states of full-length Src, including alternative drug-inhibited forms. This approach offers a rapid method to differentiate between various inhibition mechanisms at any stage of drug development, eliminating the need to resolve the structure of Src-drug complexes. Using selectively 13C-methyl-enriched methionine, spectra can be acquired in under an hour, while natural abundance spectra with comparable information are achievable within a few hours.
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Affiliation(s)
- Alejandro Fernández
- Biomolecular
NMR Laboratory, Departament de Química Inorgànica i
Orgànica, Universitat de Barcelona
(UB), Baldiri Reixac 10-12, 08028 Barcelona. Spain
- PhD
Program in Biotechnology, Faculty of Pharmacy, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Margarida Gairí
- Centres
Científics i Tecnològics de La Universitat de Barcelona
(CCiTUB), Baldiri Reixac
10-12, 08028 Barcelona. Spain
| | - María Teresa González
- Centres
Científics i Tecnològics de La Universitat de Barcelona
(CCiTUB), Baldiri Reixac
10-12, 08028 Barcelona. Spain
| | - Miquel Pons
- Biomolecular
NMR Laboratory, Departament de Química Inorgànica i
Orgànica, Universitat de Barcelona
(UB), Baldiri Reixac 10-12, 08028 Barcelona. Spain
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20
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Sengupta I. Insights into the Structure and Dynamics of Proteins from 19F Solution NMR Spectroscopy. Biochemistry 2024; 63:2958-2968. [PMID: 39495741 DOI: 10.1021/acs.biochem.4c00534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2024]
Abstract
19F NMR spectroscopy has recently witnessed a resurgence as an attractive analytical tool for the study of the structure and dynamics of biomolecules in vitro and in cells, despite reports of its applications in biomolecular NMR since the 1970s. The high gyromagnetic ratio, large chemical shift dispersion, and complete absence of the spin 1/2 19F nucleus from biomolecules results in background-free, high-resolution 19F NMR spectra. The introduction of 19F probes in a few selected locations in biomolecules reduces spectral crowding despite its increased line width in comparison to typical 1H NMR line widths and allows rapid site-specific measurements from simple 1D spectra alone. The design and synthesis of novel 19F probes with reduced line widths and increased chemical shift sensitivity to the surrounding environment, together with advances in labeling techniques, NMR methodology, and hardware, have overcome several drawbacks of 19F NMR spectroscopy. The increased interest and widespread use of 19F NMR spectroscopy of biomolecules is gradually establishing it as a sensitive and high-resolution probe of biomolecular structure and dynamics, supplementing traditional 13C/15N-based methods. This Review focuses on the advances in 19F solution NMR spectroscopy of proteins in the past 5 years, with an emphasis on novel 19F tags and labeling techniques, NMR experiments to probe protein structure and conformational dynamics in vitro, and in-cell NMR applications.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
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21
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Honfroy A, Bertouille J, Turea AM, Cauwenbergh T, Bridoux J, Lensen N, Mangialetto J, Van den Brande N, White JF, Gardiner J, Brigaud T, Ballet S, Hernot S, Chaume G, Martin C. Fluorinated Peptide Hydrogels Result in Longer In Vivo Residence Time after Subcutaneous Administration. Biomacromolecules 2024; 25:6666-6680. [PMID: 39230056 DOI: 10.1021/acs.biomac.4c00872] [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: 09/05/2024]
Abstract
Peptide-based hydrogels are of interest to biomedical applications. Herein, we have explored the introduction of fluorinated amino acids in hydrogelator H-FQFQFK-NH2 (P1) to design a series of fluorinated peptide hydrogels and evaluate the in vitro and in vivo properties of the most promising analogues. The impact of fluorinated groups on peptide gelation, secondary structure, and self-assembly processes was assessed. We show that fluorine can significantly improve hydrogel stiffness, compared to the nonfluorinated reference P1. For P15 (H-FQFQF(o-CF3)K-NH2), P18 (H-FQFQF(F5)K-NH2), and P19 (H-FQFQM(CF3)K-NH2), microscopy studies scrutinized fiber morphologies and alignment in the network. In vitro release studies of hydrogels loaded with an opioid cargo suggested improved hydrogel stability for P15 and P18. This improved stability was further validated in vivo, notably for P15, giving the most significant increased gel residence time, with more than 20% of hydrogel still present 9 days post-injection, as monitored by nuclear SPECT-CT imaging.
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Affiliation(s)
- Aurélie Honfroy
- Research Group of Organic Chemistry (ORGC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
- VUB, Molecular Imaging and Therapy Research Group (MITH), Laarbeeklaan 103, Jette 1090, Belgium
- CY Cergy Paris Université, CNRS, BioCIS UMR 8076, Cergy-Pontoise 95000, France
- Université Paris-Saclay, CNRS, BioCIS UMR 8076, Orsay 91400, France
| | - Jolien Bertouille
- Research Group of Organic Chemistry (ORGC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Ana-Maria Turea
- Research Group of Organic Chemistry (ORGC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Thibault Cauwenbergh
- Research Group of Organic Chemistry (ORGC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Jessica Bridoux
- VUB, Molecular Imaging and Therapy Research Group (MITH), Laarbeeklaan 103, Jette 1090, Belgium
| | - Nathalie Lensen
- CY Cergy Paris Université, CNRS, BioCIS UMR 8076, Cergy-Pontoise 95000, France
- Université Paris-Saclay, CNRS, BioCIS UMR 8076, Orsay 91400, France
| | - Jessica Mangialetto
- Research Group Sustainable Materials Engineering (SUME), Lab of Physical Chemistry and Polymer Science (FYSC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Niko Van den Brande
- Research Group Sustainable Materials Engineering (SUME), Lab of Physical Chemistry and Polymer Science (FYSC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Jacinta F White
- CSIRO Manufacturing, Bayview Avenue, Clayton, VIC 3169, Australia
| | - James Gardiner
- CSIRO Manufacturing, Bayview Avenue, Clayton, VIC 3169, Australia
| | - Thierry Brigaud
- CY Cergy Paris Université, CNRS, BioCIS UMR 8076, Cergy-Pontoise 95000, France
- Université Paris-Saclay, CNRS, BioCIS UMR 8076, Orsay 91400, France
| | - Steven Ballet
- Research Group of Organic Chemistry (ORGC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
| | - Sophie Hernot
- VUB, Molecular Imaging and Therapy Research Group (MITH), Laarbeeklaan 103, Jette 1090, Belgium
| | - Grégory Chaume
- CY Cergy Paris Université, CNRS, BioCIS UMR 8076, Cergy-Pontoise 95000, France
- Université Paris-Saclay, CNRS, BioCIS UMR 8076, Orsay 91400, France
| | - Charlotte Martin
- Research Group of Organic Chemistry (ORGC), Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium
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22
