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Fleck N, Heubach C, Hett T, Spicher S, Grimme S, Schiemann O. Ox-SLIM: Synthesis of and Site-Specific Labelling with a Highly Hydrophilic Trityl Spin Label. Chemistry 2021; 27:5292-5297. [PMID: 33404074 PMCID: PMC8048664 DOI: 10.1002/chem.202100013] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Indexed: 01/04/2023]
Abstract
The combination of pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) with site-directed spin labelling is a powerful tool in structural biology. Rational design of trityl-based spin labels has enabled studying biomolecular structures at room temperature and within cells. However, most current trityl spin labels suffer either from aggregation with proteins due to their hydrophobicity, or from bioconjugation groups not suitable for in-cell measurements. Therefore, we introduce here the highly hydrophilic trityl spin label Ox-SLIM. Engineered as a short-linked maleimide, it combines the most recent developments in one single molecule, as it does not aggregate with proteins, exhibits high resistance under in-cell conditions, provides a short linker, and allows for selective and efficient spin labelling via cysteines. Beyond establishing synthetic access to Ox-SLIM, its suitability as a spin label is illustrated and ultimately, highly sensitive PDS measurements are presented down to protein concentrations as low as 45 nm resolving interspin distances of up to 5.5 nm.
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Affiliation(s)
- Nico Fleck
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
| | - Caspar Heubach
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
| | - Tobias Hett
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
| | - Sebastian Spicher
- University of BonnInstitute of Physical and Theoretical ChemistryBeringstr. 453115BonnGermany
| | - Stefan Grimme
- University of BonnInstitute of Physical and Theoretical ChemistryBeringstr. 453115BonnGermany
| | - Olav Schiemann
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
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Abdullin D, Matsuoka H, Yulikov M, Fleck N, Klein C, Spicher S, Hagelueken G, Grimme S, Lützen A, Schiemann O. Pulsed EPR Dipolar Spectroscopy under the Breakdown of the High-Field Approximation: The High-Spin Iron(III) Case. Chemistry 2019; 25:8820-8828. [PMID: 31017706 DOI: 10.1002/chem.201900977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Indexed: 12/11/2022]
Abstract
Pulsed EPR dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling and thus the distance between electron-spin centers. To date, PDS measurements to metal centers were limited to ions that adhere to the high-field approximation. Here, the PDS methodology is extended to cases where the high-field approximation breaks down on the example of the high-spin Fe3+ /nitroxide spin-pair. First, the theory developed by Maryasov et al. (Appl. Magn. Reson. 2006, 30, 683-702) was adapted to derive equations for the dipolar coupling constant, which revealed that the dipolar spectrum does not only depend on the length and orientation of the interspin distance vector with respect to the applied magnetic field but also on its orientation to the effective g-tensor of the Fe3+ ion. Then, it is shown on a model system and a heme protein that a PDS method called relaxation-induced dipolar modulation enhancement (RIDME) is well-suited to measuring such spectra and that the experimentally obtained dipolar spectra are in full agreement with the derived equations. Finally, a RIDME data analysis procedure was developed, which facilitates the determination of distance and angular distributions from the RIDME data. Thus, this study enables the application of PDS to for example, the highly relevant class of high-spin Fe3+ heme proteins.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.,Current address: Graduate School of Science, Osaka City University, Osaka, Japan
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nico Fleck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Christoph Klein
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.,Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Arne Lützen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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Jassoy JJ, Meyer A, Spicher S, Wuebben C, Schiemann O. Synthesis of Nanometer Sized Bis- and Tris-trityl Model Compounds with Different Extent of Spin-Spin Coupling. Molecules 2018; 23:E682. [PMID: 29562622 PMCID: PMC6017437 DOI: 10.3390/molecules23030682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022] Open
Abstract
Tris(2,3,5,6-tetrathiaaryl)methyl radicals, so-called trityl radicals, are emerging as spin labels for distance measurements in biological systems based on Electron Paramagnetic Resonance (EPR). Here, the synthesis and characterization of rigid model systems carrying either two or three trityl moieties is reported. The monofunctionalized trityl radicals are connected to the molecular bridging scaffold via an esterification reaction employing the Mukaiyama reagent 2-chloro-methylpyridinium iodide. The bis- and tris-trityl compounds exhibit different inter-spin distances, strength of electron-electron exchange and dipolar coupling and can give rise to multi-spin effects. They are to serve as benchmark systems in comparing EPR distance measurement methods.
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Affiliation(s)
- J Jacques Jassoy
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Andreas Meyer
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany.
