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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: 35] [Impact Index Per Article: 17.5] [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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2
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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: 23] [Impact Index Per Article: 11.5] [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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3
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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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Miao Q, Liu WM, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019; 58:13093-13100. [PMID: 31314159 PMCID: PMC6771572 DOI: 10.1002/anie.201906049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/15/2019] [Indexed: 01/20/2023]
Abstract
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.
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Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New, Taipei City, 24205, Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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Miao Q, Liu W, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double‐Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Wei‐Min Liu
- Department of Chemistry Fu Jen Catholic University No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205 Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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6
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Lee MD, Dennis ML, Graham B, Swarbrick JD. Short two-armed lanthanide-binding tags for paramagnetic NMR spectroscopy based on chiral 1,4,7,10-tetrakis(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane scaffolds. Chem Commun (Camb) 2018; 53:13205-13208. [PMID: 29165449 DOI: 10.1039/c7cc07961c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A new pair of enantiomeric two-armed lanthanide-binding tags have been developed for paramagnetic NMR studies of proteins. The tags produce large and significantly different paramagnetic effects to one another when bound to the same tagging site. Additionally, they are less sensitive to sample pH than our previous two-armed tag designs.
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Affiliation(s)
- Michael D Lee
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville VIC 3052, Australia.
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Welegedara AP, Yang Y, Lee MD, Swarbrick JD, Huber T, Graham B, Goldfarb D, Otting G. Double‐Arm Lanthanide Tags Deliver Narrow Gd
3+
–Gd
3+
Distance Distributions in Double Electron–Electron Resonance (DEER) Measurements. Chemistry 2017; 23:11694-11702. [DOI: 10.1002/chem.201702521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Yin Yang
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Thomas Huber
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Daniella Goldfarb
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Gottfried Otting
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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8
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Seebald LM, DeMott CM, Ranganathan S, Asare-Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M. Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR. J Inorg Biochem 2017; 170:202-208. [PMID: 28260679 PMCID: PMC5956527 DOI: 10.1016/j.jinorgbio.2017.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/16/2016] [Accepted: 02/10/2017] [Indexed: 11/16/2022]
Abstract
Paramagnetic resonance enhancement (PRE) is an NMR technique that allows studying three-dimensional structures of RNA-protein complexes in solution. RNA strands are typically spin labeled using nitroxide reagents, which provide minimal perturbation to the native structure. The current work describes an alternative approach, which is based on a Co2+-based probe that can be covalently attached to RNA in the vicinity of the protein's binding site using 'click' chemistry. Similar to nitroxide spin labels, the transition metal based probe is capable of attenuating NMR signal intensities from protein residues localized <40Å away. The extent of attenuation is related to the probe's distance, thus allowing for construction of the protein's contact surface map. This new paradigm has been applied to study binding of HIV-1 nucleocapsid protein 7, NCp7, to a model RNA pentanucleotide.
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Affiliation(s)
- Leah M Seebald
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Srivathsan Ranganathan
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Papa Nii Asare-Okai
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Anastasia Glazunova
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Alan Chen
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States
| | - Maksim Royzen
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave. Albany, NY 12222, United States.
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9
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Nitsche C, Otting G. Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 98-99:20-49. [PMID: 28283085 DOI: 10.1016/j.pnmrs.2016.11.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Christoph Nitsche
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia. http://www.rsc.anu.edu.au/~go/index.html
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10
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Lee MD, Dennis ML, Swarbrick JD, Graham B. Enantiomeric two-armed lanthanide-binding tags for complementary effects in paramagnetic NMR spectroscopy. Chem Commun (Camb) 2016; 52:7954-7. [DOI: 10.1039/c6cc02325h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new pair of two-armed lanthanide-binding tags provide distinct sets of structural restraints when attached to the same site of a protein.
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Affiliation(s)
- Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Matthew L. Dennis
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
- CSIRO Biosciences Program
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
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