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Suleiman M, Frere GA, Törner R, Tabunar L, Bhole GV, Taverner K, Tsuchimura N, Pichugin D, Lichtenecker RJ, Vozny O, Gunning P, Arthanari H, Sljoka A, Prosser RS. Characterization of conformational states of the homodimeric enzyme fluoroacetate dehalogenase by 19F- 13C two-dimensional NMR. RSC Chem Biol 2024:d4cb00176a. [PMID: 39398890 PMCID: PMC11465415 DOI: 10.1039/d4cb00176a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 09/10/2024] [Indexed: 10/15/2024] Open
Abstract
Tryptophan plays a critical role in proteins by contributing to stability, allostery, and catalysis. Using fluorine (19F) nuclear magnetic resonance (NMR), protein conformational dynamics and structure-activity relationships (SARs) can be studied via fluorotryptophan reporters. Tryptophan analogs such as 4-, 5-, 6-, or 7-fluorotryptophan can be routinely incorporated into proteins during heterologous expression by arresting endogenous tryptophan biosynthesis. Building upon the large 19F chemical shift dispersion associated with 5-fluorotryptophan, we introduce an approach to the incorporation of 13C-enriched 5-fluorotryptophan using a direct biosynthetic precursor, 5-fluoroanthranilic acid-(phenyl-13C6). The homodimeric enzyme fluoroacetate dehalogenase (FAcD), a thermophilic alpha/beta hydrolase responsible for the hydrolysis of a C-F bond in fluoroacetate, was expressed and biosynthetically labeled with (phenyl-13C6) 5-fluorotryptophan. The resulting two-dimensional 19F-13C (transverse relaxation optimized spectroscopy) TROSY heteronuclear correlation spectra provide complete resolution of all 9 tryptophan residues in the apo enzyme and FAcD saturated with the substrate analog bromoacetate. The (19F,13C) correlation spectra also reveal a multitude of minor resonances in the apo sample. The role of each tryptophan residue in allosteric communication was validated with computational rigidity transmission allostery analysis, which in this case explores the relative interprotomer communication between all possible tryptophan pairs.
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Affiliation(s)
- Motasem Suleiman
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
| | - Geordon A Frere
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
| | - Ricarda Törner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University Boston USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston USA
| | - Lauren Tabunar
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
| | - Gaurav Vijay Bhole
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University Boston USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston USA
| | - Keith Taverner
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
| | - Nobuyuki Tsuchimura
- Kwansei Gakuin University, Department of Informatics Nishinomiya 530-0012 Japan
| | - Dmitry Pichugin
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna Währingerstr 38 1090 Vienna Austria
| | - Oleksandr Vozny
- Department of Chemistry, University of Toronto, UTSC, EV 564 - Environmental Science & Chemistry 1065 Military Trail Scarborough ON Canada M1C 1A4
| | - Patrick Gunning
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University Boston USA
- Department of Cancer Biology, Dana-Farber Cancer Institute Boston USA
| | - Adnan Sljoka
- RIKEN, Center for Advanced Intelligence Project 1-4-1 Nihombashi, Chuo-Ku Tokyo 103-0027 Japan
| | - Robert S Prosser
- Department of Chemistry, University of Toronto UTM, 3359 Mississauga Rd Mississauga ON Canada L5L 1C6
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building Room 5207 Toronto ON Canada M5S 1A8
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23
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Movellan KT, Zhu W, Banks D, Kempf J, Runge B, Gronenborn AM, Polenova T. Expanding the tool box for native structural biology: 19F dynamic nuclear polarization with fast magic angle spinning. SCIENCE ADVANCES 2024; 10:eadq3115. [PMID: 39356759 PMCID: PMC11446267 DOI: 10.1126/sciadv.adq3115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024]
Abstract
Obtaining atomic-level information on components in the cell is a major focus in structural biology. Elucidating specific structural and dynamic features of proteins and their interactions in the cellular context is crucial for understanding cellular processes. We introduce 19F dynamic nuclear polarization (DNP) combined with fast magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy as a powerful technique to study proteins in mammalian cells. We demonstrate our approach on the severe acute respiratory syndrome coronavirus 2 5F-Trp-NNTD protein, electroporated into human cells. DNP signal enhancements of 30- to 40-fold were observed, translating into over 1000-fold experimental time savings. High signal-to-noise ratio spectra were acquired on nanomole quantities of a protein in cells in minutes. 2D 19F-19F dipolar correlation spectra with remarkable sensitivity and resolution were obtained, exhibiting 19F-19F cross peaks associated with fluorine atoms as far as ~10 angstroms apart. This work paves the way for 19F DNP-enhanced MAS NMR applications in cells for probing protein structure, dynamics, and ligand interactions.
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Affiliation(s)
- Kumar Tekwani Movellan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Wenkai Zhu
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Daniel Banks
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - James Kempf
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Brent Runge
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Angela M. Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Chemistry, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
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24
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Sarkar S, Wu CQ, Manna S, Samanta D, Chen PPY, Rath SP. Probing substrate binding inside a paramagnetic cavity: a NMR spectroscopy toolbox for combined experimental and theoretical investigation. Chem Sci 2024:d4sc05432f. [PMID: 39364070 PMCID: PMC11446338 DOI: 10.1039/d4sc05432f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 09/18/2024] [Indexed: 10/05/2024] Open
Abstract
Protein cavities often rely on the paramagnetic metal present in their active site in order to catalyse various chemical transformations in biology. The selective detection and identification of the substrate is of fundamental importance in environmental monitoring and biological studies. Herein, a covalently linked Fe(iii)porphyrin dimer-based paramagnetic sensory cavity has been devised for the accurate detection and simultaneous identification of phenol (substrate) binding within the cavity that provides a unique spectroscopic signature with valuable structural and environmental information. These substrates within the paramagnetic cavity leave the fingerprints of the specific binding modes (exo vs. endo) which are well distinguished with the help of various spectroscopic studies viz. UV-vis, 1H, and 19F NMR and in their respective crystal structures also. The theoretical 19F NMR analysis plays a pivotal role in replicating the observed NMR trends with large chemical shifts of the phenolato species which in turn helps in deciphering the selective binding modes of the phenols and thereby recognizing the chemical environment within the cavity. These findings will help develop an excellent diagnostic tool for in situ monitoring of subtle conformational changes and transient interactions.
