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Chen X, Zhang X, Qin M, Chen J, Wang M, Liu Z, An L, Song X, Yao L. Protein Allostery Study in Cells Using NMR Spectroscopy. Anal Chem 2024; 96:7065-7072. [PMID: 38652079 DOI: 10.1021/acs.analchem.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Protein allostery is commonly observed in vitro. But how protein allostery behaves in cells is unknown. In this work, a protein monomer-dimer equilibrium system was built with the allosteric effect on the binding characterized using NMR spectroscopy through mutations away from the dimer interface. A chemical shift linear fitting method was developed that enabled us to accurately determine the dissociation constant. A total of 28 allosteric mutations were prepared and grouped to negative allosteric, nonallosteric, and positive allosteric modulators. ∼ 50% of mutations displayed the allosteric-state changes when moving from a buffered solution into cells. For example, there were no positive allosteric modulators in the buffered solution but eight in cells. The change in protein allostery is correlated with the interactions between the protein and the cellular environment. These interactions presumably drive the surrounding macromolecules in cells to transiently bind to the monomer and dimer mutational sites and change the free energies of the two species differently which generate new allosteric effects. These surrounding macromolecules create a new protein allostery pathway that is only present in cells.
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Affiliation(s)
- Xiaoxu Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xueying Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Qin
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Jingfei Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Mengting Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Liaoyuan An
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiangfei Song
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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Querci L, Grifagni D, Trindade IB, Silva JM, Louro RO, Cantini F, Piccioli M. Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center. JOURNAL OF BIOMOLECULAR NMR 2023; 77:247-259. [PMID: 37853207 PMCID: PMC10687126 DOI: 10.1007/s10858-023-00425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.
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Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
- Division of Biology and Biological Engineering, California Institute of Technology, CA 91125, Pasadena, USA
| | - José Malanho Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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3
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Qin Z, Wang Z, Kong F, Su J, Huang Z, Zhao P, Chen S, Zhang Q, Shi F, Du J. In situ electron paramagnetic resonance spectroscopy using single nanodiamond sensors. Nat Commun 2023; 14:6278. [PMID: 37805509 PMCID: PMC10560202 DOI: 10.1038/s41467-023-41903-5] [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: 02/15/2023] [Accepted: 09/18/2023] [Indexed: 10/09/2023] Open
Abstract
An ultimate goal of electron paramagnetic resonance (EPR) spectroscopy is to analyze molecular dynamics in place where it occurs, such as in a living cell. The nanodiamond (ND) hosting nitrogen-vacancy (NV) centers will be a promising EPR sensor to achieve this goal. However, ND-based EPR spectroscopy remains elusive, due to the challenge of controlling NV centers without well-defined orientations inside a flexible ND. Here, we show a generalized zero-field EPR technique with spectra robust to the sensor's orientation. The key is applying an amplitude modulation on the control field, which generates a series of equidistant Floquet states with energy splitting being the orientation-independent modulation frequency. We acquire the zero-field EPR spectrum of vanadyl ions in aqueous glycerol solution with embedded single NDs, paving the way towards in vivo EPR.
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Affiliation(s)
- Zhuoyang Qin
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Zhecheng Wang
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Fei Kong
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China.
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, 230088, China.
| | - Jia Su
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Zhehua Huang
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Pengju Zhao
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Sanyou Chen
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
- School of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Qi Zhang
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China
- School of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Fazhan Shi
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China.
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, 230088, China.
- School of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China.
| | - Jiangfeng Du
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China.
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, 230026, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, 230088, China.
- School of Physics, Zhejiang University, Hangzhou, 310027, China.
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Chen JL, Yang Y, Shi T, Su XC. Effective assessment of lanthanide ion delivery into live cells by paramagnetic NMR spectroscopy. Chem Commun (Camb) 2023; 59:10552-10555. [PMID: 37575089 DOI: 10.1039/d3cc03135g] [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: 08/15/2023]
Abstract
We report an effective assessment of lanthanide ion (Ln3+) delivery into live cells by paramagnetic NMR spectroscopy. Free Ln3+ ions are toxic to live cells resulting in a gradual leakage of target proteins to the extracellular media. The citrate-Ln3+ complex is an efficient and mild reagent over the free Ln3+ form for live cell delivery.
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Affiliation(s)
- Jia-Liang Chen
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang, Shandong, 277160, China.
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Tiesheng Shi
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang, Shandong, 277160, China.
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
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5
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Wang M, Song X, Chen J, Chen X, Zhang X, Yang Y, Liu Z, Yao L. Intracellular environment can change protein conformational dynamics in cells through weak interactions. SCIENCE ADVANCES 2023; 9:eadg9141. [PMID: 37478178 PMCID: PMC10361600 DOI: 10.1126/sciadv.adg9141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.
