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Mercurio I, D’Abrosca G, della Valle M, Malgieri G, Fattorusso R, Isernia C, Russo L, Di Gaetano S, Pedone EM, Pirone L, Del Gatto A, Zaccaro L, Alberga D, Saviano M, Mangiatordi GF. Molecular interactions between a diphenyl scaffold and PED/PEA15: Implications for type II diabetes therapeutics targeting PED/PEA15 - Phospholipase D1 interaction. Comput Struct Biotechnol J 2024; 23:2001-2010. [PMID: 38770160 PMCID: PMC11103223 DOI: 10.1016/j.csbj.2024.04.063] [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] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
In a recent study, we have identified BPH03 as a promising scaffold for the development of compounds aimed at modulating the interaction between PED/PEA15 (Phosphoprotein Enriched in Diabetes/Phosphoprotein Enriched in Astrocytes 15) and PLD1 (phospholipase D1), with potential applications in type II diabetes therapy. PED/PEA15 is known to be overexpressed in certain forms of diabetes, where it binds to PLD1, thereby reducing insulin-stimulated glucose transport. The inhibition of this interaction reestablishes basal glucose transport, indicating PED as a potential target of ligands capable to recover glucose tolerance and insulin sensitivity. In this study, we employ computational methods to provide a detailed description of BPH03 interaction with PED, evidencing the presence of a hidden druggable pocket within its PLD1 binding surface. We also elucidate the conformational changes that occur during PED interaction with BPH03. Moreover, we report new NMR data supporting the in-silico findings and indicating that BPH03 disrupts the PED/PLD1 interface displacing PLD1 from its interaction with PED. Our study represents a significant advancement toward the development of potential therapeutics for the treatment of type II diabetes.
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Affiliation(s)
- Ivan Mercurio
- Institute of Crystallography, CNR, Via Amendola 122/o, 70126 Bari, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D’Abrosca
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
- Institute of Crystallography, CNR, Via Vivaldi 43, 81100, Caserta, Italy
| | - Maria della Valle
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Domenico Alberga
- Institute of Crystallography, CNR, Via Amendola 122/o, 70126 Bari, Italy
| | - Michele Saviano
- Institute of Crystallography, CNR, Via Vivaldi 43, 81100, Caserta, Italy
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Wat JH, Pizzala NJ, Reppert M. Isotope Reverse-Labeled Infrared Spectroscopy as a Probe of In-Cell Protein Structure. J Phys Chem B 2024; 128:9923-9934. [PMID: 39358675 DOI: 10.1021/acs.jpcb.4c03068] [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: 10/04/2024]
Abstract
While recent years have seen great progress in determining the three-dimensional structure of isolated proteins, monitoring protein structure inside live cells remains extremely difficult. Here, we examine the utility of Fourier transform infrared (FTIR) spectroscopy as a probe of protein structure in live bacterial cells. Selective isotope enrichment is used both to distinguish recombinantly expressed NuG2b protein from the cellular background and to examine the conformation of specific residues in the protein. To maximize labeling flexibility and to improve spectral resolution between label and main-band peaks, we carry out isotope-labeling experiments in "reverse-labeling" mode: cells are initially grown in 13C-enriched media, with specific 12C-labeled amino acids added when protein expression is induced. 1 Because FTIR measurements require only around 20 μL of sample and each measurement takes only a few minutes to complete, isotope-labeling costs are minimal, allowing us to label multiple different residues in parallel in simultaneously grown cultures. For the stable NuG2b protein, isotope difference spectra from live bacterial cultures are nearly identical to spectra from isolated proteins, confirming that the structure of the protein is unperturbed by the cellular environment. By combining such measurements with site-directed mutagenesis, we further demonstrate that the local conformation of individual amino acids can be monitored, allowing us to determine, for example, whether a specific site in the protein contributes to α-helix or β-sheet structures.
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Affiliation(s)
- Jacob H Wat
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicolas J Pizzala
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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3
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Xiao X, Zhan J, Liu B, Zhu Q, Wang G, Zeng D, Liu C, Jiang B, He L, Gong Z, Zhou X, Zhang X, Liu M. Lysine methylation: A strategy to improve in-cell NMR spectroscopy of proteins. Anal Chim Acta 2024; 1324:343099. [PMID: 39218580 DOI: 10.1016/j.aca.2024.343099] [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: 02/07/2024] [Revised: 07/26/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND In-cell NMR is a valuable technique for investigating protein structure and function in cellular environments. However, challenges arise due to highly crowded cellular environment, where nonspecific interactions between the target protein and other cellular components can lead to signals broadening or disappearance in NMR spectra. RESULTS We implemented chemical reduction methylation to selectively modify lysine residues on protein surfaces aiming to weaken charge interactions and recover obscured NMR signals. This method was tested on six proteins varying in molecular size and lysine content. While methylation did not disrupt the protein's native conformation, it successful restored some previously obscured in-cell NMR signals, particularly for proteins with high isoelectric points that decreased post-methylation. SIGNIFICANCE This study affirms lysine methylation as a feasible approach to enhance the sensitivity of in-cell NMR spectra for protein studies. By mitigating signal loss due to nonspecific interactions, this method expands the utility of in-cell NMR for investigating proteins in their natural cellular environment, potentially leading to more accurate structural and functional insights.
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Affiliation(s)
- Xiong Xiao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Zhan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Biao Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qinjun Zhu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Danyun Zeng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, 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 for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China; Optics Valley Laboratory, Wuhan, 430074, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China; Optics Valley Laboratory, Wuhan, 430074, China.
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China; Optics Valley Laboratory, Wuhan, 430074, China.
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4
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Rosati M, Barbieri L, Hlavac M, Kratzwald S, Lichtenecker RJ, Konrat R, Luchinat E, Banci L. Towards cost-effective side-chain isotope labelling of proteins expressed in human cells. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00447-6. [PMID: 39172315 DOI: 10.1007/s10858-024-00447-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Side chain isotope labelling is a powerful tool to study protein structure and interactions by NMR spectroscopy. 1H,13C labelling of side-chain methyl groups in a deuterated background allows studying large molecules, while side-chain aromatic groups are highly sensitive to the interaction with ligands, drugs, and other proteins. In E. coli, side chain labelling is performed by substituting amino acids with isotope-labelled precursors. However, proteins that can only be produced in mammalian cells require expensive isotope-labelled amino acids. Here we provide a simple and cost-effective method to label side chains in mammalian cells, which exploits the reversible reaction catalyzed by endogenous transaminases to convert isotope-labelled α-ketoacid precursors. We show by in-cell and in-lysate NMR spectroscopy that replacing an amino acid in the medium with its cognate precursor is sufficient to achieve selective labelling without scrambling, and how this approach allows monitoring conformational changes such as those arising from ligand binding.