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Van Eps N, Altenbach C, Caro LN, Latorraca NR, Hollingsworth SA, Dror RO, Ernst OP, Hubbell WL. G i- and G s-coupled GPCRs show different modes of G-protein binding. Proc Natl Acad Sci U S A 2018; 115:2383-8. [PMID: 29463720 DOI: 10.1073/pnas.1721896115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation of G protein-coupled receptors (GPCRs) initiates conformational shifts that trigger interaction with a specific G-protein subtype from a structurally homologous set. A major unsolved problem is the mechanism by which this selectivity is achieved. Structures of GPCR–G protein complexes so far fail to reveal the origin of selectivity because they all involve one G-protein subtype (Gs). In this work, we report a structural model of the activated GPCR rhodopsin in complex with another G-protein subtype (Gi) derived from intermolecular distance mapping with DEER-EPR and refinement with modeling. Comparison of the model with structures of complexes involving Gs reveals distinct GPCR–G protein-binding modes, the differences of which suggest key features of the structural selectivity filter. More than two decades ago, the activation mechanism for the membrane-bound photoreceptor and prototypical G protein-coupled receptor (GPCR) rhodopsin was uncovered. Upon light-induced changes in ligand–receptor interaction, movement of specific transmembrane helices within the receptor opens a crevice at the cytoplasmic surface, allowing for coupling of heterotrimeric guanine nucleotide-binding proteins (G proteins). The general features of this activation mechanism are conserved across the GPCR superfamily. Nevertheless, GPCRs have selectivity for distinct G-protein family members, but the mechanism of selectivity remains elusive. Structures of GPCRs in complex with the stimulatory G protein, Gs, and an accessory nanobody to stabilize the complex have been reported, providing information on the intermolecular interactions. However, to reveal the structural selectivity filters, it will be necessary to determine GPCR–G protein structures involving other G-protein subtypes. In addition, it is important to obtain structures in the absence of a nanobody that may influence the structure. Here, we present a model for a rhodopsin–G protein complex derived from intermolecular distance constraints between the activated receptor and the inhibitory G protein, Gi, using electron paramagnetic resonance spectroscopy and spin-labeling methodologies. Molecular dynamics simulations demonstrated the overall stability of the modeled complex. In the rhodopsin–Gi complex, Gi engages rhodopsin in a manner distinct from previous GPCR–Gs structures, providing insight into specificity determinants.
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Abstract
Nanometre distance measurements by pulsed electron-electron double resonance (PELDOR) spectroscopy have become an increasingly important tool in structural biology. The theoretical underpinning of the experiment is well defined for systems containing two nitroxide spin-labels (spin pairs); however, recently experiments have been reported on homo-oligomeric membrane proteins consisting of up to eight spin-labelled monomers. We have explored the theory behind these systems by examining model systems based on multiple spins arranged in rotationally symmetric polygons. The results demonstrate that with a rising number of spins within the test molecule, increasingly strong distortions appear in distance distributions obtained from an analysis based on the simple spin pair approach. These distortions are significant over a range of system sizes and remain so even when random errors are introduced into the symmetry of the model. We present an alternative approach to the extraction of distances on such systems based on a minimisation that properly treats multi-spin correlations. We demonstrate the utility of this approach on a spin-labelled mutant of the heptameric Mechanosensitive Channel of Small Conductance of E. coli.
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Affiliation(s)
- Angeliki Giannoulis
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Richard Ward
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Emma Branigan
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, Scotland, UK
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Abstract
The growing recognition of the many roles that disordered protein states play in biology places an increasing importance on developing approaches to characterize the structural properties of this class of proteins and to clarify the links between these properties and the associated biological functions. Disordered proteins, when isolated in solution, do not adopt a fixed structure, but can and often do contain detectable and significant residual or transient structure, including both secondary and long-range structure. Such residual structure can play a role in nucleating local structural transitions as well as modulating intramolecular or intermolecular tertiary interactions, including those involved in ordered protein aggregation. An increasing array of tools has been recruited to help characterize the structural properties of disordered proteins. While a number of methods can report on residual secondary structure, detecting and quantifying transient long-range structure has proven to be more difficult. This chapter describes the use of paramagnetic spin labeling in combination with paramagnetic relaxation enhancement (PRE) in NMR spectroscopy and pulsed dipolar ESR spectroscopy (PDS) for this purpose.
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Affiliation(s)
- David Eliezer
- Department of Biochemistry and Program in Structural Biology, Weill Cornell Medical College, New York, NY, USA.
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