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Affiliation(s)
- Sabyasachi Sarkar
- Department of Chemistry, Indian Institute of Technology Kanpur Kanpur-208016 India
| | - Chang-Quan Wu
- Department of Chemistry, National Chung Hsing University 145 Xingda Rd. South Dist. Taichung City 402 Taiwan
| | - Santanu Manna
- Department of Chemistry, Indian Institute of Technology Kanpur Kanpur-208016 India
| | - Deepannita Samanta
- Department of Chemistry, Indian Institute of Technology Kanpur Kanpur-208016 India
| | - Peter P-Y Chen
- Department of Chemistry, National Chung Hsing University 145 Xingda Rd. South Dist. Taichung City 402 Taiwan
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur Kanpur-208016 India
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25
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Bell D, Lindemann F, Gerland L, Aucharova H, Klein A, Friedrich D, Hiller M, Grohe K, Meier T, van Rossum B, Diehl A, Hughes J, Mueller LJ, Linser R, Miller AF, Oschkinat H. Sedimentation of large, soluble proteins up to 140 kDa for 1H-detected MAS NMR and 13C DNP NMR - practical aspects. JOURNAL OF BIOMOLECULAR NMR 2024; 78:179-192. [PMID: 38904893 PMCID: PMC7616530 DOI: 10.1007/s10858-024-00444-9] [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: 02/20/2024] [Accepted: 05/08/2024] [Indexed: 06/22/2024]
Abstract
Solution NMR is typically applied to biological systems with molecular weights < 40 kDa whereas magic-angle-spinning (MAS) solid-state NMR traditionally targets very large, oligomeric proteins and complexes exceeding 500 kDa in mass, including fibrils and crystalline protein preparations. Here, we propose that the gap between these size regimes can be filled by the approach presented that enables investigation of large, soluble and fully protonated proteins in the range of 40-140 kDa. As a key step, ultracentrifugation produces a highly concentrated, gel-like state, resembling a dense phase in spontaneous liquid-liquid phase separation (LLPS). By means of three examples, a Sulfolobus acidocaldarius bifurcating electron transfer flavoprotein (SaETF), tryptophan synthases from Salmonella typhimurium (StTS) and their dimeric β-subunits from Pyrococcus furiosus (PfTrpB), we show that such samples yield well-resolved proton-detected 2D and 3D NMR spectra at 100 kHz MAS without heterogeneous broadening, similar to diluted liquids. Herein, we provide practical guidance on centrifugation conditions and tools, sample behavior, and line widths expected. We demonstrate that the observed chemical shifts correspond to those obtained from µM/low mM solutions or crystalline samples, indicating structural integrity. Nitrogen line widths as low as 20-30 Hz are observed. The presented approach is advantageous for proteins or nucleic acids that cannot be deuterated due to the expression system used, or where relevant protons cannot be re-incorporated after expression in deuterated medium, and it circumvents crystallization. Importantly, it allows the use of low-glycerol buffers in dynamic nuclear polarization (DNP) NMR of proteins as demonstrated with the cyanobacterial phytochrome Cph1.
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Affiliation(s)
- Dallas Bell
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Florian Lindemann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Lisa Gerland
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Hanna Aucharova
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Alexander Klein
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Friedrich
- Department of Chemistry and Biochemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
| | - Matthias Hiller
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Kristof Grohe
- Bruker BioSpin GmbH & Co. KG, Rudolf-Plank-Str. 23, 76275, Ettlingen, Germany
| | - Tobias Meier
- Bruker BioSpin GmbH & Co. KG, Rudolf-Plank-Str. 23, 76275, Ettlingen, Germany
| | - Barth van Rossum
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Anne Diehl
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Jon Hughes
- Institute for Plant Physiology, Justus Liebig University, Senckenbergstr. 3, 35360, Gießen, Germany
- Department of Physics, Free University of Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Leonard J Mueller
- Department of Chemistry, University of California - Riverside, Riverside, CA, 92521, USA
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Anne-Frances Miller
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA.
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
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26
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Pan B, Guo C, Liu D, Wüthrich K. Fluorine-19 labeling of the tryptophan residues in the G protein-coupled receptor NK1R using the 5-fluoroindole precursor in Pichia pastoris expression. JOURNAL OF BIOMOLECULAR NMR 2024; 78:133-138. [PMID: 38554216 DOI: 10.1007/s10858-024-00439-6] [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: 11/14/2023] [Accepted: 02/16/2024] [Indexed: 04/01/2024]
Abstract
In NMR spectroscopy of biomolecular systems, the use of fluorine-19 probes benefits from a clean background and high sensitivity. Therefore, 19F-labeling procedures are of wide-spread interest. Here, we use 5-fluoroindole as a precursor for cost-effective residue-specific introduction of 5-fluorotryptophan (5F-Trp) into G protein-coupled receptors (GPCRs) expressed in Pichia pastoris. The method was successfully implemented with the neurokinin 1 receptor (NK1R). The 19F-NMR spectra of 5F-Trp-labeled NK1R showed one well-separated high field-shifted resonance, which was assigned by mutational studies to the "toggle switch tryptophan". Residue-selective labeling thus enables site-specific investigations of this functionally important residue. The method described here is inexpensive, requires minimal genetic manipulation and can be expected to be applicable for yeast expression of GPCRs at large.
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Affiliation(s)
- Benxun Pan
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Canyong Guo
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA.
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, Zürich, 8093, Switzerland.
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27
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Hanson GSM, Coxon CR. Fluorinated Tags to Study Protein Conformation and Interactions Using 19F NMR. Chembiochem 2024; 25:e202400195. [PMID: 38744671 DOI: 10.1002/cbic.202400195] [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: 03/01/2024] [Revised: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
The incorporation of fluorine atoms into a biomacromolecule provides a background-free and environmentally sensitive reporter of structure, conformation and interactions using 19F NMR. There are several methods to introduce the 19F reporter - either by synthetic incorporation via solid phase peptide synthesis; by suppressing the incorporation or biosynthesis of a natural amino acid and supplementing the growth media with a fluorinated counterpart during protein expression; and by genetic code expansion to add new amino acids to the amino acid alphabet. This review aims to discuss progress in the field of introducing fluorinated handles into biomolecules for NMR studies by post-translational bioconjugation or 'fluorine-tagging'. We will discuss the range of chemical tagging 'warheads' that have been used, explore the applications of fluorine tags, discuss ways to enhance reporter sensitivity and how the signal to noise ratios can be boosted. Finally, we consider some key challenges of the field and offer some ideas for future directions.