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Affiliation(s)
- Martina Rosati
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy
| | | | | | - Roman J Lichtenecker
- MAG-LAB GmbH, Vienna, Austria
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Robert Konrat
- MAG-LAB GmbH, Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Enrico Luchinat
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
| | - Lucia Banci
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
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5
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Annecke HTP, Eidelpes R, Feyrer H, Ilgen J, Gürdap CO, Dasgupta R, Petzold K. Optimising in-cell NMR acquisition for nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00448-5. [PMID: 39162911 DOI: 10.1007/s10858-024-00448-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/08/2024] [Indexed: 08/21/2024]
Abstract
Understanding the structure and function of nucleic acids in their native environment is crucial to structural biology and one focus of in-cell NMR spectroscopy. Many challenges hamper in-cell NMR in human cell lines, e.g. sample decay through cell death and RNA degradation. The resulting low signal intensities and broad line widths limit the use of more complex NMR experiments, reducing the possible structural and dynamic information that can be extracted. Here, we optimize the detection of imino proton signals, indicators of base-pairing and therefore secondary structure, of a double-stranded DNA oligonucleotide in HeLa cells, using selective excitation. We demonstrate the reproducible quantification of in-cell selective longitudinal relaxation times (selT1), which are reduced compared to the in vitro environment, as a result of interactions with the complex cellular environment. By measuring the intracellular selT1, we optimize the existing proton pulse sequences, and shorten measurement time whilst enhancing the signal gained per unit of time. This exemplifies an advantage of selective excitation over conventional methods like jump-return water suppression for in-cell NMR. Furthermore, important experimental controls are discussed, including intracellular quantification, supernatant control measurements, as well as the processing of lowly concentrated in-cell NMR samples. We expect that robust and fast in-cell NMR experiments of nucleic acids will facilitate the study of structure and dynamics and reveal their functional correlation.
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Affiliation(s)
- Henry T P Annecke
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Reiner Eidelpes
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
| | - Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
| | - Julian Ilgen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden
| | - Cenk Onur Gürdap
- Department of Women's and Children's Health, Karolinska Institutet, 171 65, Solna, Sweden
- Science for Life Laboratory, 171 65, Solna, Sweden
| | - Rubin Dasgupta
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 1, 171 65, Stockholm, Sweden.
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden.
- Science for Life Laboratory, 171 65, Solna, Sweden.
- Center of Excellence for the Chemical Mechanisms of Life, Uppsala University, 752 37, Uppsala, Sweden.
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6
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Jegadheeshwari S, Velayutham M, Gunasekaran K, Kesavan M. DbGTi: Thermostable trypsin inhibitor from Dioscorea bulbifera L. ground tubers: assessment of antioxidant and antibacterial properties and cytotoxicity evaluation using zebrafish model. Int J Biol Macromol 2024; 263:130244. [PMID: 38387638 DOI: 10.1016/j.ijbiomac.2024.130244] [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: 09/24/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024]
Abstract
Oxidative stress disorders and diseases caused by drug-resistant bacteria have emerged as significant public health concerns. Plant-based medications like protease inhibitors are growing despite adverse effects therapies. Consecutively, in this study, trypsin inhibitors from Dioscorea bulbifera L. (DbGTi trypsin inhibitor) ground tubers were isolated, purified, characterized, and evaluated for their potential cytotoxicity, antibacterial, and antioxidant activities. DbGTi protein was purified by Q-Sepharose matrix, followed by trypsin inhibitory activity. The molecular weight of the DbGTi protein was found to be approximately 31 kDa by SDS-PAGE electrophoresis. The secondary structure analysis by circular dichroism (CD) spectroscopy revealed that the DbGTi protein predominantly comprises β sheets followed by α helix. DbGTi protein showed competitive type of inhibition with Vmax = 2.1372 × 10-1 μM/min, Km = 1.1805 × 102 μM, & Ki = 8.4 × 10-9 M and was stable up to 70 °C. DbGTi protein exhibited 58 % similarity with Dioscorin protein isolated from Dioscorea alata L. as revealed by LC-MS/MS analysis. DbGTi protein showed a non-toxic effect, analyzed by MTT, Haemolytic assay and in vivo studies on zebrafish model. DbGTi protein significantly inhibited K. pneumoniae and has excellent antioxidant properties, confirmed by various antioxidant assays. The results of anti-microbial, cytotoxicity and antioxidant assays demonstrate its bioactive potential and non-toxic nature.
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Affiliation(s)
- S Jegadheeshwari
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India; Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Manikandan Velayutham
- Institute of Biotechnology, Department of Medical Biotechnology, Integrative Physiology, Saveetha Institute of Medical and Technical Sciences, Saveetha Nagar, Thandalam, Kanchipuram, India
| | - K Gunasekaran
- Department of Crystallography and Biophysics, University of Madras, Chennai, India
| | - M Kesavan
- Interdisciplinary Institute of Indian System of Medicine, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India; Department of Physics and Nanotechnology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India.
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7
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Moon J, Hu G, Hayashi T. Application of Machine Learning in the Quantitative Analysis of the Surface Characteristics of Highly Abundant Cytoplasmic Proteins: Toward AI-Based Biomimetics. Biomimetics (Basel) 2024; 9:162. [PMID: 38534847 DOI: 10.3390/biomimetics9030162] [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: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantified the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was used for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, the B-factor, the proportion of beta structures, roughness, and the proportion of disordered regions. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments.
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Affiliation(s)
- Jooa Moon
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Guanghao Hu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8502, Japan
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-0882, Japan
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8
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Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L. Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells. J Med Chem 2024; 67:1115-1126. [PMID: 38215028 PMCID: PMC10823471 DOI: 10.1021/acs.jmedchem.3c01600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/14/2024]
Abstract
The development of more effective drugs requires knowledge of their bioavailability and binding efficacy directly in the native cellular environment. In-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating ligand-target interactions directly in living cells. However, the target molecule may be NMR-invisible due to interactions with cellular components, while observing the ligand by 1H NMR is impractical due to the cellular background. Such limitations can be overcome by observing fluorinated ligands by 19F in-cell NMR as they bind to the intracellular target. Here we report a novel approach based on real-time in-cell 19F NMR that allows measuring ligand binding affinities in human cells by competition binding, using a fluorinated compound as a reference. The binding of a set of compounds toward Hsp90α was investigated. In principle, this approach could be applied to other pharmacologically relevant targets, thus aiding the design of more effective compounds in the early stages of drug development.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, Cesena 47521, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Letizia Barbieri
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Ben Davis
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Paul A. Brough
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Matteo Pennestri
- Pharmaceutical
Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, U.K.
| | - Lucia Banci
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Centro
di Risonanze Magnetiche—CERM, Università
degli Studi di Firenze, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, Sesto Fiorentino 50019, Italy
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9
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Vallina Estrada E, Zhang N, Wennerström H, Danielsson J, Oliveberg M. Diffusive intracellular interactions: On the role of protein net charge and functional adaptation. Curr Opin Struct Biol 2023; 81:102625. [PMID: 37331204 DOI: 10.1016/j.sbi.2023.102625] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
A striking feature of nucleic acids and lipid membranes is that they all carry net negative charge and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal intermolecular repulsion that keeps the cytosolic content suitably 'fluid' for function. We focus in this review on the experimental, theoretical and genetic findings which serve to underpin this idea and the new questions they raise. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the 'random' protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. It is further evident that this dynamic protein-protein interplay is under evolutionary control and finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long-range but also the collective properties of the cellular interior as a whole.
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Affiliation(s)
- Eloy Vallina Estrada
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Nannan Zhang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Håkan Wennerström
- Division of Physical Chemistry, Department of Chemistry, Lund University, Box 124, 22100 Lund, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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10
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Watkin SAJ, Bennie RZ, Gilkes JM, Nock VM, Pearce FG, Dobson RCJ. On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:459-471. [PMID: 36583735 PMCID: PMC9801160 DOI: 10.1007/s00249-022-01626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jenna M Gilkes
- Protein Science and Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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11
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Kurbatov I, Dolgalev G, Arzumanian V, Kiseleva O, Poverennaya E. The Knowns and Unknowns in Protein-Metabolite Interactions. Int J Mol Sci 2023; 24:4155. [PMID: 36835565 PMCID: PMC9964805 DOI: 10.3390/ijms24044155] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Increasing attention has been focused on the study of protein-metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein-protein interactions, protein-metabolite interactions are still not clearly defined. Existing assays for detecting protein-metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein-metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term "interaction" to advance the field of interactomics further.
