51
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short-Linked, Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020; 59:9767-9772. [PMID: 32329172 PMCID: PMC7318235 DOI: 10.1002/anie.202004452] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/15/2022]
Abstract
The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site-directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in-cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide-functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm, and shows high stability against reduction. Using this label, the guanine-nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.
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Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
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52
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Kong F, Zhao P, Yu P, Qin Z, Huang Z, Wang Z, Wang M, Shi F, Du J. Kilohertz electron paramagnetic resonance spectroscopy of single nitrogen centers at zero magnetic field. SCIENCE ADVANCES 2020; 6:eaaz8244. [PMID: 32766444 PMCID: PMC7385428 DOI: 10.1126/sciadv.aaz8244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/20/2020] [Indexed: 06/01/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is among the most important analytical tools in physics, chemistry, and biology. The emergence of nitrogen-vacancy (NV) centers in diamond, serving as an atomic-sized magnetometer, has promoted this technique to single-spin level, even under ambient conditions. Despite the enormous progress in spatial resolution, the current megahertz spectral resolution is still insufficient to resolve key heterogeneous molecular information. A major challenge is the short coherence times of the sample electron spins. Here, we address this challenge by using a magnetic noise-insensitive transition between states of different symmetry. We demonstrate a 27-fold narrower spectrum of single substitutional nitrogen (P1) centers in diamond with a linewidth of several kilohertz, and then some weak couplings can be resolved. Those results show both spatial and spectral advances of NV center-based EPR and provide a route toward analytical (EPR) spectroscopy at the single-molecule level.
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Affiliation(s)
- Fei Kong
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Pengju Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Pei Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhuoyang Qin
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhehua Huang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhecheng Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Mengqi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Fazhan Shi
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jiangfeng Du
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
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53
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EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility. Arch Biochem Biophys 2020; 684:108323. [DOI: 10.1016/j.abb.2020.108323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
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54
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short‐Linked, Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004452] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Römerstr. 164 53117 Bonn Germany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Römerstr. 164 53117 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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55
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K A, Kathirvelu V. Electron spin relaxation time of Ni(II) ion in hexapyrazole zinc(II) dinitrate at 300 K. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:329-333. [PMID: 32017195 DOI: 10.1002/mrc.5007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/27/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Understanding the electron spin relaxation properties of paramagnetic species is a fundamental requirement to use them as a probe to measure distances between sites in biomolecules by electron paramagnetic resonance (EPR) spectroscopy. Even though Ni(II) ion is an essential trace element for many species, relaxation properties are not well understood. Herein, the polycrystalline sample of Ni(II) ion magnetically diluted in Zn(Pyrazole)6 (NO3 )2 (Ni/ZPN) has been studied in detail by EPR spectroscopy to explore the electron spin relaxation time. Progressive continuous-wave (CW) EPR power saturation study on Ni/ZPN at 300 K yielded 907 mW as the P1/2 value. The cavity constant (KQ ) has been calculated using tempol in PVA-BA glass matrix and the product of electron spin-lattice relaxation time (T1 ) and spin-spin relaxation time (T2 ) for Ni/ZPN at 300 K has been reported for the first time.
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Affiliation(s)
- Amrutha K
- 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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56
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Abdullin D, Schiemann O. Pulsed Dipolar EPR Spectroscopy and Metal Ions: Methodology and Biological Applications. Chempluschem 2020; 85:353-372. [DOI: 10.1002/cplu.201900705] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/16/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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57
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Juliusson HY, Sigurdsson ST. Reduction Resistant and Rigid Nitroxide Spin-Labels for DNA and RNA. J Org Chem 2020; 85:4036-4046. [PMID: 32103670 DOI: 10.1021/acs.joc.9b02988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy, coupled with site-directed spin labeling (SDSL), is a useful method for studying conformational changes of biomolecules in cells. To employ in-cell EPR using nitroxide-based spin labels, the structure of the nitroxides must confer reduction resistance to withstand the reductive environment within cells. Here, we report the synthesis of two new spin labels, EÇ and EÇm, both of which possess the rigidity and the reduction resistance needed for extracting detailed structural information by EPR spectroscopy. EÇ and EÇm were incorporated into DNA and RNA, respectively, by oligonucleotide synthesis. Both labels were shown to be nonperturbing of the duplex structure. The partial reduction of EÇm during RNA synthesis was circumvented by the protection of the nitroxide as a benzoylated hydroxylamine.
