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Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. J Struct Biol X 2022; 7:100079. [PMID: 36578472 PMCID: PMC9791609 DOI: 10.1016/j.yjsbx.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
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Zhu W, Guseman AJ, Bhinderwala F, Lu M, Su XC, Gronenborn AM. Visualizing Proteins in Mammalian Cells by 19 F NMR Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202201097. [PMID: 35278268 PMCID: PMC9156538 DOI: 10.1002/anie.202201097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Indexed: 12/20/2022]
Abstract
In-cell NMR spectroscopy is a powerful tool to investigate protein behavior in physiologically relevant environments. Although proven valuable for disordered proteins, we show that in commonly used 1 H-15 N HSQC spectra of globular proteins, interactions with cellular components often broaden resonances beyond detection. This contrasts 19 F spectra in mammalian cells, in which signals are readily observed. Using several proteins, we demonstrate that surface charges and interaction with cellular binding partners modulate linewidths and resonance frequencies. Importantly, we establish that 19 F paramagnetic relaxation enhancements using stable, rigid Ln(III) chelate pendants, attached via non-reducible thioether bonds, provide an effective means to obtain accurate distances for assessing protein conformations in the cellular milieu.
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Affiliation(s)
- Wenkai Zhu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Alex J Guseman
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Fatema Bhinderwala
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Manman Lu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 300071, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, 300071, Tianjin, China
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
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Liu Z, Zheng X, Wang J. Bioinspired Ice-Binding Materials for Tissue and Organ Cryopreservation. J Am Chem Soc 2022; 144:5685-5701. [PMID: 35324185 DOI: 10.1021/jacs.2c00203] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cryopreservation of tissues and organs can bring transformative changes to medicine and medical science. In the past decades, limited progress has been achieved, although cryopreservation of tissues and organs has long been intensively pursued. One key reason is that the cryoprotective agents (CPAs) currently used for cell cryopreservation cannot effectively preserve tissues and organs because of their cytotoxicity and tissue destructive effect as well as the low efficiency in controlling ice formation. In stark contrast, nature has its unique ways of controlling ice formation, and many living organisms can effectively prevent freezing damage. Ice-binding proteins (IBPs) are regarded as the essential materials identified in these living organisms for regulating ice nucleation and growth. Note that controversial results have been reported on the utilization of IBPs and their mimics for the cryopreservation of tissues and organs, that is, some groups revealed that IBPs and mimics exhibited unique superiorities in tissues cryopreservation, while other groups showed detrimental effects. In this perspective, we analyze possible reasons for the controversy and predict future research directions in the design and construction of IBP inspired ice-binding materials to be used as new CPAs for tissue cryopreservation after briefly introducing the cryo-injuries and the challenges of conventional CPAs in the cryopreservation of tissues and organs.
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Affiliation(s)
- Zhang Liu
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xia Zheng
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jianjun Wang
- Key Laboratory of Green Printing, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, PR China.,School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100190, PR China
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Gronenborn AM, Zhu W, Guseman AJ, Bhinderwala F, Lu M, Su XC. Visualizing Proteins in Mammalian Cells by 19F NMR spectroscopy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Angela M Gronenborn
- University of Pittsburgh, School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Wenkai Zhu
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Alex J Guseman
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Fatema Bhinderwala
- University of Pittsburgh School of Medicine Department of Structural Biology UNITED STATES
| | - Manman Lu
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Xun-Cheng Su
- Nankai University College of Chemistry State Key Laboratory of Elemento-Organic Chemistry 300071 Tianjin CHINA
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Welte H, Sinn P, Kovermann M. Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate. Chembiochem 2021; 22:2973-2980. [PMID: 34390111 PMCID: PMC8596521 DOI: 10.1002/cbic.202100304] [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: 06/19/2021] [Revised: 07/30/2021] [Indexed: 11/12/2022]
Abstract
The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution 19 F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.
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Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Pia Sinn
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
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Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L. Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Enrico Luchinat
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di Scienze Biomediche Sperimentali e Cliniche “Mario Serio”Università degli Studi di Firenze Viale Morgagni 50 50134 Florence Italy
| | - Letizia Barbieri
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Consorzio Interuniversitario Risonanze Magnetiche di, Metalloproteine Via Luigi Sacconi 6 Sesto Fiorentino Italy
| | - Matteo Cremonini
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
| | - Alessio Nocentini
- Dipartimento NeurofarbaSezione di Scienze FarmaceuticheUniversità degli Studi di Firenze Via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Claudiu T. Supuran
- Dipartimento NeurofarbaSezione di Scienze FarmaceuticheUniversità degli Studi di Firenze Via Ugo Schiff 6 50019 Sesto Fiorentino Italy
- Dipartimento di ChimicaUniversità degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Banci
- CERM—Magnetic Resonance CenterUniversità degli Studi di Firenze via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Dipartimento di ChimicaUniversità degli Studi di Firenze Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L. Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency. Angew Chem Int Ed Engl 2020; 59:6535-6539. [PMID: 32022355 PMCID: PMC7187179 DOI: 10.1002/anie.201913436] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Structure-based drug development is often hampered by the lack of in vivo activity of promising compounds screened in vitro, due to low membrane permeability or poor intracellular binding selectivity. Herein, we show that ligand screening can be performed in living human cells by "intracellular protein-observed" NMR spectroscopy, without requiring enzymatic activity measurements or other cellular assays. Quantitative binding information is obtained by fast, inexpensive 1 H NMR experiments, providing intracellular dose- and time-dependent ligand binding curves, from which kinetic and thermodynamic parameters linked to cell permeability and binding affinity and selectivity are obtained. The approach was applied to carbonic anhydrase and, in principle, can be extended to any NMR-observable intracellular target. The results obtained are directly related to the potency of candidate drugs, that is, the required dose. The application of this approach at an early stage of the drug design pipeline could greatly increase the low success rate of modern drug development.
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Affiliation(s)
- Enrico Luchinat
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.,Dipartimento di Scienze Biomediche Sperimentali e Cliniche "Mario Serio", Università degli Studi di Firenze, Viale Morgagni 50, 50134, Florence, Italy
| | - Letizia Barbieri
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di, Metalloproteine, Via Luigi Sacconi 6, Sesto Fiorentino, Italy
| | - Matteo Cremonini
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy.,Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Banci
- CERM-Magnetic Resonance Center, Università degli Studi di Firenze, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.,Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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Welte H, Zhou T, Mihajlenko X, Mayans O, Kovermann M. What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein. Sci Rep 2020; 10:2640. [PMID: 32060391 PMCID: PMC7021800 DOI: 10.1038/s41598-020-59446-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/29/2020] [Indexed: 11/21/2022] Open
Abstract
Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.
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Affiliation(s)
- Hannah Welte
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.,Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Tiankun Zhou
- Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Xenia Mihajlenko
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Olga Mayans
- Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.,Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. .,Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. .,Zukunftskolleg, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.
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