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Affiliation(s)
| | | | | | - Olga Kiseleva
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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12
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Kadavath H, Cecilia Prymaczok N, Eichmann C, Riek R, Gerez JA. Multi-Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In-Cell NMR. Angew Chem Int Ed Engl 2023; 62:e202213976. [PMID: 36379877 PMCID: PMC10107511 DOI: 10.1002/anie.202213976] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Governing function, half-life and subcellular localization, the 3D structure and dynamics of proteins are in nature constantly changing in a tightly regulated manner to fulfill the physiological and adaptive requirements of the cells. To find evidence for this hypothesis, we applied in-cell NMR to three folded model proteins and propose that the splitting of cross peaks constitutes an atomic fingerprint of distinct structural states that arise from multiple target binding co-existing inside mammalian cells. These structural states change upon protein loss of function or subcellular localisation into distinct cell compartments. In addition to peak splitting, we observed NMR signal intensity attenuations indicative of transient interactions with other molecules and dynamics on the microsecond to millisecond time scale.
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Affiliation(s)
| | | | - Cédric Eichmann
- ETH Zurich, Vladimir-Prelog-weg 2, 8093, Zurich, Switzerland
| | - Roland Riek
- ETH Zurich, Vladimir-Prelog-weg 2, 8093, Zurich, Switzerland
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13
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In-cell NMR: From target structure and dynamics to drug screening. Curr Opin Struct Biol 2022; 74:102374. [DOI: 10.1016/j.sbi.2022.102374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 11/18/2022]
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14
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Luchinat E, Cremonini M, Banci L. Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. Chem Rev 2022; 122:9267-9306. [PMID: 35061391 PMCID: PMC9136931 DOI: 10.1021/acs.chemrev.1c00790] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 12/12/2022]
Abstract
A detailed knowledge of the complex processes that make cells and organisms alive is fundamental in order to understand diseases and to develop novel drugs and therapeutic treatments. To this aim, biological macromolecules should ideally be characterized at atomic resolution directly within the cellular environment. Among the existing structural techniques, solution NMR stands out as the only one able to investigate at high resolution the structure and dynamic behavior of macromolecules directly in living cells. With the advent of more sensitive NMR hardware and new biotechnological tools, modern in-cell NMR approaches have been established since the early 2000s. At the coming of age of in-cell NMR, we provide a detailed overview of its developments and applications in the 20 years that followed its inception. We review the existing approaches for cell sample preparation and isotopic labeling, the application of in-cell NMR to important biological questions, and the development of NMR bioreactor devices, which greatly increase the lifetime of the cells allowing real-time monitoring of intracellular metabolites and proteins. Finally, we share our thoughts on the future perspectives of the in-cell NMR methodology.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum−Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019 Sesto Fiorentino, Italy
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15
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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16
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On the osmotic pressure of cells. QRB DISCOVERY 2022. [PMID: 37529285 PMCID: PMC10392628 DOI: 10.1017/qrd.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
The chemical potential of water (
$ {\mu}_{{\mathrm{H}}_2\mathrm{O}} $
) provides an essential thermodynamic characterization of the environment of living organisms, and it is of equal significance as the temperature. For cells,
$ {\mu}_{{\mathrm{H}}_2\mathrm{O}} $
is conventionally expressed in terms of the osmotic pressure (πosm). We have previously suggested that the main contribution to the intracellular πosm of the bacterium E. coli is from soluble negatively-charged proteins and their counter-ions. Here, we expand on this analysis by examining how evolutionary divergent cell types cope with the challenge of maintaining πosm within viable values. Complex organisms, like mammals, maintain constant internal πosm ≈ 0.285 osmol, matching that of 0.154 M NaCl. For bacteria it appears that optimal growth conditions are found for similar or slightly higher πosm (0.25-0.4 osmol), despite that they represent a much earlier stage in evolution. We argue that this value reflects a general adaptation for optimising metabolic function under crowded intracellular conditions. Environmental πosm that differ from this optimum require therefore special measures, as exemplified with gram-positive and gram-negative bacteria. To handle such situations, their membrane encapsulations allow for a compensating turgor pressure that can take both positive and negative values, where positive pressures allow increased frequency of metabolic events through increased intracellular protein concentrations. A remarkable exception to the rule of 0.25-0.4 osmol, is found for halophilic archaea with internal πosm ≈ 15 osmol. The internal organization of these archaea differs in that they utilize a repulsive electrostatic mechanism operating only in the ionic-liquid regime to avoid aggregation, and that they stand out from other organisms by having no turgor pressure.
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17
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Farina B, Pirone L, D’Abrosca G, Della Valle M, Russo L, Isernia C, Sassano M, Del Gatto A, Di Gaetano S, Zaccaro L, Malgieri G, Pedone EM, Fattorusso R. Screening a Molecular Fragment Library to Modulate the PED/PEA15-Phospholipase D1 Interaction in Cellular Lysate Environments. ACS Chem Biol 2021; 16:2798-2807. [PMID: 34825823 DOI: 10.1021/acschembio.1c00688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The overexpression of PED/PEA15, the phosphoprotein enriched in diabetes/phosphoprotein enriched in the astrocytes 15 protein (here referred simply to as PED), observed in some forms of type II diabetes, reduces the transport of insulin-stimulated glucose by binding to the phospholipase D1 (PLD1). The inhibition of the PED/PLD1 interaction was shown to restore basal glucose transport, indicating PED as a pharmacological target for the development of drugs capable of improving insulin sensitivity and glucose tolerance. We here report the identification and selection of PED ligands by means of NMR screening of a library of small organic molecules, NMR characterization of the PED/PLD1 interaction in lysates of cells expressing PLD1, and modulation of such interactions using BPH03, the best selected ligand. Overall, we complement the available literature data by providing detailed information on the structural determinants of the PED/PLD1 interaction in a cellular lysate environment and indicate BPH03 as a precious scaffold for the development of novel compounds that are able to modulate such interactions with possible therapeutic applications in type II diabetes.
