1
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Wieneke R, Tampé R. Multivalent Chelators for In Vivo Protein Labeling. Angew Chem Int Ed Engl 2019; 58:8278-8290. [PMID: 30919542 DOI: 10.1002/anie.201811293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 01/09/2023]
Abstract
With the advent of single-molecule methods, chemoselective and site-specific labeling of proteins evolved to become a central aspect in chemical biology as well as cell biology. Protein labeling demands high specificity, rapid as well as efficient conjugation, while maintaining low concentration and biocompatibility under physiological conditions. Generic methods that do not interfere with the function, dynamics, subcellular localization of proteins, and crosstalk with other factors are crucial to probe and image proteins in vitro and in living cells. Alternatives to enzyme-based tags or autofluorescent proteins are short peptide-based recognition tags. These tags provide high specificity, enhanced binding rates, bioorthogonality, and versatility. Here, we report on recent applications of multivalent chelator heads, recognizing oligohistidine-tagged proteins. The striking features of this system has facilitated the analysis of protein complexes by single-molecule approaches.
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Affiliation(s)
- Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M., Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M., Germany
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2
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Wieneke R, Tampé R. Multivalent Chelators for In Vivo Protein Labeling. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ralph Wieneke
- Institute of BiochemistryBiocenterGoethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt/M. Germany
| | - Robert Tampé
- Institute of BiochemistryBiocenterGoethe University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt/M. Germany
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3
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Braun T, Drescher M, Summerer D. Expanding the Genetic Code for Site-Directed Spin-Labeling. Int J Mol Sci 2019; 20:ijms20020373. [PMID: 30654584 PMCID: PMC6359334 DOI: 10.3390/ijms20020373] [Citation(s) in RCA: 24] [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: 12/19/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 02/04/2023] Open
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy enables studies of the structure, dynamics, and interactions of proteins in the noncrystalline state. The scope and analytical value of SDSL⁻EPR experiments crucially depends on the employed labeling strategy, with key aspects being labeling chemoselectivity and biocompatibility, as well as stability and spectroscopic properties of the resulting label. The use of genetically encoded noncanonical amino acids (ncAA) is an emerging strategy for SDSL that holds great promise for providing excellent chemoselectivity and potential for experiments in complex biological environments such as living cells. We here give a focused overview of recent advancements in this field and discuss their potentials and challenges for advancing SDSL⁻EPR studies.
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Affiliation(s)
- Theresa Braun
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany.
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4
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Giannoulis A, Yang Y, Gong YJ, Tan X, Feintuch A, Carmieli R, Bahrenberg T, Liu Y, Su XC, Goldfarb D. DEER distance measurements on trityl/trityl and Gd(iii)/trityl labelled proteins. Phys Chem Chem Phys 2019; 21:10217-10227. [DOI: 10.1039/c8cp07249c] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Trityl–trityl and trityl–Gd(iii) DEER distance measurements in proteins are performed using a new trityl spin label affording thioether–protein conjugation.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yin Yang
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
- China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics
- School of Pharmacy
- Tianjin Medical University
- Tianjin 300070
- China
| | - Akiva Feintuch
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Raanan Carmieli
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics
- School of Pharmacy
- Tianjin Medical University
- Tianjin 300070
- China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
- China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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5
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Application of Lysine-specific Labeling to Detect Transient Interactions Present During Human Lysozyme Amyloid Fibril Formation. Sci Rep 2017; 7:15018. [PMID: 29101328 PMCID: PMC5670245 DOI: 10.1038/s41598-017-14739-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/16/2017] [Indexed: 11/08/2022] Open
Abstract
Populating transient and partially unfolded species is a crucial step in the formation and accumulation of amyloid fibrils formed from pathogenic variants of human lysozyme linked with a rare but fatal hereditary systemic amyloidosis. The partially unfolded species possess an unstructured β-domain and C-helix with the rest of the α-domain remaining native-like. Here we use paramagnetic relaxation enhancement (PRE) measured by NMR spectroscopy to study the transient intermolecular interactions between such intermediate species. Nitroxide spin labels, introduced specifically at three individual lysine residues, generate distinct PRE profiles, indicating the presence of intermolecular interactions between residues within the unfolded β-domain. This study describes the applicability to PRE NMR measurements of selective lysine labeling, at different sites within a protein, as an alternative to the introduction of spin labels via engineered cysteine residues. These results reveal the importance of the β-sheet region of lysozyme for initiating self-assembly into amyloid fibrils.