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Affiliation(s)
- Mengting Wang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangfei Song
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Jingfei Chen
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Xiaoxu Chen
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueying Zhang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Lishan Yao
- Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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6
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Silva JM, Cerofolini L, Carvalho AL, Ravera E, Fragai M, Parigi G, Macedo AL, Geraldes CFGC, Luchinat C. Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase. J Inorg Biochem 2023; 244:112222. [PMID: 37068394 DOI: 10.1016/j.jinorgbio.2023.112222] [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: 02/14/2023] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
Many proteins naturally carry metal centers, with a large share of them being in the active sites of several enzymes. Paramagnetic effects are a powerful source of structural information and, therefore, if the native metal is paramagnetic, or it can be functionally substituted with a paramagnetic one, paramagnetic effects can be used to study the metal sites, as well as the overall structure of the protein. One notable example is cobalt(II) substitution for zinc(II) in carbonic anhydrase. In this manuscript we investigate the effects of sodium thiocyanate on the chemical environment of the metal ion of the human carbonic anhydrase II. The electron paramagnetic resonance (EPR) titration of the cobalt(II) protein with thiocyanate shows that the EPR spectrum changes from A-type to C-type on passing from 1:1 to 1:1000-fold ligand excess. This indicates the occurrence of a change in the electronic structure, which may reflect a sizable change in the metal coordination environment in turn caused by a modification of the frozen solvent glass. However, paramagnetic nuclear magnetic resonance (NMR) data indicate that the metal coordination cage remains unperturbed even in 1:1000-fold ligand excess. This result proves that the C-type EPR spectrum observed at large ligand concentration should be ascribed to the low temperature at which EPR measurements are performed, which impacts on the structure of the protein when it is destabilized by a high concentration of a chaotropic agent.
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Affiliation(s)
- José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Ana Luísa Carvalho
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal; Coimbra Chemistry Center- Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy; Giotto Biotech, S.R.L, Sesto Fiorentino, Florence 50019, Italy.
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7
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Zhu W, Yang DT, Gronenborn AM. Ligand-Capped Cobalt(II) Multiplies the Value of the Double-Histidine Motif for PCS NMR Studies. J Am Chem Soc 2023; 145:4564-4569. [PMID: 36786809 PMCID: PMC10032564 DOI: 10.1021/jacs.2c12021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In structural studies by NMR, pseudocontact shifts (PCSs) provide both angular and distance information. For proteins, incorporation of a di-histidine (diHis) motif, coordinated to Co2+, has emerged as an important tool to measure PCS. Here, we show that using different Co(II)-chelating ligands, such as nitrilotriacetic acid (NTA) and iminodiacetic acid (IDA), resolves the isosurface ambiguity of Co2+-diHis and yields orthogonal PCS data sets with different Δχ-tensors for the same diHis-bearing protein. Importantly, such capping ligands effectively eliminate undesired intermolecular interactions, which can be detrimental to PCS studies. Devising and employing ligand-capping strategies afford versatile and powerful means to obtain multiple orthogonal PCS data sets, significantly extending the use of the diHis motif for structural studies by NMR.
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Affiliation(s)
- Wenkai Zhu
- Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Darian T Yang
- Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department of Chemistry, University of Pittsburgh, Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department of Chemistry, University of Pittsburgh, Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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8
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Dal Colle MCS, Fittolani G, Delbianco M. Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans. Chembiochem 2022; 23:e202200416. [PMID: 36005282 PMCID: PMC10087674 DOI: 10.1002/cbic.202200416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Indexed: 01/25/2023]
Abstract
NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., 13 C or 19 F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.
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Affiliation(s)
- Marlene C S Dal Colle
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
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9
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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10
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Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:169-182. [PMID: 37904871 PMCID: PMC10539774 DOI: 10.5194/mr-3-169-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2023]
Abstract
The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 + ions.
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Affiliation(s)
| | - Mithun C. Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael J. Maxwell
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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11
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Su X, Zhang L, Zhao L, Pan B, Chen B, Chen J, Zhai C, Li B. Efficient Protein–Protein Couplings Mediated by Small Molecules under Mild Conditions. Angew Chem Int Ed Engl 2022; 61:e202205597. [DOI: 10.1002/anie.202205597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Xun‐Cheng Su
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Ling‐Yang Zhang
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Li‐Na Zhao
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Bin‐Bin Pan
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Ben‐Guang Chen
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Jia‐Liang Chen
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Cheng‐Liang Zhai
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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12
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Chen JL, Li B, Ma B, Su XC. Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag. JOURNAL OF BIOMOLECULAR NMR 2022; 76:107-119. [PMID: 35841475 DOI: 10.1007/s10858-022-00399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Flexibility between the paramagnetic tag and its protein conjugates is a common yet unresolved issue in the applications of paramagnetic NMR spectroscopy in biological systems. The flexibility greatly attenuates the magnetic anisotropy and compromises paramagnetic effects especially for pseudocontact shift and residual dipolar couplings. Great efforts have been made to improve the rigidity of paramagnetic tag in the protein conjugates, however, the effect of local environment vicinal to the protein ligation site on the paramagnetic effects remains poorly understood. In the present work, the stereospecific effect of chiral tether between the protein and a tag on the paramagnetic effects produced by the tag attached via a D- and L-type linker between the protein and paramagnetic metal chelating moiety was assessed. The remarkable chiral effect of the D- and L-type tether between the tag and the protein on the rigidity of paramagnetic tag is disclosed in a number of protein-tag-Ln complexes. The chiral tether formed between the D-type tag and L-type protein surface minimizes the effect of the local environment surrounding the ligation site on the averaging of paramagnetic tag, which is helpful to preserve the rigidity of a paramagnetic tag in the protein conjugates.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bo Ma
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.