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Affiliation(s)
- Biancamaria Farina
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Luciano Pirone
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Gianluca D’Abrosca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Della Valle
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Marica Sassano
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Annarita Del Gatto
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Sonia Di Gaetano
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Laura Zaccaro
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Emilia M. Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania─L. Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
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18
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Iwakawa N, Morimoto D, Walinda E, Leeb S, Shirakawa M, Danielsson J, Sugase K. Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel. J Phys Chem B 2021; 125:2521-2532. [PMID: 33657322 DOI: 10.1021/acs.jpcb.0c11162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aggregate formation of superoxide dismutase 1 (SOD1) inside motor neurons is known as a major factor in onset of amyotrophic lateral sclerosis. The thermodynamic stability of the SOD1 β-barrel has been shown to decrease in crowded environments such as inside a cell, but it remains unclear how the thermodynamics of crowding-induced protein destabilization relate to SOD1 aggregation. Here we have examined the effects of a protein crowder, lysozyme, on fibril aggregate formation of the SOD1 β-barrel. We found that aggregate formation of SOD1 is decelerated even in mildly crowded solutions. Intriguingly, transient diffusive interactions with lysozyme do not significantly affect the static structure of the SOD1 β-barrel but stabilize an alternative excited "invisible" state. The net effect of crowding is to favor species off the aggregation pathway, thereby explaining the decelerated aggregation in the crowded environment. Our observations suggest that the intracellular environment may have a similar negative (inhibitory) effect on fibril formation of other amyloidogenic proteins in living cells. Deciphering how crowded intracellular environments affect aggregation and fibril formation of such disease-associated proteins will probably become central in understanding the exact role of aggregation in the etiology of these enigmatic diseases.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sarah Leeb
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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19
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Sörensen T, Leeb S, Danielsson J, Oliveberg M. Polyanions Cause Protein Destabilization Similar to That in Live Cells. Biochemistry 2021; 60:735-746. [PMID: 33635054 PMCID: PMC8028048 DOI: 10.1021/acs.biochem.0c00889] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/11/2021] [Indexed: 12/25/2022]
Abstract
The structural stability of proteins is found to markedly change upon their transfer to the crowded interior of live cells. For some proteins, the stability increases, while for others, it decreases, depending on both the sequence composition and the type of host cell. The mechanism seems to be linked to the strength and conformational bias of the diffusive in-cell interactions, where protein charge is found to play a decisive role. Because most proteins, nucleotides, and membranes carry a net-negative charge, the intracellular environment behaves like a polyanionic (Z:1) system with electrostatic interactions different from those of standard 1:1 ion solutes. To determine how such polyanion conditions influence protein stability, we use negatively charged polyacetate ions to mimic the net-negatively charged cellular environment. The results show that, per Na+ equivalent, polyacetate destabilizes the model protein SOD1barrel significantly more than monoacetate or NaCl. At an equivalent of 100 mM Na+, the polyacetate destabilization of SOD1barrel is similar to that observed in live cells. By the combined use of equilibrium thermal denaturation, folding kinetics, and high-resolution nuclear magnetic resonance, this destabilization is primarily assigned to preferential interaction between polyacetate and the globally unfolded protein. This interaction is relatively weak and involves mainly the outermost N-terminal region of unfolded SOD1barrel. Our findings point thus to a generic influence of polyanions on protein stability, which adds to the sequence-specific contributions and needs to be considered in the evaluation of in vivo data.
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Affiliation(s)
- Therese Sörensen
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Sarah Leeb
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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20
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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21
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Leeb S, Yang F, Oliveberg M, Danielsson J. Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. J Phys Chem B 2020; 124:10698-10707. [PMID: 33179918 PMCID: PMC7735724 DOI: 10.1021/acs.jpcb.0c08274] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/22/2020] [Indexed: 12/26/2022]
Abstract
In the cytosolic environment, protein crowding and Brownian motions result in numerous transient encounters. Each such encounter event increases the apparent size of the interacting molecules, leading to slower rotational tumbling. The extent of transient protein complexes formed in live cells can conveniently be quantified by an apparent viscosity, based on NMR-detected spin-relaxation measurements, that is, the longitudinal (T1) and transverse (T2) relaxation. From combined analysis of three different proteins and surface mutations thereof, we find that T2 implies significantly higher apparent viscosity than T1. At first sight, the effect on T1 and T2 seems thus nonunifiable, consistent with previous reports on other proteins. We show here that the T1 and T2 deviation is actually not a inconsistency but an expected feature of a system with fast exchange between free monomers and transient complexes. In this case, the deviation is basically reconciled by a model with fast exchange between the free-tumbling reporter protein and a transient complex with a uniform 143 kDa partner. The analysis is then taken one step further by accounting for the fact that the cytosolic content is by no means uniform but comprises a wide range of molecular sizes. Integrating over the complete size distribution of the cytosolic interaction ensemble enables us to predict both T1 and T2 from a single binding model. The result yields a bound population for each protein variant and provides a quantification of the transient interactions. We finally extend the approach to obtain a correction term for the shape of a database-derived mass distribution of the interactome in the mammalian cytosol, in good accord with the existing data of the cellular composition.
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Affiliation(s)
- Sarah Leeb
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Fan Yang
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics,
Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm 106 91, Sweden
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22
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Murvai N, Kalmar L, Szalaine Agoston B, Szabo B, Tantos A, Csikos G, Micsonai A, Kardos J, Vertommen D, Nguyen PN, Hristozova N, Lang A, Kovacs D, Buday L, Han KH, Perczel A, Tompa P. Interplay of Structural Disorder and Short Binding Elements in the Cellular Chaperone Function of Plant Dehydrin ERD14. Cells 2020; 9:E1856. [PMID: 32784707 PMCID: PMC7465474 DOI: 10.3390/cells9081856] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/23/2022] Open
Abstract
Details of the functional mechanisms of intrinsically disordered proteins (IDPs) in living cells is an area not frequently investigated. Here, we dissect the molecular mechanism of action of an IDP in cells by detailed structural analyses based on an in-cell nuclear magnetic resonance experiment. We show that the ID stress protein (IDSP) A. thaliana Early Response to Dehydration (ERD14) is capable of protecting E. coli cells under heat stress. The overexpression of ERD14 increases the viability of E. coli cells from 38.9% to 73.9% following heat stress (50 °C × 15 min). We also provide evidence that the protection is mainly achieved by protecting the proteome of the cells. In-cell NMR experiments performed in E. coli cells show that the protective activity is associated with a largely disordered structural state with conserved, short sequence motifs (K- and H-segments), which transiently sample helical conformations in vitro and engage in partner binding in vivo. Other regions of the protein, such as its S segment and its regions linking and flanking the binding motifs, remain unbound and disordered in the cell. Our data suggest that the cellular function of ERD14 is compatible with its residual structural disorder in vivo.
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Affiliation(s)
- Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Bianka Szalaine Agoston
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
- MTA-ELTE Protein Modelling Research Group and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, 1117 Budapest, Hungary; (A.L.); (A.P.)
| | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Gyorgy Csikos
- Department of General Zoology, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - Didier Vertommen
- Faculty of Medicine and de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Phuong N. Nguyen
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Nevena Hristozova
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Andras Lang
- MTA-ELTE Protein Modelling Research Group and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, 1117 Budapest, Hungary; (A.L.); (A.P.)
| | - Denes Kovacs
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Laszlo Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Kyou-Hoon Han
- Gene Editing Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Andras Perczel
- MTA-ELTE Protein Modelling Research Group and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, 1117 Budapest, Hungary; (A.L.); (A.P.)
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
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23
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Luchinat E, Barbieri L, Campbell TF, Banci L. Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution. Anal Chem 2020; 92:9997-10006. [PMID: 32551584 PMCID: PMC7735651 DOI: 10.1021/acs.analchem.0c01677] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
In-cell NMR can investigate
protein conformational changes at atomic
resolution, such as those changes induced by drug binding or chemical
modifications, directly in living human cells, and therefore has great
potential in the context of drug development as it can provide an
early assessment of drug potency. NMR bioreactors can greatly improve
the cell sample stability over time and, more importantly, allow for
recording in-cell NMR data in real time to monitor the evolution of
intracellular processes, thus providing unique insights into the kinetics
of drug-target interactions. However, current implementations are
limited by low cell viability at >24 h times, the reduced sensitivity
compared to “static” experiments and the lack of protocols
for automated and quantitative analysis of large amounts of data.
