151
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Evans EGB, Millhauser GL. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling. Methods Enzymol 2015; 563:503-27. [PMID: 26478497 PMCID: PMC4841275 DOI: 10.1016/bs.mie.2015.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents, should make K1 labeling an increasingly viable alternative to cysteine-based methods for SDSL in proteins.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA.
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152
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Manukovsky N, Frydman V, Goldfarb D. Gd3+ Spin Labels Report the Conformation and Solvent Accessibility of Solution and Vesicle-Bound Melittin. J Phys Chem B 2015; 119:13732-41. [DOI: 10.1021/acs.jpcb.5b03523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nurit Manukovsky
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Veronica Frydman
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daniella Goldfarb
- Departments of †Chemical Physics and ‡Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
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153
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Shevelev GY, Krumkacheva OA, Lomzov AA, Kuzhelev AA, Trukhin DV, Rogozhnikova OY, Tormyshev VM, Pyshnyi DV, Fedin MV, Bagryanskaya EG. Triarylmethyl Labels: Toward Improving the Accuracy of EPR Nanoscale Distance Measurements in DNAs. J Phys Chem B 2015; 119:13641-8. [PMID: 26011022 DOI: 10.1021/acs.jpcb.5b03026] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triarylmethyl (trityl, TAM) based spin labels represent a promising alternative to nitroxides for EPR distance measurements in biomolecules. Herewith, we report synthesis and comparative study of series of model DNA duplexes, 5'-spin-labeled with TAMs and nitroxides. We have found that the accuracy (width) of distance distributions obtained by double electron-electron resonance (DEER/PELDOR) strongly depends on the type of radical. Replacement of both nitroxides by TAMs in the same spin-labeled duplex allows narrowing of the distance distributions by a factor of 3. Replacement of one nitroxide by TAM (orthogonal labeling) leads to a less pronounced narrowing but at the same time gains sensitivity in DEER experiment due to efficient pumping on the narrow EPR line of TAM. Distance distributions in nitroxide/nitroxide pairs are influenced by the structure of the linker: the use of a short amine-based linker improves the accuracy by a factor of 2. At the same time, a negligible dependence on the linker length is found for the distribution width in TAM/TAM pairs. Molecular dynamics calculations indicate greater conformational disorder of nitroxide labels compared to TAM ones, thus rationalizing the experimentally observed trends. Thereby, we conclude that double spin-labeling using TAMs allows obtaining narrower spin-spin distance distributions and potentially more precise distances between labeling sites compared to traditional nitroxides.
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Affiliation(s)
- Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Matvey V Fedin
- International Tomography Center, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
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154
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Joseph B, Sikora A, Bordignon E, Jeschke G, Cafiso DS, Prisner TF. Distance Measurement on an Endogenous Membrane Transporter in E. coli Cells and Native Membranes Using EPR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:6196-9. [PMID: 25826642 DOI: 10.1002/anie.201501086] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Indexed: 01/21/2023]
Abstract
Membrane proteins may be influenced by the environment, and they may be unstable in detergents or fail to crystallize. As a result, approaches to characterize structures in a native environment are highly desirable. Here, we report a novel general strategy for precise distance measurements on outer membrane proteins in whole Escherichia coli cells and isolated outer membranes. The cobalamin transporter BtuB was overexpressed and spin-labeled in whole cells and outer membranes and interspin distances were measured to a spin-labeled cobalamin using pulse EPR spectroscopy. A comparative analysis of the data reveals a similar interspin distance between whole cells, outer membranes, and synthetic vesicles. This approach provides an elegant way to study conformational changes or protein-protein/ligand interactions at surface-exposed sites of membrane protein complexes in whole cells and native membranes, and provides a method to validate outer membrane protein structures in their native environment.
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Affiliation(s)
- Benesh Joseph
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum, Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany) http://www.prisner.de
| | - Arthur Sikora
- Department of Chemistry, University of Virginia, McCormick Road, Charlottesville VA22904-4319 (USA)
| | - Enrica Bordignon
- Department of Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin (Germany)
| | - Gunnar Jeschke
- Laboratory for Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich (Switzerland)
| | - David S Cafiso
- Department of Chemistry, University of Virginia, McCormick Road, Charlottesville VA22904-4319 (USA).
| | - Thomas F Prisner
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum, Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany) http://www.prisner.de.
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155
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Joseph B, Sikora A, Bordignon E, Jeschke G, Cafiso DS, Prisner TF. Distance Measurement on an Endogenous Membrane Transporter inE. coliCells and Native Membranes Using EPR Spectroscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501086] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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156
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Prisner TF, Marko A, Sigurdsson ST. Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:187-98. [PMID: 25701439 DOI: 10.1016/j.jmr.2014.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 05/22/2023]
Abstract
Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.
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Affiliation(s)
- T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - S Th Sigurdsson
- Science Institute, University of Iceland, Reykjavik, Iceland
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157
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Cunningham TF, Shannon MD, Putterman MR, Arachchige RJ, Sengupta I, Gao M, Jaroniec CP, Saxena S. Cysteine-specific Cu2+ chelating tags used as paramagnetic probes in double electron electron resonance. J Phys Chem B 2015; 119:2839-43. [PMID: 25608028 DOI: 10.1021/jp5103143] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Double electron electron resonance (DEER) is an attractive technique that is utilized for gaining insight into protein structure and dynamics via nanometer-scale distance measurements. The most commonly used paramagnetic tag in these measurements is a nitroxide spin label, R1. Here, we present the application of two types of high-affinity Cu(2+) chelating tags, based on the EDTA and cyclen metal-binding motifs as alternative X-band DEER probes, using the B1 immunoglobulin-binding domain of protein G (GB1) as a model system. Both types of tags have been incorporated into a variety of protein secondary structure environments and exhibit high spectral sensitivity. In particular, the cyclen-based tag displays distance distributions with comparable distribution widths and most probable distances within 1-3 Å when compared to homologous R1 distributions. The results display the viability of the cyclen tag as an alternative to the R1 side chain for X-band DEER distance measurements in proteins.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh , 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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158
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Martorana A, Yang Y, Zhao Y, Li QF, Su XC, Goldfarb D. Mn(ii) tags for DEER distance measurements in proteins via C–S attachment. Dalton Trans 2015; 44:20812-6. [DOI: 10.1039/c5dt04123f] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tags for Mn2+–Mn2+ distance measurements in proteins with a short and stable linker that generate narrow distance distributions were developed.