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13
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Li X, Jiang F, Liu M, Qu Y, Lan Z, Dai X, Huang C, Yue X, Zhao S, Pan X, Zhang C. Synthesis, Characterization, and Bioactivities of Polysaccharide Metal Complexes: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6922-6942. [PMID: 35639848 DOI: 10.1021/acs.jafc.2c01349] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Natural polysaccharides are critical to a wide range of fields (e.g., medicine, food production, and cosmetics) for their various remarkable physical properties and biological activities. However, the bioactivities of naturally acquired polysaccharides may be unsatisfactory and limit their further applications. It is generally known that the chemical structure exhibited by polysaccharides lays the material basis for their biological activities. Accordingly, possible structural modifications should be conducted on polysaccharides for their enhancement. Recently, polysaccharides complexed with metal ions (e.g., Fe, Zn, Mg, Cr, and Pt) have been reported to be possibly used to improve their bioactivities. Moreover, since the properties exhibited by metal ions are normally conserved, polysaccharides may be endowed with new applications. In this review, the synthesis methods, characterization methods, and bioactivities of polysaccharide metal complexes are summarized specifically. Then, the application prospects and limitations of these complexes are analyzed and discussed.
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Affiliation(s)
- Xuebo Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Fuchen Jiang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Meiyan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Yan Qu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Zhiqiong Lan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Xiaolin Dai
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Chi Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Xuan Yue
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Shiyi Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Xiaoli Pan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
| | - Chen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, P. R. China
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14
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Su XC, Zhang LY, Zhao LN, Pan BB, Chen BG, Chen JL, Zhai CL, Li B. Efficient Protein‐Protein Couplings Mediated by Small Molecules under Mild Conditions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xun-Cheng Su
- Nankai University College of Chemistry Stat Key Laboratory of Elemento-organic Chemistry Weijing Road 94 300071 Tianjin CHINA
| | | | - Li-Na Zhao
- Nankai University college of chemistry CHINA
| | - Bin-Bin Pan
- Nankai University college of chemistry CHINA
| | | | | | | | - Bin Li
- Nankai University college of chemistry CHINA
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15
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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16
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Orton HW, Abdelkader EH, Topping L, Butler SJ, Otting G. Localising nuclear spins by pseudocontact shifts from a single tagging site. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:65-76. [PMID: 37905181 PMCID: PMC10539793 DOI: 10.5194/mr-3-65-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/18/2022] [Indexed: 11/01/2023]
Abstract
Ligating a protein at a specific site with a tag molecule containing a paramagnetic metal ion provides a versatile way of generating pseudocontact shifts (PCSs) in nuclear magnetic resonance (NMR) spectra. PCSs can be observed for nuclear spins far from the tagging site, and PCSs generated from multiple tagging sites have been shown to enable highly accurate structure determinations at specific sites of interest, even when using flexible tags, provided the fitted effective magnetic susceptibility anisotropy (Δ χ ) tensors accurately back-calculate the experimental PCSs measured in the immediate vicinity of the site of interest. The present work investigates the situation where only the local structure of a protein region or bound ligand is to be determined rather than the structure of the entire molecular system. In this case, the need for gathering structural information from tags deployed at multiple sites may be queried. Our study presents a computational simulation of the structural information available from samples produced with single tags attached at up to six different sites, up to six different tags attached to a single site, and in-between scenarios. The results indicate that the number of tags is more important than the number of tagging sites. This has important practical implications, as it is much easier to identify a single site that is suitable for tagging than multiple ones. In an initial experimental demonstration with the ubiquitin mutant S57C, PCSs generated with four different tags at a single site are shown to accurately pinpoint the location of amide protons in different segments of the protein.
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Affiliation(s)
- Henry W Orton
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Lydia Topping
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Stephen J Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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17
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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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18
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Amrutha K, Kathirvelu V. Interpretation of EPR and optical spectra of Ni(II) ions in crystalline lattices at ambient temperature. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:414-421. [PMID: 34859492 DOI: 10.1002/mrc.5237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Many biologically important paramagnetic metal ions are characterized by electron paramagnetic resonance (EPR) spectroscopy to use as spin probes to investigate the structure and function of biomolecules. Though nickel(II) ions are an essential trace element and part of many biomolecules, the EPR properties are least understood. Herein, the EPR and optical absorption spectra measured at 300 K for Ni(II) ions diluted in two different diamagnetic hosts are investigated and reported. The EPR spectrum of a polycrystalline Ni/Mg(3-methylpyrazole)6 (ClO4 )2 [Ni/MMPC] shows two transitions at X-band frequency (~9.5 GHz), suggesting the zero-field splitting parameter (D) is larger than the resonance field of the free electron (Ho ). This incomplete and complex spectrum is successfully analyzed to obtain EPR parameters. The EPR spectrum of the polycrystalline Ni/Zn(pyrazole)6 (NO3 )2 [Ni/ZPN] shows a triplet spectrum indicating D < Ho . A detailed analysis of single-crystal EPR data yielded the spin Hamiltonian parameters. The optical absorption spectra are deconvoluted to understand the symmetry of the coordination environment in the complex.