Here, we report an improved bioreactor design which maintains human
cells alive and metabolically active for up to 72 h, and a semiautomated
workflow for quantitative analysis of real-time in-cell NMR data relying
on Multivariate Curve Resolution. We apply this setup to monitor protein–ligand
interactions and protein oxidation in real time. High-quality concentration
profiles can be obtained from noisy 1D and 2D NMR data with high temporal
resolution, allowing further analysis by fitting with kinetic models.
This unique approach can therefore be applied to investigate complex
kinetic behaviors of macromolecules in a cellular setting, and could
be extended in principle to any real-time NMR application in live
cells.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Center for Colloids and Surface Science - CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence Italy
| | - Letizia Barbieri
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Interuniversity Consortium for Magnetic Resonance of Metalloproteins - CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
| | - Timothy F Campbell
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
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24
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Breindel L, Yu J, Burz DS, Shekhtman A. Intact ribosomes drive the formation of protein quinary structure. PLoS One 2020; 15:e0232015. [PMID: 32330166 PMCID: PMC7182177 DOI: 10.1371/journal.pone.0232015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/05/2020] [Indexed: 01/19/2023] Open
Abstract
Transient, site-specific, or so-called quinary, interactions are omnipresent in live cells and modulate protein stability and activity. Quinary intreactions are readily detected by in-cell NMR spectroscopy as severe broadening of the NMR signals. Intact ribosome particles were shown to be necessary for the interactions that give rise to the NMR protein signal broadening observed in cell lysates and sufficient to mimic quinary interactions present in the crowded cytosol. Recovery of target protein NMR spectra that were broadened in lysates, in vitro and in the presence of purified ribosomes was achieved by RNase A digestion only after the structure of the ribosome was destabilized by removing magnesium ions from the system. Identifying intact ribosomal particles as the major protein-binding component of quinary interactions and consequent spectral peak broadening will facilitate quantitative characterization of macromolecular crowding effects in live cells and streamline models of metabolic activity.
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Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
| | - Jianchao Yu
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
| | - David S. Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, United States of America
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25
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Leeb S, Sörensen T, Yang F, Mu X, Oliveberg M, Danielsson J. Diffusive protein interactions in human versus bacterial cells. Curr Res Struct Biol 2020; 2:68-78. [PMID: 34235470 PMCID: PMC8244477 DOI: 10.1016/j.crstbi.2020.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 01/14/2023] Open
Abstract
Random encounters between proteins in crowded cells are by no means passive, but found to be under selective control. This control enables proteome solubility, helps to optimise the diffusive search for interaction partners, and allows for adaptation to environmental extremes. Interestingly, the residues that modulate the encounters act mesoscopically through protein surface hydrophobicity and net charge, meaning that their detailed signatures vary across organisms with different intracellular constraints. To examine such variations, we use in-cell NMR relaxation to compare the diffusive behaviour of bacterial and human proteins in both human and Escherichia coli cytosols. We find that proteins that ‘stick’ in E. coli are generally less restricted in mammalian cells. Furthermore, the rotational diffusion in the mammalian cytosol is less sensitive to surface-charge mutations. This implies that, in terms of protein motions, the mammalian cytosol is more forgiving to surface alterations than E. coli cells. The cellular differences seem not linked to the proteome properties per se, but rather to a 6-fold difference in protein concentrations. Our results outline a scenario in which the tolerant cytosol of mammalian cells, found in long-lived multicellular organisms, provides an enlarged evolutionary playground, where random protein-surface mutations are less deleterious than in short-generational bacteria. Random protein encounters and diffusibility in cells are controlled by surface charge. Protein rotational diffusion is less restricted in human cells than in E. coli. Human cells are less sensitive to alterations of protein charge than Escherichia coli cells.
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Affiliation(s)
- Sarah Leeb
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Therese Sörensen
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Fan Yang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Xin Mu
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91, Stockholm, Sweden
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26
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Abstract
Cellular function is generally depicted at the level of functional pathways and detailed structural mechanisms, based on the identification of specific protein–protein interactions. For an individual protein searching for its partner, however, the perspective is quite different: The functional task is challenged by a dense crowd of nonpartners obstructing the way. Adding to the challenge, there is little information about how to navigate the search, since the encountered surrounding is composed of protein surfaces that are predominantly “nonconserved” or, at least, highly variable across organisms. In this study, we demonstrate from a colloidal standpoint that such a blindfolded intracellular search is indeed favored and has more fundamental impact on the cellular organization than previously anticipated. Basically, the unique polyion composition of cellular systems renders the electrostatic interactions different from those in physiological buffer, leading to a situation where the protein net-charge density balances the attractive dispersion force and surface heterogeneity at close range. Inspection of naturally occurring proteomes and in-cell NMR data show further that the “nonconserved” protein surfaces are by no means passive but chemically biased to varying degree of net-negative repulsion across organisms. Finally, this electrostatic control explains how protein crowding is spontaneously maintained at a constant level through the intracellular osmotic pressure and leads to the prediction that the “extreme” in halophilic adaptation is not the ionic-liquid conditions per se but the evolutionary barrier of crossing its physicochemical boundaries.
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27
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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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28
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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: 46] [Impact Index Per Article: 11.5] [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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29
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Davis CM, Deutsch J, Gruebele M. An in vitro mimic of in-cell solvation for protein folding studies. Protein Sci 2020; 29:1060-1068. [PMID: 31994240 DOI: 10.1002/pro.3833] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 01/15/2023]
Abstract
Ficoll, an inert macromolecule, is a common in vitro crowder, but by itself it does not reproduce in-cell stability or kinetic trends for protein folding. Lysis buffer, which contains ions, glycerol as a simple kosmotrope, and mimics small crowders with hydrophilic/hydrophobic patches, can reproduce sticking trends observed in cells but not the crowding. We previously suggested that the proper combination of Ficoll and lysis buffer could reproduce the opposite in-cell folding stability trend of two proteins: variable major protein-like sequence expressed (VlsE) is destabilized in eukaryotic cells and phosphoglycerate kinase (PGK) is stabilized. Here, to discover a well-characterized solvation environment that mimics in-cell stabilities for these two very differently behaved proteins, we conduct a two-dimensional scan of Ficoll (0-250 mg/ml) and lysis buffer (0-75%) mixtures. Contrary to our previous expectation, we show that mixtures of Ficoll and lysis buffer have a significant nonadditive effect on the folding stability. Lysis buffer enhances the stabilizing effect of Ficoll on PGK and inhibits the stabilizing effect of Ficoll on VlsE. We demonstrate that a combination of 150 mg/ml Ficoll and 60% lysis buffer can be used as an in vitro mimic to account for both crowding and non-steric effects on PGK and VlsE stability and folding kinetics in the cell. Our results also suggest that this mixture is close to the point where phase separation will occur. The simple mixture proposed here, based on commercially available reagents, could be a useful tool to study a variety of cytoplasmic protein interactions, such as folding, binding and assembly, and enzymatic reactions. SIGNIFICANCE STATEMENT: The complexity of the in-cell environment is difficult to reproduce in the test tube. Here we validate a mimic of cellular crowding and sticking interactions in a test tube using two proteins that are differently impacted by the cell: one is stabilized and the other is destabilized. This mimic is a starting point to reproduce cellular effects on a variety of protein and biomolecular interactions, such as folding and binding.