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6
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Kankate L, Aguf A, Großmann H, Schnietz M, Tampé R, Turchanin A, Gölzhäuser A. Vapor Phase Exchange of Self-Assembled Monolayers for Engineering of Biofunctional Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3847-3854. [PMID: 28340533 DOI: 10.1021/acs.langmuir.6b04207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We show that 4'-nitro-1,1'-biphenyl-4-thiol self-assembled monolayers (NBPT SAMs) on gold can be exchanged with 11-(mercaptoundecyl)triethylene glycol (C11EG3OH) SAMs via vapor deposition (VD). The pristine and the exchanged SAMs obtained by VD as well as solution method (SM) were characterized by X-ray photoelectron spectroscopy (XPS) and polarization modulation infrared reflection-absorption spectroscopy (PM-IRRAS). Using surface plasmon resonance (SPR), it is shown that C11EG3OH SAMs on gold obtained by vapor deposition exchange (VDEx) have the same protein resistivity as SAMs obtained by the direct self-assembly process. As expected, the cross-linked NBPT SAM are found to be resistive to both exchange processes, VDEx and solution method exchange (SMEx). In this way, VDEx opens up an elegant and new approach of patterning SAM surfaces in situ at vacuum conditions without using any solvents. By combining electron irradiation-induced chemical lithography of NBPT SAMs with VDEx, biofunctional patterned substrates were engineered and used for immobilization of protein arrays.
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Affiliation(s)
- L Kankate
- Department of Physics, Physics of Supramolecular Systems and Surfaces, University of Bielefeld , 33615 Bielefeld, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - A Aguf
- Department of Physics, Physics of Supramolecular Systems and Surfaces, University of Bielefeld , 33615 Bielefeld, Germany
| | - H Großmann
- Institute of Biochemistry, Biocenter, Goethe-University , 60438 Frankfurt, Germany
| | - M Schnietz
- Department of Physics, Physics of Supramolecular Systems and Surfaces, University of Bielefeld , 33615 Bielefeld, Germany
| | - R Tampé
- Institute of Biochemistry, Biocenter, Goethe-University , 60438 Frankfurt, Germany
| | - A Turchanin
- Institute of Physical Chemistry, Friedrich Schiller University Jena , Lessingstr. 10, 07743 Jena, Germany
| | - A Gölzhäuser
- Department of Physics, Physics of Supramolecular Systems and Surfaces, University of Bielefeld , 33615 Bielefeld, Germany
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7
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Ching HYV, Mascali FC, Bertrand HC, Bruch EM, Demay-Drouhard P, Rasia RM, Policar C, Tabares LC, Un S. The Use of Mn(II) Bound to His-tags as Genetically Encodable Spin-Label for Nanometric Distance Determination in Proteins. J Phys Chem Lett 2016; 7:1072-1076. [PMID: 26938795 DOI: 10.1021/acs.jpclett.6b00362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A genetically encodable paramagnetic spin-label capable of self-assembly from naturally available components would offer a means for studying the in-cell structure and interactions of a protein by electron paramagnetic resonance (EPR). Here, we demonstrate pulse electron-electron double resonance (DEER) measurements on spin-labels consisting of Mn(II) ions coordinated to a sequence of histidines, so-called His-tags, that are ubiquitously added by genetic engineering to facilitate protein purification. Although the affinity of His-tags for Mn(II) was low (800 μM), Mn(II)-bound His-tags yielded readily detectable DEER time traces even at concentrations expected in cells. We were able to determine accurately the distance between two His-tag Mn(II) spin-labels at the ends of a rigid helical polyproline peptide of known structure, as well as at the ends of a completely cell-synthesized 3-helix bundle. This approach not only greatly simplifies the labeling procedure but also represents a first step towards using self-assembling metal spin-labels for in-cell distance measurements.
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Affiliation(s)
- H Y Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
| | - Florencia C Mascali
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , 2000 Rosario, Argentina
| | - Hélène C Bertrand
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7203 LBM , F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
| | - Eduardo M Bruch
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7203 LBM , F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
| | - Rodolfo M Rasia
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , 2000 Rosario, Argentina
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7203 LBM , F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
| | - Leandro C Tabares
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
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8
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Roser P, Schmidt MJ, Drescher M, Summerer D. Site-directed spin labeling of proteins for distance measurements in vitro and in cells. Org Biomol Chem 2016; 14:5468-76. [DOI: 10.1039/c6ob00473c] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We here review strategies for site-directed spin labeling (SDSL) of proteins and discuss their potential for EPR distance measurements to study protein function in vitro and in cells.