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Affiliation(s)
- Kamalon Amrutha
- Department of Applied Sciences, National Institute of Technology Goa, Ponda, India
| | - Velavan Kathirvelu
- Department of Applied Sciences, National Institute of Technology Goa, Ponda, India
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19
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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20
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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21
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Ma B, Chen JL, Cui CY, Yang F, Gong YJ, Su XC. Rigid, Highly Reactive and Stable DOTA-like Tags Containing a Thiol-Specific Phenylsulfonyl Pyridine Moiety for Protein Modification and NMR Analysis*. Chemistry 2021; 27:16145-16152. [PMID: 34595784 DOI: 10.1002/chem.202102495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 11/06/2022]
Abstract
Site specific installation of a paramagnetic ion with magnetic anisotropy in a biomolecule generates valuable structural restraints, such as pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs). These paramagnetic effects can be used to characterize the structures, interactions and dynamics of biological macromolecules and their complexes. Two single-armed DOTA-like tags, BrPSPy-DO3M(S)A-Ln and BrPSPy-6M-DO3M(S)A-Ln, each containing a thiol-specific reacting group, that is, a phenylsulfonyl pyridine moiety, are demonstrated as rigid, reactive and stable paramagnetic tags for protein modification by formation of a reducing resistant thioether bond between the protein and the tag. The two tags present high reactivity with the solvent exposed thiol group in aqueous solution at room temperature. The introduction of Br at the meta-position in pyridine enhances the reactivity of 4-phenylsulfonyl pyridine towards the solvent exposed thiol group in a protein, whereas the ortho-methyl group in pyridine increases the rigidity of the tag in the protein conjugates. The high performance of these two tags has been demonstrated in different cysteine mutants of ubiquitin and GB1. The high reactivity and rigidity of these two tags can be added in the toolbox of paramagnetic tags suitable for the high-resolution NMR measurements of biological macromolecules and their complexes.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
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22
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Herath ID, Breen C, Hewitt SH, Berki TR, Kassir AF, Dodson C, Judd M, Jabar S, Cox N, Otting G, Butler SJ. A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time-Resolved Luminescence Studies. Chemistry 2021; 27:13009-13023. [PMID: 34152643 PMCID: PMC8518945 DOI: 10.1002/chem.202101143] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A lanthanide-binding tag site-specifically attached to a protein presents a tool to probe the protein by multiple spectroscopic techniques, including nuclear magnetic resonance, electron paramagnetic resonance and time-resolved luminescence spectroscopy. Here a new stable chiral LnIII tag, referred to as C12, is presented for spontaneous and quantitative reaction with a cysteine residue to generate a stable thioether bond. The synthetic protocol of the tag is relatively straightforward, and the tag is stable for storage and shipping. It displays greatly enhanced reactivity towards selenocysteine, opening a route towards selective tagging of selenocysteine in proteins containing cysteine residues. Loaded with TbIII or TmIII ions, the C12 tag readily generates pseudocontact shifts (PCS) in protein NMR spectra. It produces a relatively rigid tether between lanthanide and protein, which is beneficial for interpretation of the PCSs by single magnetic susceptibility anisotropy tensors, and it is suitable for measuring distance distributions in double electron-electron resonance experiments. Upon reaction with cysteine or other thiol compounds, the TbIII complex exhibits a 100-fold enhancement in luminescence quantum yield, affording a highly sensitive turn-on luminescence probe for time-resolved FRET assays and enzyme reaction monitoring.