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Affiliation(s)
- Caitlin M Davis
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jonathan Deutsch
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Martin Gruebele
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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30
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Alshamleh I, Krause N, Richter C, Kurrle N, Serve H, Günther UL, Schwalbe H. Real-Time NMR Spectroscopy for Studying Metabolism. Angew Chem Int Ed Engl 2020; 59:2304-2308. [PMID: 31730253 PMCID: PMC7004128 DOI: 10.1002/anie.201912919] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/12/2019] [Indexed: 12/19/2022]
Abstract
Current metabolomics approaches utilize cellular metabolite extracts, are destructive, and require high cell numbers. We introduce here an approach that enables the monitoring of cellular metabolism at lower cell numbers by observing the consumption/production of different metabolites over several kinetic data points of up to 48 hours. Our approach does not influence cellular viability, as we optimized the cellular matrix in comparison to other materials used in a variety of in-cell NMR spectroscopy experiments. We are able to monitor real-time metabolism of primary patient cells, which are extremely sensitive to external stress. Measurements are set up in an interleaved manner with short acquisition times (approximately 7 minutes per sample), which allows the monitoring of up to 15 patient samples simultaneously. Further, we implemented our approach for performing tracer-based assays. Our approach will be important not only in the metabolomics fields, but also in individualized diagnostics.
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Affiliation(s)
- Islam Alshamleh
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Nina Krause
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Nina Kurrle
- German Cancer Consortium (DKTK) and DKFZ69120HeidelbergGermany
- Department of Medicine 2, Hematology/OncologyGoethe University60590Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)60590Frankfurt am MainGermany
| | - Hubert Serve
- German Cancer Consortium (DKTK) and DKFZ69120HeidelbergGermany
- Department of Medicine 2, Hematology/OncologyGoethe University60590Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)60590Frankfurt am MainGermany
| | - Ulrich L. Günther
- Institute of Chemistry and MetabolomicsUniversity of LuebeckRatzeburger Allee 16023562LuebeckGermany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
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31
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Alshamleh I, Krause N, Richter C, Kurrle N, Serve H, Günther UL, Schwalbe H. Real‐Time NMR Spectroscopy for Studying Metabolism. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Islam Alshamleh
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Nina Krause
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Nina Kurrle
- German Cancer Consortium (DKTK) and DKFZ 69120 Heidelberg Germany
- Department of Medicine 2, Hematology/OncologyGoethe University 60590 Frankfurt am Main Germany
- Frankfurt Cancer Institute (FCI) 60590 Frankfurt am Main Germany
| | - Hubert Serve
- German Cancer Consortium (DKTK) and DKFZ 69120 Heidelberg Germany
- Department of Medicine 2, Hematology/OncologyGoethe University 60590 Frankfurt am Main Germany
- Frankfurt Cancer Institute (FCI) 60590 Frankfurt am Main Germany
| | - Ulrich L. Günther
- Institute of Chemistry and MetabolomicsUniversity of Luebeck Ratzeburger Allee 160 23562 Luebeck Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
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32
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Abstract
Cells of the vast majority of organisms are subject to temperature, pressure, pH, ionic strength, and other stresses. We discuss these effects in the light of protein folding and protein interactions in vitro, in complex environments, in cells, and in vivo. Protein phase diagrams provide a way of organizing different structural ensembles that occur under stress and how one can move among ensembles. Experiments that perturb biomolecules in vitro or in cells by stressing them have revealed much about the underlying forces that are competing to control protein stability, folding, and function. Two phenomena that emerge and serve to broadly classify effects of the cellular environment are crowding (mainly due to repulsive forces) and sticking (mainly due to attractive forces). The interior of cells is closely balanced between these emergent effects, and stress can tip the balance one way or the other. The free energy scale involved is small but significant on the scale of the "on/off switches" that control signaling in cells or of protein-protein association with a favorable function such as increased enzyme processivity. Quantitative tools from biophysical chemistry will play an important role in elucidating the world of crowding and sticking under stress.
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Affiliation(s)
- Mayank Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
- Department of Chemistry, Department of Physics, Center for the Physics of Living Cells, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
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33
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Siegal G, Selenko P. Cells, drugs and NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:202-212. [PMID: 31358370 DOI: 10.1016/j.jmr.2019.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/08/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for investigating cellular structures and their compositions. While in vivo and whole-cell NMR have a long tradition in cell-based approaches, high-resolution in-cell NMR spectroscopy is a new addition to these methods. In recent years, technological advancements in multiple areas provided converging benefits for cellular MR applications, especially in terms of robustness, reproducibility and physiological relevance. Here, we review the use of cellular NMR methods for drug discovery purposes in academia and industry. Specifically, we discuss how developments in NMR technologies such as miniaturized bioreactors and flow-probe perfusion systems have helped to consolidate NMR's role in cell-based drug discovery efforts.
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Affiliation(s)
- Gregg Siegal
- ZoBio B.V., BioPartner 2 Building, J.H. Oortweg 19, 2333 Leiden, the Netherlands
| | - Philipp Selenko
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000 Rehovot, Israel.
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34
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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35
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Nishida N, Ito Y, Shimada I. In situ structural biology using in-cell NMR. Biochim Biophys Acta Gen Subj 2019; 1864:129364. [PMID: 31103749 DOI: 10.1016/j.bbagen.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Accumulating evidence from the experimental and computational studies indicated that the functional properties of proteins are different between in vitro and living cells, raising the necessity to examine the protein structure under the native intracellular milieu. To gain structural information of the proteins inside the living cells at an atomic resolution, in-cell NMR method has been developed for the past two decades. SCOPE OF REVIEW In this review, we will overview the recent progress in the methodological developments and the biological applications of in-cell NMR, and discuss the advances and challenges in this filed. MAJOR CONCLUSIONS A number of methods were developed to enrich the isotope-labeled proteins inside the cells, enabling the in-cell NMR observation of bacterial cells as well as eukaryotic cells. In-cell NMR has been applied to various biological systems, including de novo structure determinations, protein/protein or protein/drug interactions, and monitoring of chemical reactions exerted by the endogenous enzymes. The bioreactor system, in which the cells in the NMR tube are perfused by fresh culture medium, enabled the long-term in-cell NMR measurements, and the real-time observations of intracellular responses upon external stimuli. GENERAL SIGNIFICANCE In-cell NMR has become a unique technology for its ability to obtain the function-related structural information of the target proteins under the physiological or pathological cellular environments, which cannot be reconstituted in vitro.
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Affiliation(s)
- Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan.
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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36
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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37
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The Inescapable Effects of Ribosomes on In-Cell NMR Spectroscopy and the Implications for Regulation of Biological Activity. Int J Mol Sci 2019; 20:ijms20061297. [PMID: 30875837 PMCID: PMC6471074 DOI: 10.3390/ijms20061297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/05/2019] [Accepted: 03/09/2019] [Indexed: 12/16/2022] Open
Abstract
The effects of RNA on in-cell NMR spectroscopy and ribosomes on the kinetic activity of several metabolic enzymes are reviewed. Quinary interactions between labelled target proteins and RNA broaden in-cell NMR spectra yielding apparent megadalton molecular weights in-cell. The in-cell spectra can be resolved by using cross relaxation-induced polarization transfer (CRINEPT), heteronuclear multiple quantum coherence (HMQC), transverse relaxation-optimized, NMR spectroscopy (TROSY). The effect is reproduced in vitro by using reconstituted total cellular RNA and purified ribosome preparations. Furthermore, ribosomal binding antibiotics alter protein quinary structure through protein-ribosome and protein-mRNA-ribosome interactions. The quinary interactions of Adenylate kinase, Thymidylate synthase and Dihydrofolate reductase alter kinetic properties of the enzymes. The results demonstrate that ribosomes may specifically contribute to the regulation of biological activity.