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Affiliation(s)
- George S M Hanson
- EaStChem School of Chemistry, University of Edinburgh, Joseph Black Building, Kings Buildings, West Mains Road, EH9 3FJ, Edinburgh, UK
| | - Christopher R Coxon
- EaStChem School of Chemistry, University of Edinburgh, Joseph Black Building, Kings Buildings, West Mains Road, EH9 3FJ, Edinburgh, UK
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28
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Wehrhan L, Keller BG. Fluorinated Protein-Ligand Complexes: A Computational Perspective. J Phys Chem B 2024; 128:5925-5934. [PMID: 38886167 PMCID: PMC11215785 DOI: 10.1021/acs.jpcb.4c01493] [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: 03/06/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Fluorine is an element renowned for its unique properties. Its powerful capability to modulate molecular properties makes it an attractive substituent for protein binding ligands; however, the rational design of fluorination can be challenging with effects on interactions and binding energies being difficult to predict. In this Perspective, we highlight how computational methods help us to understand the role of fluorine in protein-ligand binding with a focus on molecular simulation. We underline the importance of an accurate force field, present fluoride channels as a showcase for biomolecular interactions with fluorine, and discuss fluorine specific interactions like the ability to form hydrogen bonds and interactions with aryl groups. We put special emphasis on the disruption of water networks and entropic effects.
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Affiliation(s)
- Leon Wehrhan
- Department of Chemistry,
Biology and Pharmacy, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Chemistry,
Biology and Pharmacy, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
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29
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Kurfiřt M, Hamala V, Beránek J, Červenková Šťastná L, Červený J, Dračínský M, Bernášková J, Spiwok V, Bosáková Z, Bojarová P, Karban J. Synthesis and unexpected binding of monofluorinated N,N'-diacetylchitobiose and LacdiNAc to wheat germ agglutinin. Bioorg Chem 2024; 147:107395. [PMID: 38705105 DOI: 10.1016/j.bioorg.2024.107395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024]
Abstract
Fluorination of carbohydrate ligands of lectins is a useful approach to examine their binding profile, improve their metabolic stability and lipophilicity, and convert them into 19F NMR-active probes. However, monofluorination of monovalent carbohydrate ligands often leads to a decreased or completely lost affinity. By chemical glycosylation, we synthesized the full series of methyl β-glycosides of N,N'-diacetylchitobiose (GlcNAcβ(1-4)GlcNAcβ1-OMe) and LacdiNAc (GalNAcβ(1-4)GlcNAcβ1-OMe) systematically monofluorinated at all hydroxyl positions. A competitive enzyme-linked lectin assay revealed that the fluorination at the 6'-position of chitobioside resulted in an unprecedented increase in affinity to wheat germ agglutinin (WGA) by one order of magnitude. For the first time, we have characterized the binding profile of a previously underexplored WGA ligand LacdiNAc. Surprisingly, 4'-fluoro-LacdiNAc bound WGA even stronger than unmodified LacdiNAc. These observations were interpreted using molecular dynamic calculations along with STD and transferred NOESY NMR techniques, which gave evidence for the strengthening of CH/π interactions after deoxyfluorination of the side chain of the non-reducing GlcNAc. These results highlight the potential of fluorinated glycomimetics as high-affinity ligands of lectins and 19F NMR-active probes.
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Affiliation(s)
- Martin Kurfiřt
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic; University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic
| | - Vojtěch Hamala
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic; University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic
| | - Jan Beránek
- University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic
| | - Lucie Červenková Šťastná
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic
| | - Jakub Červený
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 00 Praha 4, Czech Republic; Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-128 43 Praha 2, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 542/2, CZ-160 00 Praha 6, Czech Republic
| | - Jana Bernášková
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic
| | - Vojtěch Spiwok
- University of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic
| | - Zuzana Bosáková
- Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-128 43 Praha 2, Czech Republic
| | - Pavla Bojarová
- Laboratory of Biotransformation, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 00 Praha 4, Czech Republic
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic.
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30
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Chai Z, Li C. In-Cell 19F NMR of Proteins: Recent Progress and Future Opportunities. Chemistry 2024; 30:e202303988. [PMID: 38269421 DOI: 10.1002/chem.202303988] [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: 11/29/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
In vitro, 19F NMR methodology is preferably selected as a complementary and straightforward method for unveiling the conformations, dynamics, and interactions of biological molecules. Its effectiveness in vivo has seen continuous improvement, addressing challenges faced by conventional heteronuclear NMR experiments on structured proteins, such as severe line broadening, low signal-to-noise ratio, and background signals. Herein, we summarize the distinctive advantages of 19F NMR, along with recent progress in sample preparation and applications within the realm of in-cell NMR. Additionally, we offer insights into the future directions and prospects of this methodology based on our understanding.
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Affiliation(s)
- Zhaofei Chai
- 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
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31
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Schweipert M, Nehls T, Frühauf A, Debarnot C, Kumar A, Knapp S, Lermyte F, Meyer‐Almes F. The catalytic domain of free or ligand bound histone deacetylase 4 occurs in solution predominantly in closed conformation. Protein Sci 2024; 33:e4917. [PMID: 38358265 PMCID: PMC10868454 DOI: 10.1002/pro.4917] [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: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Human histone deacetylase 4 (HDAC4) is a key epigenetic regulator involved in a number of important cellular processes. This makes HDAC4 a promising target for the treatment of several cancers and neurodegenerative diseases, in particular Huntington's disease. HDAC4 is highly regulated by phosphorylation and oxidation, which determine its nuclear or cytosolic localization, and exerts its function through multiple interactions with other proteins, forming multiprotein complexes of varying composition. The catalytic domain of HDAC4 is known to interact with the SMRT/NCOR corepressor complex when the structural zinc-binding domain (sZBD) is intact and forms a closed conformation. Crystal structures of the HDAC4 catalytic domain have been reported showing an open conformation of HDAC4 when bound to certain ligands. Here, we investigated the relevance of this HDAC4 conformation under physiological conditions in solution. We show that proper zinc chelation in the sZBD is essential for enzyme function. Loss of the structural zinc ion not only leads to a massive decrease in enzyme activity, but it also has serious consequences for the overall structural integrity and stability of the protein. However, the Zn2+ free HDAC4 structure in solution is incompatible with the open conformation. In solution, the open conformation of HDAC4 was also not observed in the presence of a variety of structurally divergent ligands. This suggests that the open conformation of HDAC4 cannot be induced in solution, and therefore cannot be exploited for the development of HDAC4-specific inhibitors.