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Affiliation(s)
- Iresha D. Herath
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Colum Breen
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Sarah H. Hewitt
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Thomas R. Berki
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Ahmad F. Kassir
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Charlotte Dodson
- Department of Pharmacy & PharmacologyUniversity of Bath Claverton DownBathBA2 7AYUK
| | - Martyna Judd
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Shereen Jabar
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Nicholas Cox
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Gottfried Otting
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Stephen J. Butler
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
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23
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Hou XN, Sekiyama N, Ohtani Y, Yang F, Miyanoiri Y, Akagi KI, Su XC, Tochio H. Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins. Chemphyschem 2021; 22:1505-1517. [PMID: 33928740 DOI: 10.1002/cphc.202100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Indexed: 11/06/2022]
Abstract
Linear polyubiquitin chains regulate diverse signaling proteins, in which the chains adopt various conformations to recognize different target proteins. Thus, the structural plasticity of the chains plays an important role in controlling the binding events. Herein, paramagnetic NMR spectroscopy is employed to explore the conformational space sampled by linear diubiquitin, a minimal unit of linear polyubiquitin, in its free state. Rigorous analysis of the data suggests that, regarding the relative positions of the ubiquitin units, particular regions of conformational space are preferentially sampled by the molecule. By combining these results with further data collected for charge-reversal derivatives of linear diubiquitin, structural insights into the factors underlying the binding events of linear diubiquitin are obtained.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yasuko Ohtani
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ken-Ichi Akagi
- NIBIOHN, Section of Laboratory Equipment, Osaka, 567-0085, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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24
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Chen JL, Chen BG, Li B, Yang F, Su XC. Assessing multiple conformations of lanthanide binding tags for proteins using a sensitive 19F-reporter. Chem Commun (Camb) 2021; 57:4291-4294. [PMID: 33913982 DOI: 10.1039/d1cc00791b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantifying the isomeric species of metal complexes in solution is difficult. 19F NMR herein was used to determine the abundance of isomeric species and dynamic properties of lanthanide binding tags. The results suggest that 19F is an efficient reporter in assessing and screening paramagnetic tags suitable for protein NMR analysis.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Ben-Guang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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25
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Gauto D, Dakhlaoui O, Marin-Montesinos I, Hediger S, De Paëpe G. Targeted DNP for biomolecular solid-state NMR. Chem Sci 2021; 12:6223-6237. [PMID: 34084422 PMCID: PMC8115112 DOI: 10.1039/d0sc06959k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022] Open
Abstract
High-field dynamic nuclear polarization is revolutionizing the scope of solid-state NMR with new applications in surface chemistry, materials science and structural biology. In this perspective article, we focus on a specific DNP approach, called targeted DNP, in which the paramagnets introduced to polarize are not uniformly distributed in the sample but site-specifically located on the biomolecular system. After reviewing the various targeting strategies reported to date, including a bio-orthogonal chemistry-based approach, we discuss the potential of targeted DNP to improve the overall NMR sensitivity while avoiding the use of glass-forming DNP matrix. This is especially relevant to the study of diluted biomolecular systems such as, for instance, membrane proteins within their lipidic environment. We also discuss routes towards extracting structural information from paramagnetic relaxation enhancement (PRE) induced by targeted DNP at cryogenic temperature, and the possibility to recover site-specific information in the vicinity of the paramagnetic moieties using high-resolution selective DNP spectra. Finally, we review the potential of targeted DNP for in-cell NMR studies and how it can be used to extract a given protein NMR signal from a complex cellular background.
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Affiliation(s)
- Diego Gauto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- Univ. Grenoble Alpes, CNRS, CERMAV Grenoble France
| | - Ildefonso Marin-Montesinos
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- University of Aveiro, CICECO Chem. Dept. Aveiro Portugal
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
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26
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Ma DL, Wu C, Liu H, Wu KJ, Leung CH. Luminescence approaches for the rapid detection of disease-related receptor proteins using transition metal-based probes. J Mater Chem B 2021; 8:3249-3260. [PMID: 31647090 DOI: 10.1039/c9tb01889a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein biomarkers, particularly abnormally expressed receptor proteins, have been proved to be one of the crucial biomarkers for the rapid assessment, diagnosis, prognosis and prediction of specific human diseases. Transition metal based strategies in particular possess delightful strengths in the in-field and real-time visualization of receptor proteins owing to their unique photophysical properties. In this review, we highlight recent advances in the development of detection methods for receptor protein biomarkers using transition metal based approaches, particularly those employing transition metal complexes. We first discuss the strengths and weaknesses of various strategies used for protein biomarker monitoring in live cells. We then describe the principles of the various sensing platforms and their application for receptor protein detection. Finally, we discuss the challenges and future inspirations in this specific field.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR 999077, China.
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27
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Wu L, Zhou M, Liu C, Chen X, Chen Y. Double-enzymes-mediated Fe 2+/Fe 3+ conversion as magnetic relaxation switch for pesticide residues sensing. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123619. [PMID: 32827859 DOI: 10.1016/j.jhazmat.2020.123619] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 05/25/2023]
Abstract
It is a great challenge to develop a newly rapid and accurate detection method for pesticide residues. In this work, based on acetylcholinesterase (AChE) and choline oxidase (CHO), a double-enzymes-mediated Fe2+/Fe3+ conversion as magnetic relaxation switch was explored for the measurement of acetamiprid residue. In the double-enzymes reactions, acetylcholine chloride (ACh) can be catalyzed to produce choline by AChE, which is successively hydrolyzed to betaine and hydrogen peroxide (H2O2) by CHO. According to the enzyme inhibition principle, AChE activity will be inactivated in the presence of acetamiprid, thus leading to the less production of H2O2. Wherein, Fe2+, ACh, AChE and CHO were optimized as the reaction substrates. In the reaction system, acetamiprid can be reflected by the transverse relaxation time (T2) that related with H2O2 mediated Fe2+ variations, which was further developed as an enzyme cascade amplification method. The detection linear range is 0.01∼1000 μg mL-1 (R2 = 0.99), and the limit of detection (LOD) is 2.66 ng mL-1 (S/N = 3, n = 3), behaving a 335-fold improvement in LOD than that of traditional enzyme inhibition method (0.89 μg mL-1). This method can realize "one-step mixing" detection of acetamiprid, which makes it a promising analytical tool for monitoring pesticide residue in complicated samples.