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38
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In-Cell NMR: Analysis of Protein-Small Molecule Interactions, Metabolic Processes, and Protein Phosphorylation. Int J Mol Sci 2019; 20:ijms20020378. [PMID: 30658393 PMCID: PMC6359726 DOI: 10.3390/ijms20020378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 01/31/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy enables the non-invasive observation of biochemical processes, in living cells, at comparably high spectral and temporal resolution. Preferably, means of increasing the detection limit of this powerful analytical method need to be applied when observing cellular processes under physiological conditions, due to the low sensitivity inherent to the technique. In this review, a brief introduction to in-cell NMR, protein–small molecule interactions, posttranslational phosphorylation, and hyperpolarization NMR methods, used for the study of metabolites in cellulo, are presented. Recent examples of method development in all three fields are conceptually highlighted, and an outlook into future perspectives of this emerging area of NMR research is given.
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Breindel L, Burz DS, Shekhtman A. Interaction proteomics by using in-cell NMR spectroscopy. J Proteomics 2019; 191:202-211. [PMID: 29427760 PMCID: PMC6082733 DOI: 10.1016/j.jprot.2018.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/31/2018] [Accepted: 02/04/2018] [Indexed: 12/17/2022]
Abstract
A synopsis of in-cell NMR spectroscopic approaches to study interaction proteomics in prokaryotic and eukaryotic cells is presented. We describe the use of in-cell NMR spectroscopy to resolve high resolution protein structures, discuss methodologies for determining and analyzing high and low affinity protein-target structural interactions, including intrinsically disordered proteins, and detail important functional interactions that result from these interactions. SIGNIFICANCE: The ultimate goal of structural and biochemical research is to understand how macromolecular interactions give rise to and regulate biological activity in living cells. The challenge is formidable due to the complexity that arises not only from the number of proteins (genes) expressed by the organism, but also from the combinatorial interactions between them. Despite ongoing efforts to decipher the complex nature of protein interactions, new methods for structurally characterizing protein complexes are needed to fully understand molecular networks. With the onset of in-cell NMR spectroscopy, molecular structures and interactions can be studied under physiological conditions shedding light on the structural underpinning of biological activity.
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Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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40
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Applications of In-Cell NMR in Structural Biology and Drug Discovery. Int J Mol Sci 2019; 20:ijms20010139. [PMID: 30609728 PMCID: PMC6337603 DOI: 10.3390/ijms20010139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/23/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) is a method to provide the structural information of a target at an atomic level under physiological conditions and a full view of the conformational changes of a protein caused by ligand binding, post-translational modifications or protein⁻protein interactions in living cells. Previous in-cell NMR studies have focused on proteins that were overexpressed in bacterial cells and isotopically labeled proteins injected into oocytes of Xenopus laevis or delivered into human cells. Applications of in-cell NMR in probing protein modifications, conformational changes and ligand bindings have been carried out in mammalian cells by monitoring isotopically labeled proteins overexpressed in living cells. The available protocols and successful examples encourage wide applications of this technique in different fields such as drug discovery. Despite the challenges in this method, progress has been made in recent years. In this review, applications of in-cell NMR are summarized. The successful applications of this method in mammalian and bacterial cells make it feasible to play important roles in drug discovery, especially in the step of target engagement.
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41
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Schneider R, Blackledge M, Jensen MR. Elucidating binding mechanisms and dynamics of intrinsically disordered protein complexes using NMR spectroscopy. Curr Opin Struct Biol 2018; 54:10-18. [PMID: 30316104 DOI: 10.1016/j.sbi.2018.09.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 01/10/2023]
Abstract
Advances in characterizing complexes of intrinsically disordered proteins (IDPs) have led to the discovery of a remarkably diverse interaction landscape that includes folding-upon-binding, highly dynamic complexes, multivalent interactions as well as regulatory switches controlled by post-translational modifications. Nuclear magnetic resonance (NMR) spectroscopy has in recent years made significant contributions to this field by describing the binding mechanisms and mapping conformational dynamics on multiple time scales. Importantly, this progress has been associated with specific methodological developments in NMR, for example in exchange techniques, allowing challenging biological systems to be studied at atomic resolution. In general, the level of dynamics observed in IDP complexes does not correlate with binding affinities, demonstrating the intricate relationship between conformational dynamics and IDP regulatory function.
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Affiliation(s)
- Robert Schneider
- Univ. Lille, CNRS, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
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42
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Davis CM, Gruebele M. Non-Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells. Chemphyschem 2018; 19:2290-2294. [PMID: 29877016 DOI: 10.1002/cphc.201800534] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 01/15/2023]
Abstract
Although biomolecules evolved to function in the cell, most biochemical assays are carried out in vitro. In-cell studies highlight how steric and non-steric interactions modulate protein folding and interactions. VlsE and PGK present two extremes of chemical behavior in the cell: the extracellular protein VlsE is destabilized in eukaryotic cells, whereas the cytoplasmic protein PGK is stabilized. VlsE and PGK are benchmarks in a systematic series of solvation environments to distinguish contributions from non-steric and steric interactions to protein stability, compactness, and folding rate by comparing cell lysate, a crowding agent, ionic buffer and lysate buffer with in-cell results. As anticipated, crowding stabilizes proteins, causes compaction, and can speed folding. Protein flexibility determines its sensitivity to steric interactions or crowding. Non-steric interactions alone predict in-cell stability trends, while crowding provides an offset towards greater stabilization. We suggest that a simple combination of lysis buffer and Ficoll is an effective new in vitro mimic of the intracellular environment on protein folding and stability.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States.,Department of Chemistry and Department of Physics, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States
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43
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Luchinat E, Banci L. In-Cell NMR in Human Cells: Direct Protein Expression Allows Structural Studies of Protein Folding and Maturation. Acc Chem Res 2018; 51:1550-1557. [PMID: 29869502 DOI: 10.1021/acs.accounts.8b00147] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cellular structural biology methods are needed to characterize biological processes at atomic resolution in the physiological environment of the cell. Toward this goal, solution in-cell NMR is a powerful approach because it provides structural and dynamic data on macromolecules inside living cells. Several approaches have been developed for in-cell NMR in cultured human cells, which are needed to study processes related to human diseases that rely on the delivery of exogenous macromolecules to the cells. Such strategies, however, may not be applicable to proteins that are sensitive to the external environment or prone to aggregate and can introduce artifacts during protein purification or delivery. As a complementary approach, direct protein expression for in-cell NMR in human cells was developed. This strategy is especially useful when studying processes like protein folding, maturation, and post-translational modification, starting right after protein synthesis. Compared with the protein expression techniques in mammalian cells commonly used in cellular biology, the low sensitivity of NMR requires higher protein levels. Among the cell lines used for high-yield protein expression, the HEK293T cell line was chosen, as it can be efficiently transfected with a cost-effective reagent. A vector originally designed for secreted proteins allows high-level cytosolic protein expression. For isotopic labeling, commercially available or homemade labeled media are employed. Uniform or amino acid type-selective labeling strategies are possible. Protein expression can be targeted to specific organelles (e.g., mitochondria), allowing for in organello NMR applications. A variant of the approach was developed that allows the sequential expression