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Affiliation(s)
- Markus Schweipert
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Thomas Nehls
- Department of ChemistryClemens‐Schöpf‐Institute of Chemistry and Biochemistry, Technical University of DarmstadtDarmstadtGermany
| | - Anton Frühauf
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Cecilé Debarnot
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
| | - Adarsh Kumar
- Fachbereich Biochemie, Chemie und PharmazieInstitut für Pharmazeutische Chemie, Goethe‐University FrankfurtFrankfurt Am MainGermany
| | - Stefan Knapp
- Fachbereich Biochemie, Chemie und PharmazieInstitut für Pharmazeutische Chemie, Goethe‐University FrankfurtFrankfurt Am MainGermany
| | - Frederik Lermyte
- Department of ChemistryClemens‐Schöpf‐Institute of Chemistry and Biochemistry, Technical University of DarmstadtDarmstadtGermany
| | - Franz‐Josef Meyer‐Almes
- Department of Chemical Engineering and BiotechnologyUniversity of Applied SciencesDarmstadtGermany
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32
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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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33
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Höfurthner T, Toscano G, Kontaxis G, Beier A, Mayer M, Geist L, McConnell DB, Weinstabl H, Lichtenecker R, Konrat R. Synthesis of a 13C-methylene-labeled isoleucine precursor as a useful tool for studying protein side-chain interactions and dynamics. JOURNAL OF BIOMOLECULAR NMR 2024; 78:1-8. [PMID: 37816933 PMCID: PMC10981609 DOI: 10.1007/s10858-023-00427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
In this study, we present the synthesis and incorporation of a metabolic isoleucine precursor compound for selective methylene labeling. The utility of this novel α-ketoacid isotopologue is shown by incorporation into the protein Brd4-BD1, which regulates gene expression by binding to acetylated histones. High quality single quantum 13C-1 H-HSQC were obtained, as well as triple quantum HTQC spectra, which are superior in terms of significantly increased 13C-T2 times. Additionally, large chemical shift perturbations upon ligand binding were observed. Our study thus proves the great sensitivity of this precursor as a reporter for side-chain dynamic studies and for investigations of CH-π interactions in protein-ligand complexes.
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Affiliation(s)
- Theresa Höfurthner
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, 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
| | - Giorgia Toscano
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währingerstraße 42, 1090, Vienna, Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121, Vienna, Austria
| | - Roman Lichtenecker
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria.
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, 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, Campus Vienna Biocenter 5, 1030, Vienna, Austria.
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34
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Zhang Z, Zhao Q, Gong Z, Du R, Liu M, Zhang Y, Zhang L, Li C. Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology. JACS AU 2024; 4:369-383. [PMID: 38425916 PMCID: PMC10900494 DOI: 10.1021/jacsau.3c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution identification of these protein structures and interactions within living cells presents a technical challenge. In this Perspective, we summarize the recent advancements in in-cell nuclear magnetic resonance (NMR) and in vivo cross-linking mass spectrometry (XL-MS) for studying protein structures and interactions within a cellular context. Additionally, we discuss the challenges, opportunities, and potential benefits of integrating in-cell NMR and in vivo XL-MS in future research to offer an exhaustive approach to studying proteins in their natural habitat.
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Affiliation(s)
- Zeting 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 of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Zhao
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- 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 of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruichen Du
- 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 of Precision Measurement, Chinese Academy of Sciences, 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 of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yukui Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, 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 of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
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35
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Bell D, Lindemann F, Gerland L, Aucharova H, Klein A, Friedrich D, Hiller M, Grohe K, van Rossum B, Diehl A, Hughes J, Mueller LJ, Linser R, Miller AF, Oschkinat H. Sedimentation of large, soluble proteins up to 140 kDa for 1H-detected MAS NMR and 13C DNP NMR - practical aspects. RESEARCH SQUARE 2024:rs.3.rs-3972885. [PMID: 38464080 PMCID: PMC10925473 DOI: 10.21203/rs.3.rs-3972885/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Solution NMR is typically applied to biological systems with molecular weights < 40 kDa whereas magic-angle-spinning (MAS) solid-state NMR traditionally targets very large, oligomeric proteins and complexes exceeding 500 kDa in mass, including fibrils and crystalline protein preparations. Here, we propose that the gap between these size regimes can be filled by the approach presented that enables investigation of large, soluble and fully protonated proteins in the range of 40-140 kDa. As a key step, ultracentrifugation produces a highly concentrated, gel-like state, resembling a dense phase in spontaneous liquid-liquid phase separation (LLPS). By means of three examples, a Sulfolobus acidocaldarius bifurcating electron transfer flavoprotein (SulfETF), tryptophan synthases from Salmonella typhimurium (StTS) and the dimeric β-subunits from Pyrococcus furiosus (PfTrpB), we show that such samples yield well-resolved proton-detected 2D and 3D NMR spectra at 100 kHz MAS without heterogeneous broadening, similar to diluted liquids. Herein, we provide practical guidance on centrifugation conditions and tools, sample behavior, and line widths expected. We demonstrate that the observed chemical shifts correspond to those obtained from μM/low mM solutions or crystalline samples, indicating structural integrity. Nitrogen line widths as low as 20-30 Hz are observed. The presented approach is advantageous for proteins or nucleic acids that cannot be deuterated due to the expression system used, or where relevant protons cannot be re-incorporated after expression in deuterated medium, and it circumvents crystallization. Importantly, it allows the use of low-glycerol buffers in dynamic nuclear polarization (DNP) NMR of proteins as demonstrated with the cyanobacterial phytochrome Cph1.