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Affiliation(s)
- Long Wu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), College of Bioengineering and Food, Hubei University of Technology, Wuhan, Hubei, 430068, PR China
| | - Min Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), College of Bioengineering and Food, Hubei University of Technology, Wuhan, Hubei, 430068, PR China
| | - Chen Liu
- Leibniz Institute of Photonic Technology, Jena-Member of the research alliance Leibniz Health Technologies, Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Albert-Einstein-Street 9, 07745, Jena, Germany; Leibniz Institute of Photonic Technology Jena - Member of the research alliance, Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745, Jena, Germany
| | - Xiaoqiang Chen
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), College of Bioengineering and Food, Hubei University of Technology, Wuhan, Hubei, 430068, PR China.
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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28
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Mekkattu Tharayil S, Mahawaththa M, Loh CT, Adekoya I, Otting G. Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:1-13. [PMID: 37904776 PMCID: PMC10539748 DOI: 10.5194/mr-2-1-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/12/2020] [Indexed: 11/01/2023]
Abstract
Pseudocontact shifts (PCSs) generated by paramagnetic lanthanide ions provide valuable long-range structural information in nuclear magnetic resonance (NMR) spectroscopic analyses of biological macromolecules such as proteins, but labelling proteins site-specifically with a single lanthanide ion remains an ongoing challenge, especially for proteins that are not suitable for ligation with cysteine-reactive lanthanide complexes. We show that a specific lanthanide-binding site can be installed on proteins by incorporation of phosphoserine in conjunction with other negatively charged residues, such as aspartate, glutamate or a second phosphoserine residue. The close proximity of the binding sites to the protein backbone leads to good immobilization of the lanthanide ion, as evidenced by the excellent quality of fits between experimental PCSs and PCSs calculated with a single magnetic susceptibility anisotropy (Δ χ ) tensor. An improved two-plasmid system was designed to enhance the yields of proteins with genetically encoded phosphoserine, and good lanthanide ion affinities were obtained when the side chains of the phosphoserine and aspartate residues are not engaged in salt bridges, although the presence of too many negatively charged residues in close proximity can also lead to unfolding of the protein. In view of the quality of the Δ χ tensors that can be obtained from lanthanide-binding sites generated by site-specific incorporation of phosphoserine, this method presents an attractive tool for generating PCSs in stable proteins, particularly as it is independent of cysteine residues.
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Affiliation(s)
- Sreelakshmi Mekkattu Tharayil
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Mithun Chamikara Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Choy-Theng Loh
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
- present address: Hangzhou Wayland Bioscience Co. Ltd, Hangzhou
310030, PR China
| | - Ibidolapo Adekoya
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
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29
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Collauto A, Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Sören Bülow
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Dnyaneshwar B. Gophane
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Subham Saha
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Lukas S. Stelzl
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
- Institute for Biophysics Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Snorri T. Sigurdsson
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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30
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Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell*. Angew Chem Int Ed Engl 2020; 59:23025-23029. [PMID: 32804430 PMCID: PMC7756485 DOI: 10.1002/anie.202009800] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/15/2022]
Abstract
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus laevis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
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Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
| | - Sören von Bülow
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Subham Saha
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
- Institute for BiophysicsGoethe University FrankfurtMax-von-Laue-Str. 960438Frankfurt am MainGermany
| | - Snorri T. Sigurdsson
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
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31
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Wang Y, An L, Yang Y, Yao L. Generating Five Independent Molecular Alignments for Simultaneous Protein Structure and Dynamics Determination Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2020; 92:15263-15269. [PMID: 33166130 DOI: 10.1021/acs.analchem.0c02882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are commonly used in NMR for protein structure and dynamics studies, but it is challenging to generate five independent RDC data sets (required for simultaneous structure and dynamics determination) for most protein molecules in the magnetic field. In this work, a reporter protein with a lanthanide tag is introduced to create five independent alignments. This reporter protein is then attached to target proteins where five independent sets of RDCs are also obtained for the target proteins. The fitting of RDCs provides important information about the structure and dynamics of the target proteins. The method is simple and effective and, in principle, can be used to generate complete sets of RDCs for different protein molecules.
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Affiliation(s)
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing 100049, China
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32
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Chai Z, Wu Q, Cheng K, Liu X, Jiang L, Liu M, Li C. Simultaneous detection of small molecule thiols with a simple 19F NMR platform. Chem Sci 2020; 12:1095-1100. [PMID: 34163876 PMCID: PMC8179020 DOI: 10.1039/d0sc04664g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Thiols play critical roles in regulating biological functions and have wide applications in pharmaceutical and biomedical industries. However, we still lack a general approach for the simultaneous detection of various thiols, especially in complex systems. Herein, we establish a 19F NMR platform where thiols are selectively fused into a novelly designed fluorinated receptor that has two sets of environmentally different 19F atoms with fast kinetics (k 2 = 0.73 mM-1 min-1), allowing us to generate unique two-dimensional codes for about 20 thiols. We demonstrate the feasibility of the approach by reliably quantifying thiol drug content in tablets, discriminating thiols in living cells, and for the first time monitoring the thiol related metabolism pathway at the atomic level. Moreover, the method can be easily extended to detect the activity of thiol related enzymes such as γ-glutamyl transpeptidase. We envision that the versatile platform will be a useful tool for detecting thiols and elucidating thiol-related processes in complex systems.