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Affiliation(s)
- P. Roser
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - M. J. Schmidt
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - M. Drescher
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - D. Summerer
- Department of Chemistry and Chemical Biology
- Technical University of Dortmund
- 44227 Dortmund
- Germany
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9
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Schmidt MJ, Fedoseev A, Bücker D, Borbas J, Peter C, Drescher M, Summerer D. EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels. ACS Chem Biol 2015; 10:2764-71. [PMID: 26421438 DOI: 10.1021/acschembio.5b00512] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic encoding of nitroxide amino acids in combination with electron paramagnetic resonance (EPR) distance measurements enables precise structural studies of native proteins, i.e. without the need for mutations to create unique reactive sites for chemical labeling and thus with minimal structural perturbation. We here report on in vitro DEER measurements in native E. coli thioredoxin (TRX) that establish the nitroxide amino acid SLK-1 as a spectroscopic probe that reports distances and conformational flexibilities in the enzyme with nonmutated catalytic centers that are not accessible by the use of the traditional methanethiosulfonate spin label (MTSSL). We generated a rotamer library for SLK-1 that in combination with molecular dynamics (MD) simulation enables predictions of distance distributions between two SLK-1 labels incorporated into a target protein. Toward a routine use of SLK-1 for EPR distance measurements in proteins and the advancement of the approach to intracellular environments, we study the stability of SLK-1 in E. coli cultures and lysates and establish guidelines for protein expression and purification that offer maximal nitroxide stability. These advancements and insights provide new perspectives for facile structural studies of native, endogenous proteins by EPR distance measurements.
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Affiliation(s)
- Moritz J. Schmidt
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Artem Fedoseev
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Dennis Bücker
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Julia Borbas
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Summerer
- Department of Chemistry,
Zukunftskolleg and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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10
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Schmidt MJ, Fedoseev A, Summerer D, Drescher M. Genetically Encoded Spin Labels for In Vitro and In-Cell EPR Studies of Native Proteins. Methods Enzymol 2015; 563:483-502. [PMID: 26478496 DOI: 10.1016/bs.mie.2015.05.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful approach to study the structure, dynamics, and interactions of proteins. The genetic encoding of the noncanonical amino acid spin-labeled lysine 1 (SLK-1) eliminates the need for any chemical labeling steps in SDSL-EPR studies and enables the investigation of native, endogenous proteins with minimal structural perturbation, and without the need to create unique reactive sites for chemical labeling. We report detailed experimental procedures for the efficient synthesis of SLK-1, the expression and purification of SLK-1-containing proteins under conditions that ensure maximal integrity of the nitroxide radical moiety, and procedures for intramolecular EPR distance measurements in proteins by double electron-electron resonance.
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Affiliation(s)
- M J Schmidt
- Department of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - A Fedoseev
- Department of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - D Summerer
- Department of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - M Drescher
- Department of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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11
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New developments in spin labels for pulsed dipolar EPR. Molecules 2014; 19:16998-7025. [PMID: 25342554 PMCID: PMC6271499 DOI: 10.3390/molecules191016998] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
Spin labelling is a chemical technique that enables the integration of a molecule containing an unpaired electron into another framework for study. Given the need to understand the structure, dynamics, and conformational changes of biomacromolecules, spin labelling provides a relatively non-intrusive technique and has certain advantages over X-ray crystallography; which requires high quality crystals. The technique relies on the design of binding probes that target a functional group, for example, the thiol group of a cysteine residue within a protein. The unpaired electron is typically supplied through a nitroxide radical and sterically shielded to preserve stability. Pulsed electron paramagnetic resonance (EPR) techniques allow small magnetic couplings to be measured (e.g., <50 MHz) providing information on single label probes or the dipolar coupling between multiple labels. In particular, distances between spin labels pairs can be derived which has led to many protein/enzymes and nucleotides being studied. Here, we summarise recent examples of spin labels used for pulse EPR that serve to illustrate the contribution of chemistry to advancing discoveries in this field.
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12
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You C, Piehler J. Multivalent chelators for spatially and temporally controlled protein functionalization. Anal Bioanal Chem 2014; 406:3345-57. [DOI: 10.1007/s00216-014-7803-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 03/26/2014] [Accepted: 03/31/2014] [Indexed: 12/30/2022]
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