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Affiliation(s)
- Dallas Bell
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin
| | | | - Lisa Gerland
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie
| | - Hanna Aucharova
- Department of Chemistry and Chemical Biology, TU Dortmund University
| | - Alexander Klein
- Department of Chemistry and Chemical Biology, TU Dortmund University
| | | | | | | | | | - Anne Diehl
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie
| | - Jon Hughes
- Justus Liebig University, Institute for Plant Physiology
| | | | - Rasmus Linser
- Department of Chemistry and Chemical Biology, TU Dortmund University
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36
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Kara H, Axer A, Muskett FW, Bueno-Alejo CJ, Paschalis V, Taladriz-Sender A, Tubasum S, Vega MS, Zhao Z, Clark AW, Hudson AJ, Eperon IC, Burley GA, Dominguez C. 2'- 19F labelling of ribose in RNAs: a tool to analyse RNA/protein interactions by NMR in physiological conditions. Front Mol Biosci 2024; 11:1325041. [PMID: 38419689 PMCID: PMC10899400 DOI: 10.3389/fmolb.2024.1325041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Protein-RNA interactions are central to numerous cellular processes. In this work, we present an easy and straightforward NMR-based approach to determine the RNA binding site of RNA binding proteins and to evaluate the binding of pairs of proteins to a single-stranded RNA (ssRNA) under physiological conditions, in this case in nuclear extracts. By incorporation of a 19F atom on the ribose of different nucleotides along the ssRNA sequence, we show that, upon addition of an RNA binding protein, the intensity of the 19F NMR signal changes when the 19F atom is located near the protein binding site. Furthermore, we show that the addition of pairs of proteins to a ssRNA containing two 19F atoms at two different locations informs on their concurrent binding or competition. We demonstrate that such studies can be done in a nuclear extract that mimics the physiological environment in which these protein-ssRNA interactions occur. Finally, we demonstrate that a trifluoromethoxy group (-OCF3) incorporated in the 2'ribose position of ssRNA sequences increases the sensitivity of the NMR signal, leading to decreased measurement times, and reduces the issue of RNA degradation in cellular extracts.
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Affiliation(s)
- Hesna Kara
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Alexander Axer
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Frederick W Muskett
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Carlos J Bueno-Alejo
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Vasileios Paschalis
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Andrea Taladriz-Sender
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Sumera Tubasum
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Marina Santana Vega
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Zhengyun Zhao
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Alasdair W Clark
- Biomedical Engineering Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J Hudson
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- School of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Ian C Eperon
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
| | - Glenn A Burley
- WestCHEM and Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Cyril Dominguez
- Department of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, United Kingdom
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37
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Bhuvaneshwari RA, Shivamani A, Sengupta I. Line Shape Analysis of 19F NMR-Monitored Chemical Denaturation of a Fold-Switching Protein RfaH Reveals Its Slow Folding Dynamics. J Phys Chem B 2024; 128:465-471. [PMID: 37991741 DOI: 10.1021/acs.jpcb.3c06550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The recent discovery of metamorphic proteins, which can switch between multiple conformations under native conditions, has challenged the well-established one sequence-one structure paradigm of protein folding. This is exemplified in the C-terminal domain of the multidomain transcription factor RfaH, which converts from an α-helical coiled-coil conformation in its autoinhibited state to a β-barrel conformation upon activation. Here, we use multisite line shape analysis of 19F NMR-monitored equilibrium chemical denaturation measurements of two 19F-labeled variants of full-length RfaH, to show that it folds/unfolds slowly on the NMR time scale, in an apparent all-or-none fashion at physiological pH and room temperature in the 3.3-4.8 M urea concentration range. The significant thermodynamic stability and slow unfolding rate (kinetic stability) are likely responsible for maintaining the closed autoinhibited state of RfaH, preventing spurious interactions with RNA polymerase (RNAP) when not functional. Our results provide a quantitative understanding of the folding-function relationship in the model fold-switching protein RfaH.
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Affiliation(s)
| | - Anish Shivamani
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
| | - Ishita Sengupta
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
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38
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Bai XC, Gonen T, Gronenborn AM, Perrakis A, Thorn A, Yang J. Challenges and opportunities in macromolecular structure determination. Nat Rev Mol Cell Biol 2024; 25:7-12. [PMID: 37848590 DOI: 10.1038/s41580-023-00659-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 10/19/2023]
Affiliation(s)
- Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA.
| | | | - Anastassis Perrakis
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Andrea Thorn
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany.
| | - Jianyi Yang
- MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.
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39
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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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40
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Eichler C, Himmelstoß M, Plangger R, Weber LI, Hartl M, Kreutz C, Micura R. Advances in RNA Labeling with Trifluoromethyl Groups. Chemistry 2023; 29:e202302220. [PMID: 37534701 PMCID: PMC10947337 DOI: 10.1002/chem.202302220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
Fluorine labeling of ribonucleic acids (RNA) in conjunction with 19 F NMR spectroscopy has emerged as a powerful strategy for spectroscopic analysis of RNA structure and dynamics, and RNA-ligand interactions. This study presents the first syntheses of 2'-OCF3 guanosine and uridine phosphoramidites, their incorporation into oligoribonucleotides by solid-phase synthesis and a comprehensive study of their properties. NMR spectroscopic analysis showed that the 2'-OCF3 modification is associated with preferential C2'-endo conformation of the U and G ribose in single-stranded RNA. When paired to the complementary strand, slight destabilization of the duplex caused by the modification was revealed by UV melting curve analysis. Moreover, the power of the 2'-OCF3 label for NMR spectroscopy is demonstrated by dissecting RNA pseudoknot folding and its binding to a small molecule. Furthermore, the 2'-OCF3 modification has potential for applications in therapeutic oligonucleotides. To this end, three 2'-OCF3 modified siRNAs were tested in silencing of the BASP1 gene which indicated enhanced performance for one of them. Importantly, together with earlier work, the present study completes the set of 2'-OCF3 nucleoside phosphoramidites to all four standard nucleobases (A, U, C, G) and hence enables applications that utilize the favorable properties of the 2'-OCF3 group without any restrictions in placing the modification into the RNA target sequence.
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Affiliation(s)
- Clemens Eichler
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Maximilian Himmelstoß
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Leonie I. Weber
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Markus Hartl
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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41
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Ramachandran S, Makukhin N, Haubrich K, Nagala M, Forrester B, Lynch DM, Casement R, Testa A, Bruno E, Gitto R, Ciulli A. Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2. Nat Commun 2023; 14:6345. [PMID: 37816714 PMCID: PMC10564737 DOI: 10.1038/s41467-023-41894-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
The Src homology 2 (SH2) domain recognizes phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signaling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we use structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signaling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach reveals covalent modification of Cys111 in a co-crystal structure, which we leverage to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We report the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in-cell 19F NMR spectroscopy. Covalent engagement at Cys111 competitively blocks recruitment of cellular SOCS2 protein to its native substrate. The qualified inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.