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Affiliation(s)
- Zhaofei Chai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 China
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 China .,Graduate University of Chinese Academy of Sciences Beijing 100049 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 China
| | - Xiaoli 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 China .,Graduate University of Chinese Academy of Sciences Beijing 100049 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 China .,Graduate University of Chinese Academy of Sciences Beijing 100049 China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences Wuhan 430071 China .,Graduate University of Chinese Academy of Sciences Beijing 100049 China
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33
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Chen JL, Li B, Li XY, Su XC. Dynamic Exchange of the Metal Chelating Moiety: A Key Factor in Determining the Rigidity of Protein-Tag Conjugates in Paramagnetic NMR. J Phys Chem Lett 2020; 11:9493-9500. [PMID: 33108729 DOI: 10.1021/acs.jpclett.0c02196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Site-specific labeling of proteins with a paramagnetic tag is an efficient way to provide atomic-resolution information about the dynamics, interactions, and structures of the proteins and protein-ligand complexes. The paramagnetic effects manifested in NMR spectroscopy generally contain paramagnetic relaxation enhancement, pseudocontact shifts (PCSs), and residual dipolar coupling (RDC), and these effects correlate closely with the flexibility of protein-tag conjugates. The rigidity of the paramagnetic tag is greatly important in decoding the structural details of macromolecular complexes, because paramagnetic averaging reduces the PCSs and RDCs. Here we show that the dynamic exchange of the metal chelating moiety is a key factor in determining the rigidity of the paramagnetic tag in the protein conjugates. Decreasing the conformational exchange rates in the metal chelating moiety greatly minimizes the paramagnetic averaging and thus increases PCSs and RDCs. This effect has been demonstrated in an open-chain tag, Py-l-Cys-DTPA, which generates large PCSs and RDCs that are comparable to those of the reported cyclic DOTA-like tags. The proposed route offers a unique way to design suitable paramagnetic tags for applications in biological systems.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xia-Yan Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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34
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Lehr M, Paschelke T, Trumpf E, Vogt A, Näther C, Sönnichsen FD, McConnell AJ. A Paramagnetic NMR Spectroscopy Toolbox for the Characterisation of Paramagnetic/Spin-Crossover Coordination Complexes and Metal-Organic Cages. Angew Chem Int Ed Engl 2020; 59:19344-19351. [PMID: 33448544 PMCID: PMC7590057 DOI: 10.1002/anie.202008439] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Indexed: 12/14/2022]
Abstract
The large paramagnetic shifts and short relaxation times resulting from the presence of a paramagnetic centre complicate NMR data acquisition and interpretation in solution. As a result, NMR analysis of paramagnetic complexes is limited in comparison to diamagnetic compounds and often relies on theoretical models. We report a toolbox of 1D (1H, proton-coupled 13C, selective 1H-decoupling 13C, steady-state NOE) and 2D (COSY, NOESY, HMQC) paramagnetic NMR methods that enables unprecedented structural characterisation and in some cases, provides more structural information than would be observable for a diamagnetic analogue. We demonstrate the toolbox's broad versatility for fields from coordination chemistry and spin-crossover complexes to supramolecular chemistry through the characterisation of CoII and high-spin FeII mononuclear complexes as well as a Co4L6 cage.
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Affiliation(s)
- Marc Lehr
- Otto Diels Institute of Organic ChemistryChristian-Albrechts-Universität zu KielOtto-Hahn-Platz 4Kiel24098Germany
| | - Tobias Paschelke
- Otto Diels Institute of Organic ChemistryChristian-Albrechts-Universität zu KielOtto-Hahn-Platz 4Kiel24098Germany
| | - Eicke Trumpf
- Otto Diels Institute of Organic ChemistryChristian-Albrechts-Universität zu KielOtto-Hahn-Platz 4Kiel24098Germany
| | - Anna‐Marlene Vogt
- Otto Diels Institute of Organic ChemistryChristian-Albrechts-Universität zu KielOtto-Hahn-Platz 4Kiel24098Germany
| | - Christian Näther
- Institute of Inorganic ChemistryChristian-Albrechts-Universität zu KielMax-Eyth-Straße 2Kiel24118Germany
| | - Frank D. Sönnichsen
- Otto Diels Institute of Organic ChemistryChristian-Albrechts-Universität zu KielOtto-Hahn-Platz 4Kiel24098Germany
| | - Anna J. McConnell
- Otto Diels Institute of Organic ChemistryChristian-Albrechts-Universität zu KielOtto-Hahn-Platz 4Kiel24098Germany
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35
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Lehr M, Paschelke T, Trumpf E, Vogt A, Näther C, Sönnichsen FD, McConnell AJ. Ein Methodenrepertoire für die paramagnetische NMR‐Spektroskopie zur Charakterisierung von paramagnetischen/Spin‐Crossover‐ Komplexen und Metall‐organischen Käfigverbindungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Marc Lehr
- Otto-Diels-Institut für Organische Chemie Christian-Albrechts-Universität zu Kiel Otto-Hahn-Platz 4 Kiel 24098 Deutschland
| | - Tobias Paschelke
- Otto-Diels-Institut für Organische Chemie Christian-Albrechts-Universität zu Kiel Otto-Hahn-Platz 4 Kiel 24098 Deutschland
| | - Eicke Trumpf
- Otto-Diels-Institut für Organische Chemie Christian-Albrechts-Universität zu Kiel Otto-Hahn-Platz 4 Kiel 24098 Deutschland