of two or more proteins, with only one selectively labeled. Protein expression in HEK293T cells was applied to recapitulate the maturation steps of intracellular superoxide dismutase 1 (SOD1) and to study the effect of mutations linked to familial amyotrophic lateral sclerosis (fALS) by in-cell NMR. Intracellular wild-type SOD1 spontaneously binds zinc, while it needs the copper chaperone for superoxide dismutase (CCS) for copper delivery and disulfide bond formation. Some fALS-linked mutations impair zinc binding and cause SOD1 to irreversibly unfold, likely forming the precursor of cytotoxic aggregates. The SOD-like domain of CCS acts as a molecular chaperone toward mutant SOD1, stabilizing its folding and allowing zinc binding and correct maturation. Changes in protein redox state distributions can also be investigated by in-cell NMR. Mitochondrial proteins require the redox-regulating partners glutaredoxin 1 (Grx1) and thioredoxin (Trx) to remain in the reduced, import-competent state in the cytosol, whereas SOD1 requires CCS for disulfide bond formation. In both cases, the proteins do not equilibrate with the cytosolic redox pool. Cysteine oxidation in response to oxidative stress can also be monitored. In the near future, in-cell NMR in human cells will likely benefit from technological advancements in NMR hardware, the development of bioreactor systems for increased sample lifetime, the application of paramagnetic NMR to obtain structural restraints, and advanced tools for genome engineering and should be increasingly integrated with advanced cellular imaging techniques.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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44
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New structural and functional insights from in-cell NMR. Emerg Top Life Sci 2018; 2:29-38. [PMID: 33525780 DOI: 10.1042/etls20170136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 11/17/2022]
Abstract
In recent years, it has become evident that structural characterization would gain significantly in terms of biological relevance if framed within a cellular context, while still maintaining the atomic resolution. Therefore, major efforts have been devoted to developing Cellular Structural Biology approaches. In this respect, in-cell NMR can provide and has provided relevant contributions to the field, not only to investigate the structural and dynamical properties of macromolecules in solution but, even more relevant, to understand functional processes directly in living cells and the factors that modulate them, such as exogenous molecules, partner proteins, and oxidative stress. In this commentary, we review and discuss some of the main contributions to the understanding of protein structural and functional properties achieved by in-cell NMR.
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45
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Becker W, Bhattiprolu KC, Gubensäk N, Zangger K. Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy. Chemphyschem 2018; 19:895-906. [PMID: 29314603 PMCID: PMC5915746 DOI: 10.1002/cphc.201701253] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution.
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Affiliation(s)
- Walter Becker
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | | | - Nina Gubensäk
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Klaus Zangger
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
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46
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Inomata K, Kamoshida H, Ikari M, Ito Y, Kigawa T. Impact of cellular health conditions on the protein folding state in mammalian cells. Chem Commun (Camb) 2018; 53:11245-11248. [PMID: 28960222 DOI: 10.1039/c7cc06004a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By using in-cell NMR experiments, we have demonstrated that the protein folding state in cells is significantly influenced by the cellular health conditions. hAK1 was denatured in cells under stressful culture conditions, while it remained functional and properly folded in cells continuously supplied with a fresh medium.
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Affiliation(s)
- Kohsuke Inomata
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. and PRESTO/Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hajime Kamoshida
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Masaomi Ikari
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Takanori Kigawa
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. and Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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47
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Lippens G, Cahoreau E, Millard P, Charlier C, Lopez J, Hanoulle X, Portais JC. In-cell NMR: from metabolites to macromolecules. Analyst 2018; 143:620-629. [PMID: 29333554 DOI: 10.1039/c7an01635b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.
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Affiliation(s)
- G Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - E Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - P Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - C Charlier
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - J Lopez
- CERMN, Seccion Quimica, Departemento de Ciencias, Pontificia Universidad Catolica del Peru, Lima 32, Peru
| | - X Hanoulle
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), University of Lille, CNRS UMR8576, Lille, France
| | - J C Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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48
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Breindel L, DeMott C, Burz DS, Shekhtman A. Real-Time In-Cell Nuclear Magnetic Resonance: Ribosome-Targeted Antibiotics Modulate Quinary Protein Interactions. Biochemistry 2018; 57:540-546. [PMID: 29266932 DOI: 10.1021/acs.biochem.7b00938] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How ribosome antibiotics affect a wide range of biochemical pathways is not well understood; changes in RNA-mediated protein quinary interactions and consequent activity inside the crowded cytosol may provide one possible mechanism. We developed real-time (RT) in-cell nuclear magnetic resonance (NMR) spectroscopy to monitor temporal changes in protein quinary structure, for ≥24 h, in response to external and internal stimuli. RT in-cell NMR consists of a bioreactor containing gel-encapsulated cells inside a 5 mm NMR tube, a gravity siphon for continuous exchange of medium, and a horizontal drip irrigation system to supply nutrients to the cells during the experiment. We showed that adding antibiotics that bind to the small ribosomal subunit results in more extensive quinary interactions between thioredoxin and mRNA. The results substantiate the idea that RNA-mediated modulation of quinary protein interactions may provide the physical basis for ribosome inhibition and other regulatory pathways.
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Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher DeMott
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
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49
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Mitri E, Barbieri L, Vaccari L, Luchinat E. 15N isotopic labelling for in-cell protein studies by NMR spectroscopy and single-cell IR synchrotron radiation FTIR microscopy: a correlative study. Analyst 2018; 143:1171-1181. [DOI: 10.1039/c7an01464c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The effect of 15N-enrichment on human cells analyzed by correlative in-cell NMR and single-cell SR-FTIR experiments.
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Affiliation(s)
- E. Mitri
- Elettra – Sincrotrone Trieste S.C.p.A
- SISSI Beamline – Chemical and Life Sciences Branch
- 34149, Basovizza
- Italy
| | - L. Barbieri
- Magnetic Resonance Centre (CERM)
- University of Florence
- 50019 Sesto Fiorentino
- Italy
- Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP)
| | - L. Vaccari
- Elettra – Sincrotrone Trieste S.C.p.A
- SISSI Beamline – Chemical and Life Sciences Branch
- 34149, Basovizza
- Italy
| | - E. Luchinat
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”
- University of Florence
- 50134 Florence
- Italy
- Magnetic Resonance Centre (CERM)
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Burz DS, DeMott CM, Aldousary A, Dansereau S, Shekhtman A. Quantitative Determination of Interacting Protein Surfaces in Prokaryotes and Eukaryotes by Using In-Cell NMR Spectroscopy. Methods Mol Biol 2018; 1688:423-444. [PMID: 29151221 DOI: 10.1007/978-1-4939-7386-6_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper describes three protocols for identifying interacting surfaces on 15N-labeled target proteins of known structure by using in-cell NMR spectroscopy. The first protocol describes how to identify protein quinary structure interaction surfaces in prokaryotes by using cross-relaxation-induced polarization transfer, CRIPT, based in-cell NMR. The second protocol describes how to introduce labeled protein into eukaryotic (HeLa) cells via electroporation for CRIPT-based in-cell studies. The third protocol describes how to quantitatively map protein interacting surfaces by utilizing singular value decomposition, SVD, analysis of STructural INTeractions by in-cell NMR, STINT-NMR, data.
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Affiliation(s)
- David S Burz
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Asma Aldousary
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Stephen Dansereau
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA.
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