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Affiliation(s)
- Sarath Ramachandran
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Nikolai Makukhin
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Kevin Haubrich
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Manjula Nagala
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Beth Forrester
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Dylan M Lynch
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Ryan Casement
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Andrea Testa
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Elvira Bruno
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno D'Alcontres 31, Pole Papardo, 98166, Messina, Italy
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom.
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42
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Smith MJ, Bramham JE, Nilsson M, Morris GA, Castañar L, Golovanov AP. Lighting up spin systems: enhancing characteristic 1H signal patterns of fluorinated molecules. Chem Commun (Camb) 2023; 59:11692-11695. [PMID: 37698544 DOI: 10.1039/d3cc03557c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Fluorine is becoming increasingly prevalent in medicinal chemistry, both in drug molecules and in molecular probes. The presence of fluorine allows convenient monitoring of such molecules in complex environments by NMR spectroscopy. However, sensitivity is a persistent limitation of NMR, especially when molecules are present at low concentrations. Here, sensitivity issues with 1H NMR are mitigated by sharing 19F photochemically-induced dynamic nuclear polarisation with 1H nuclei. Unlike direct 1H enhancement, this method enhances 1H signals without significantly distorting multiplet intensities, and has the potential to enable the use of suitable molecules as low-concentration probes.
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Affiliation(s)
- Marshall J Smith
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Jack E Bramham
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Mathias Nilsson
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Gareth A Morris
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Laura Castañar
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
- Department of Organic Chemistry, Faculty of Chemical Science, Complutense University of Madrid, Ciudad Universitaria s/n, Madrid 28040, Spain.
| | - Alexander P Golovanov
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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43
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Gregorc J, Lensen N, Chaume G, Iskra J, Brigaud T. Trifluoromethylthiolation of Tryptophan and Tyrosine Derivatives: A Tool for Enhancing the Local Hydrophobicity of Peptides. J Org Chem 2023; 88:13169-13177. [PMID: 37672679 PMCID: PMC10507666 DOI: 10.1021/acs.joc.3c01373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 09/08/2023]
Abstract
The incorporation of fluorinated groups into peptides significantly affects their biophysical properties. We report herein the synthesis of Fmoc-protected trifluoromethylthiolated tyrosine (CF3S-Tyr) and tryptophan (CF3S-Trp) analogues on a gram scale (77-93% yield) and demonstrate their use as highly hydrophobic fluorinated building blocks for peptide chemistry. The developed methodology was successfully applied to the late-stage regioselective trifluoromethylthiolation of Trp residues in short peptides (66-80% yield) and the synthesis of various CF3S-analogues of biologically active monoamines. To prove the concept, Fmoc-(CF3S)Tyr and -Trp were incorporated into the endomorphin-1 chain (EM-1) and into model tripeptides by solid-phase peptide synthesis. A remarkable enhancement of the local hydrophobicity of the trifluoromethylthiolated peptides was quantified by the chromatographic hydrophobicity index determination method, demonstrating the high potential of CF3S-containing amino acids for the rational design of bioactive peptides.
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Affiliation(s)
- Jure Gregorc
- Chair
of Organic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Nathalie Lensen
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Grégory Chaume
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Jernej Iskra
- Chair
of Organic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Thierry Brigaud
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
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44
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Cosottini L, Zineddu S, Massai L, Ghini V, Turano P. 19F: A small probe for a giant protein. J Inorg Biochem 2023; 244:112236. [PMID: 37146532 DOI: 10.1016/j.jinorgbio.2023.112236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023]
Abstract
Herein we describe a method for the efficient production (∼90% fluorination) of 5-F-Trp human H ferritin via the selective incorporation of 19F into the side chain of W93 using 5-fluoroindole as the fluorinated precursor of the amino acid. Human H ferritin is a nanocage composed of 24 identical subunits, each containing a single Trp belonging to a loop exposed on the external surface of the protein nanocage. This makes 5-F-Trp a potential probe for the study of intermolecular interactions in solution by exploiting its intrinsic fluorescence. More interestingly, albeit the large size of the cage (12 nm external diameter, ∼500 kDa molecular mass) we observe a broad but well defined NMR 19F resonance that can be used for the dual purpose of detecting solution intermolecular interactions via chemical shift perturbation mapping and monitoring the uptake of ferritin by cells treated with ferritin-based drug carriers, the latter being an application area of increasing importance.
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Affiliation(s)
- Lucrezia Cosottini
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Stefano Zineddu
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Lara Massai
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy.
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45
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Krempl C, Sprangers R. Assessing the applicability of 19F labeled tryptophan residues to quantify protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2023; 77:55-67. [PMID: 36639431 PMCID: PMC10149471 DOI: 10.1007/s10858-022-00411-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/20/2022] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited to study the dynamics of biomolecules in solution. Most NMR studies exploit the spins of proton, carbon and nitrogen isotopes, as these atoms are highly abundant in proteins and nucleic acids. As an alternative and complementary approach, fluorine atoms can be introduced into biomolecules at specific sites of interest. These labels can then be used as sensitive probes for biomolecular structure, dynamics or interactions. Here, we address if the replacement of tryptophan with 5-fluorotryptophan residues has an effect on the overall dynamics of proteins and if the introduced fluorine probe is able to accurately report on global exchange processes. For the four different model proteins (KIX, Dcp1, Dcp2 and DcpS) that we examined, we established that 15N CPMG relaxation dispersion or EXSY profiles are not affected by the 5-fluorotryptophan, indicating that this replacement of a proton with a fluorine has no effect on the protein motions. However, we found that the motions that the 5-fluorotryptophan reports on can be significantly faster than the backbone motions. This implies that care needs to be taken when interpreting fluorine relaxation data in terms of global protein motions. In summary, our results underscore the great potential of fluorine NMR methods, but also highlight potential pitfalls that need to be considered.