| | - Anna‐Marlene Vogt
- Otto-Diels-Institut für Organische Chemie Christian-Albrechts-Universität zu Kiel Otto-Hahn-Platz 4 Kiel 24098 Deutschland
| | - Christian Näther
- Institut für Anorganische Chemie Christian-Albrechts-Universität zu Kiel Max-Eyth-Straße 2 Kiel 24118 Deutschland
| | - Frank D. Sönnichsen
- Otto-Diels-Institut für Organische Chemie Christian-Albrechts-Universität zu Kiel Otto-Hahn-Platz 4 Kiel 24098 Deutschland
| | - Anna J. McConnell
- Otto-Diels-Institut für Organische Chemie Christian-Albrechts-Universität zu Kiel Otto-Hahn-Platz 4 Kiel 24098 Deutschland
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A water-soluble and incubate-free fluorescent environment-sensitive probe for ultrafast visualization of protein thiols within living cells. Anal Chim Acta 2020; 1126:72-81. [DOI: 10.1016/j.aca.2020.06.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/22/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022]
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Denis M, Softley C, Giuntini S, Gentili M, Ravera E, Parigi G, Fragai M, Popowicz G, Sattler M, Luchinat C, Cerofolini L, Nativi C. The Photocatalyzed Thiol-ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins. Chemphyschem 2020; 21:863-869. [PMID: 32092218 PMCID: PMC7384118 DOI: 10.1002/cphc.202000071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Indexed: 11/18/2022]
Abstract
Paramagnetic restraints have been used in biomolecular NMR for the last three decades to elucidate and refine biomolecular structures, but also to characterize protein-ligand interactions. A common technique to generate such restraints in proteins, which do not naturally contain a (paramagnetic) metal, consists in the attachment to the protein of a lanthanide-binding-tag (LBT). In order to design such LBTs, it is important to consider the efficiency and stability of the conjugation, the geometry of the complex (conformational exchanges and coordination) and the chemical inertness of the ligand. Here we describe a photo-catalyzed thiol-ene reaction for the cysteine-selective paramagnetic tagging of proteins. As a model, we designed an LBT with a vinyl-pyridine moiety which was used to attach our tag to the protein GB1 in fast and irreversible fashion. Our tag T1 yields magnetic susceptibility tensors of significant size with different lanthanides and has been characterized using NMR and relaxometry measurements.
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Affiliation(s)
- Maxime Denis
- Giotto Biotech, S.R.LVia Madonna del piano 650019Sesto Fiorentino (FI)Italy
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
| | - Charlotte Softley
- Biomolecular NMR, Department ChemieTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Stefano Giuntini
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Matteo Gentili
- Giotto Biotech, S.R.LVia Madonna del piano 650019Sesto Fiorentino (FI)Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Giacomo Parigi
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Marco Fragai
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Grzegorz Popowicz
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Michael Sattler
- Biomolecular NMR, Department ChemieTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
- Institute of Structural BiologyHelmholtz Center MunichNeuherbergGermany
| | - Claudio Luchinat
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (C.I.R.M.M.P)Via L. Sacconi 650019Sesto FIorentino (FI)Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 350019Sesto Fiorentino (FI), Italy
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Cysteine-specific protein multi-functionalization and disulfide bridging using 3-bromo-5-methylene pyrrolones. Nat Commun 2020; 11:1015. [PMID: 32081914 PMCID: PMC7035330 DOI: 10.1038/s41467-020-14757-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Many reagents have been developed for cysteine-specific protein modification. However, few of them allow for multi-functionalization of a single Cys residue and disulfide bridging bioconjugation. Herein, we report 3-bromo-5-methylene pyrrolones (3Br-5MPs) as a simple, robust, and versatile class of reagents for cysteine-specific protein modification. These compounds can be facilely synthesized via a one-pot mild reaction and they show comparable tagging efficiency but higher cysteine specificity than the maleimide counterparts. The addition of cysteine to 3Br-5MPs generates conjugates that are amenable to secondary addition by another thiol or cysteine, making 3Br-5MPs valuable for multi-functionalization of a single cysteine and disulfide bridging bioconjugation. The labeling reaction and subsequent treatments are mild enough to produce stable and active protein conjugates for biological applications. Many reagents have been developed for cysteine-specific protein modification. However, few of them allow for multi-functionalization of a single Cys residue and disulfide bridging bioconjugation. Here the authors report 3-bromo-5-methylene pyrrolones as a simple, robust and versatile class of reagents for cysteine-specific protein modification.
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Joss D, Häussinger D. Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:284-312. [PMID: 31779884 DOI: 10.1016/j.pnmrs.2019.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 05/14/2023]
Abstract
In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, CB-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.
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Affiliation(s)
- Daniel Joss
- University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
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