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Affiliation(s)
- Andrea Martorana
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Yu Zhao
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Qing-Feng Li
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- China
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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159
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Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S. Nanometric distance measurements between Mn(ii)DOTA centers. Phys Chem Chem Phys 2015; 17:23368-77. [DOI: 10.1039/c5cp03487f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The distance between two Mn(ii)DOTA complexes attached to the ends of polyproline helices of varying lengths was measured by 94 GHz PELDOR spectroscopy with good accuracy demonstrating their effectiveness as spin-labels.
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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
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
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160
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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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161
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Dalaloyan A, Qi M, Ruthstein S, Vega S, Godt A, Feintuch A, Goldfarb D. Gd(iii)–Gd(iii) EPR distance measurements – the range of accessible distances and the impact of zero field splitting. Phys Chem Chem Phys 2015; 17:18464-76. [DOI: 10.1039/c5cp02602d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gd rulers were designed in the 2–8 nm range for in-depth evaluation of Gd(iii) complexes as spin labels for EPR distance measurements.
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Affiliation(s)
- Arina Dalaloyan
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Mian Qi
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Sharon Ruthstein
- Department of Chemistry
- Faculty of Exact Sciences
- Bar-Ilan University
- Ramat Gan
- Israel
| | - Shimon Vega
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Adelheid Godt
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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162
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Feintuch A, Otting G, Goldfarb D. Gd3+ Spin Labeling for Measuring Distances in Biomacromolecules. Methods Enzymol 2015; 563:415-57. [DOI: 10.1016/bs.mie.2015.07.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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163
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Yang Y, Wang JT, Pei YY, Su XC. Site-specific tagging proteins via a rigid, stable and short thiolether tether for paramagnetic spectroscopic analysis. Chem Commun (Camb) 2015; 51:2824-7. [DOI: 10.1039/c4cc08493d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of phenylsulfonated pyridine derivatives and protein thiols is suitable for high-resolution spectroscopic analysis by generation of a rigid, stable and short thiolether tether.
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Affiliation(s)
- Yin Yang
- State-Key Laboratory of Elemento-organic Chemistry
- Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin
- China
| | - Jin-Tao Wang
- State-Key Laboratory of Elemento-organic Chemistry
- Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin
- China
| | - Ying-Ying Pei
- State-Key Laboratory of Elemento-organic Chemistry
- Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin
- China
| | - Xun-Cheng Su
- State-Key Laboratory of Elemento-organic Chemistry
- Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin
- China
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164
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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution. Methods Enzymol 2015; 558:279-331. [DOI: 10.1016/bs.mie.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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165
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166
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Doll A, Qi M, Pribitzer S, Wili N, Yulikov M, Godt A, Jeschke G. Sensitivity enhancement by population transfer in Gd(iii) spin labels. Phys Chem Chem Phys 2015; 17:7334-44. [DOI: 10.1039/c4cp05893c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Frequency-swept chirp pulses with bandwidths > 1 GHz rearrange electron spin populations in the S = 7/2 spin of Gd(iii) ions for better sensitivity, as demonstrated with distance measurements between Gd(iii) ions.
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Affiliation(s)
- Andrin Doll
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials
- Bielefeld University
- 33615 Bielefeld
- Germany
| | | | - Nino Wili
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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167
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Valera S, Bode BE. Strategies for the synthesis of yardsticks and abaci for nanometre distance measurements by pulsed EPR. Molecules 2014; 19:20227-56. [PMID: 25479188 PMCID: PMC6271543 DOI: 10.3390/molecules191220227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/19/2014] [Accepted: 11/27/2014] [Indexed: 01/18/2023] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) techniques have been found to be efficient tools for the elucidation of structure in complex biological systems as they give access to distances in the nanometre range. These measurements can provide additional structural information such as relative orientations, structural flexibility or aggregation states. A wide variety of model systems for calibration and optimisation of pulsed experiments has been synthesised. Their design is based on mimicking biological systems or materials in specific properties such as the distances themselves and the distance distributions. Here, we review selected approaches to the synthesis of chemical systems bearing two or more spin centres, such as nitroxide or trityl radicals, metal ions or combinations thereof and outline their application in pulsed EPR distance measurements.
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Affiliation(s)
- Silvia Valera
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK.
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168
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Qi M, Groß A, Jeschke G, Godt A, Drescher M. Gd(III)-PyMTA Label Is Suitable for In-Cell EPR. J Am Chem Soc 2014; 136:15366-78. [DOI: 10.1021/ja508274d] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Mian Qi
- Faculty
of Chemistry and Center for Molecular Materials, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Andreas Groß
- Department
of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical
Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Gunnar Jeschke
- Laboratory
of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Faculty
of Chemistry and Center for Molecular Materials, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Malte Drescher
- Department
of Chemistry, Zukunftskolleg, and Konstanz Research School Chemical
Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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