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Affiliation(s)
- Christina Krempl
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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46
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Wohl S, Zheng W. Interpreting Transient Interactions of Intrinsically Disordered Proteins. J Phys Chem B 2023; 127:2395-2406. [PMID: 36917561 PMCID: PMC10038935 DOI: 10.1021/acs.jpcb.3c00096] [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] [Indexed: 03/16/2023]
Abstract
The flexible nature of intrinsically disordered proteins (IDPs) gives rise to a conformational ensemble with a diverse set of conformations. The simplest way to describe this ensemble is through a homopolymer model without any specific interactions. However, there has been growing evidence that the conformational properties of IDPs and their relevant functions can be affected by transient interactions between specific and even nonlocal pairs of amino acids. Interpreting these interactions from experimental methods, each of which is most sensitive to a different distance regime referred to as probing length, remains a challenging and unsolved problem. Here, we first show that transient interactions can be realized between short fragments of charged amino acids by generating conformational ensembles using model disordered peptides and coarse-grained simulations. Using these ensembles, we investigate how sensitive different types of experimental measurements are to the presence of transient interactions. We find methods with shorter probing lengths to be more appropriate for detecting these transient interactions, but one experimental method is not sufficient due to the existence of other weak interactions typically seen in IDPs. Finally, we develop an adjusted polymer model with an additional short-distance peak which can robustly reproduce the distance distribution function from two experimental measurements with complementary short and long probing lengths. This new model can suggest whether a homopolymer model is insufficient for describing a specific IDP and meets the challenge of quantitatively identifying specific, transient interactions from a background of nonspecific, weak interactions.
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Affiliation(s)
- Samuel Wohl
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
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47
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Lete MG, Franconetti A, Bertuzzi S, Delgado S, Azkargorta M, Elortza F, Millet O, Jiménez-Osés G, Arda A, Jiménez-Barbero J. NMR Investigation of Protein-Carbohydrate Interactions: The Recognition of Glycans by Galectins Engineered with Fluorotryptophan Residues. Chemistry 2023; 29:e202202208. [PMID: 36343278 PMCID: PMC10107428 DOI: 10.1002/chem.202202208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
Fluorine (19 F) incorporation into glycan-binding proteins (lectins) has been achieved and exploited to monitor the binding to carbohydrate ligands by nuclear magnetic resonance (NMR) spectroscopy. Galectins are a family of lectins that bind carbohydrates, generally with weak affinities, through a combination of intermolecular interactions including a key CH-π stacking involving a conserved tryptophan residue. Herein, Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were selected. Gal3 contains one Trp, whereas Gal8 contains three, one at each binding site and a third one not involved in sugar binding; these were substituted by the corresponding F-Trp analogues. The presence of fluorine did not significantly modify the affinity for glycan binding, which was in slow exchange on the 19 F NMR chemical-shift timescale, even for weak ligands, and allowed binding events taking place at two different binding sites within the same lectin to be individualized.
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Affiliation(s)
- Marta G Lete
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Antonio Franconetti
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sara Bertuzzi
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sandra Delgado
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Félix Elortza
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Oscar Millet
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Gonzalo Jiménez-Osés
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Ana Arda
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain.,Department of Organic Chemistry II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
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48
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Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. 19F fast MAS (60-111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101831. [PMID: 36182713 DOI: 10.1016/j.ssnmr.2022.101831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
19F magic angle spinning (MAS) NMR spectroscopy is a powerful tool for characterization of fluorinated solids. The recent development of 19F MAS NMR probes, operating at spinning frequencies of 60-111 kHz, enabled analysis of systems spanning from organic molecules to pharmaceutical formulations to biological assemblies, with unprecedented resolution. Herein, we systematically evaluate the benefits of high MAS frequencies (60-111 kHz) for 1D and 2D 19F-detected experiments in two pharmaceuticals, the antimalarial drug mefloquine and a formulation of the cholesterol-lowering drug atorvastatin calcium. We demonstrate that 1H decoupling is essential and that scalar-based, heteronuclear single quantum coherence (HSQC) and heteronuclear multiple quantum coherence (HMQC) correlation experiments become feasible and efficient at the MAS frequency of 100 kHz. This study opens doors for the applications of high frequency 19F MAS NMR to a wide range of problems in chemistry and biology.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States.
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49
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Cell-free synthesis of amyloid fibrils with infectious properties and amenable to sub-milligram magic-angle spinning NMR analysis. Commun Biol 2022; 5:1202. [DOI: 10.1038/s42003-022-04175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractStructural investigations of amyloid fibrils often rely on heterologous bacterial overexpression of the protein of interest. Due to their inherent hydrophobicity and tendency to aggregate as inclusion bodies, many amyloid proteins are challenging to express in bacterial systems. Cell-free protein expression is a promising alternative to classical bacterial expression to produce hydrophobic proteins and introduce NMR-active isotopes that can improve and speed up the NMR analysis. Here we implement the cell-free synthesis of the functional amyloid prion HET-s(218-289). We present an interesting case where HET-s(218-289) directly assembles into infectious fibril in the cell-free expression mixture without the requirement of denaturation procedures and purification. By introducing tailored 13C and 15N isotopes or CF3 and 13CH2F labels at strategic amino-acid positions, we demonstrate that cell-free synthesized amyloid fibrils are readily amenable to high-resolution magic-angle spinning NMR at sub-milligram quantity.
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50
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Cyril D, Giugni A, Bangar SS, Mirzaeipoueinak M, Shrivastav D, Sharabi M, Tipper JL, Tavakoli J. Elastic Fibers in the Intervertebral Disc: From Form to Function and toward Regeneration. Int J Mol Sci 2022; 23:8931. [PMID: 36012198 PMCID: PMC9408956 DOI: 10.3390/ijms23168931] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Despite extensive efforts over the past 40 years, there is still a significant gap in knowledge of the characteristics of elastic fibers in the intervertebral disc (IVD). More studies are required to clarify the potential contribution of elastic fibers to the IVD (healthy and diseased) function and recommend critical areas for future investigations. On the other hand, current IVD in-vitro models are not true reflections of the complex biological IVD tissue and the role of elastic fibers has often been ignored in developing relevant tissue-engineered scaffolds and realistic computational models. This has affected the progress of IVD studies (tissue engineering solutions, biomechanics, fundamental biology) and translation into clinical practice. Motivated by the current gap, the current review paper presents a comprehensive study (from the early 1980s to 2022) that explores the current understanding of structural (multi-scale hierarchy), biological (development and aging, elastin content, and cell-fiber interaction), and biomechanical properties of the IVD elastic fibers, and provides new insights into future investigations in this domain.
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Affiliation(s)
- Divya Cyril
- Centre for Health Technologies, School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Amelia Giugni
- Centre for Health Technologies, School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Saie Sunil Bangar
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Melika Mirzaeipoueinak
- Centre for Health Technologies, School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Dipika Shrivastav
- Centre for Health Technologies, School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mirit Sharabi
- Department of Mechanical Engineering and Mechatronics, Ariel University, Ariel 407000, Israel
| | - Joanne L. Tipper
- Centre for Health Technologies, School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Javad Tavakoli
- Centre for Health Technologies, School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
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