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Affiliation(s)
- Haraldur Y Juliusson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
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58
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Yang Y, Pan BB, Tan X, Yang F, Liu Y, Su XC, Goldfarb D. In-Cell Trityl-Trityl Distance Measurements on Proteins. J Phys Chem Lett 2020; 11:1141-1147. [PMID: 31951412 PMCID: PMC7307952 DOI: 10.1021/acs.jpclett.9b03208] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Double-electron electron resonance (DEER) can be used to track the structural dynamics of proteins in their native environment, the cell. This method provides the distance distribution between two spin labels attached at specific, well-defined positions in a protein. For the method to be viable under in-cell conditions, the spin label and its attachment to the protein should exhibit high chemical stability in the cell. Here we present low-temperature, trityl-trityl DEER distance measurements on two model proteins, PpiB (prolyl cis-trans isomerase from E. coli) and GB1 (immunoglobulin G-binding protein), doubly labeled with the trityl spin label, CT02MA. Both proteins gave in-cell distance distributions similar to those observed in vitro, with maxima at 4.5-5 nm, and the data were further compared with in-cell Gd(III)-Gd(III) DEER obtained for PpiB labeled with BrPSPy-DO3A-Gd(III) at the same positions. These results highlight the challenges of designing trityl tags suitable for in-cell distance determination at ambient temperatures on live cells.
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Affiliation(s)
- Yin Yang
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Bin-Bin Pan
- 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
| | - Feng Yang
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - 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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59
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Tormyshev VM, Chubarov AS, Krumkacheva OA, Trukhin DV, Rogozhnikova OY, Spitsyna AS, Kuzhelev AA, Koval VV, Fedin MV, Godovikova TS, Bowman MK, Bagryanskaya EG. Methanethiosulfonate Derivative of OX063 Trityl: A Promising and Efficient Reagent for Side-Directed Spin Labeling of Proteins. Chemistry 2020; 26:2705-2712. [PMID: 31851392 DOI: 10.1002/chem.201904587] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Indexed: 12/20/2022]
Abstract
Trityl radicals (TAMs) have recently appeared as an alternative source of spin labels for measuring long distances in biological systems. Finland trityl radical (FTAM) served as the basis for this new generation of spin labels, but FTAM is rather lipophilic and susceptible to self-aggregation, noncovalent binding with lipophilic sites of proteins, and noncovalent docking at the termini of duplex DNA. In this paper the very hydrophilic OX063 TAM with very low toxicity and little tendency for aggregation is used as the basis for a spin label. Human serum albumin (HSA) labeled with OX063 has an intense narrow line typical of TAM radicals in solution, whereas HSA labeled with FTAM shows broad lines and extensive aggregation. In pulse EPR measurements, the measured phase memory time TM for HSA labeled with OX063 is 6.3 μs at 50 K, the longest yet obtained with a TAM-based spin label. The lowered lipophilicity also decreases side products in the labeling reaction.
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Affiliation(s)
- Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk, 630090, Russia
| | - Dmitry V Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Olga Yu Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Anna S Spitsyna
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk, 630090, Russia
| | - Tatyana S Godovikova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Michael K Bowman
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama, 35487-0336, USA
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
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60
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Galazzo L, Meier G, Timachi MH, Hutter CAJ, Seeger MA, Bordignon E. Spin-labeled nanobodies as protein conformational reporters for electron paramagnetic resonance in cellular membranes. Proc Natl Acad Sci U S A 2020; 117:2441-2448. [PMID: 31964841 PMCID: PMC7007536 DOI: 10.1073/pnas.1913737117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nanobodies are emerging tools in a variety of fields such as structural biology, cell imaging, and drug discovery. Here we pioneer the use of their spin-labeled variants as reporters of conformational dynamics of membrane proteins using DEER spectroscopy. At the example of the bacterial ABC transporter TM287/288, we show that two gadolinium-labeled nanobodies allow us to quantify, via analysis of the modulation depth of DEER traces, the fraction of transporters adopting the outward-facing state under different experimental conditions. Additionally, we quantitatively follow the interconversion from the outward- to the inward-facing state in the conformational ensemble under ATP turnover conditions. We finally show that the specificity of the nanobodies for the target protein allows the direct attainment of structural information on the wild-type TM287/288 expressed in cellular membranes without the need to purify or label the investigated membrane protein.
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Affiliation(s)
- Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - M Hadi Timachi
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany;
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61
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Accelerating structural life science by paramagnetic lanthanide probe methods. Biochim Biophys Acta Gen Subj 2020; 1864:129332. [DOI: 10.1016/j.bbagen.2019.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 02/08/2023]
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62
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Kucher S, Korneev S, Klare JP, Klose D, Steinhoff HJ. In cell Gd3+-based site-directed spin labeling and EPR spectroscopy of eGFP. Phys Chem Chem Phys 2020; 22:13358-13362. [DOI: 10.1039/d0cp01930e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newly synthesized Gd3+ chelate complex allows in cell spin labeling and detection of eGFP by EPR spectroscopy.
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Affiliation(s)
| | - Sergej Korneev
- Department of Biology
- Osnabrück University
- Osnabrück
- Germany
| | | | - Daniel Klose
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- Zurich
- Switzerland
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63
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Widder P, Schuck J, Summerer D, Drescher M. Combining site-directed spin labeling in vivo and in-cell EPR distance determination. Phys Chem Chem Phys 2020; 22:4875-4879. [DOI: 10.1039/c9cp05584c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Non-canonical amino acid incorporation via amber stop codon suppression and in vivo site-directed spin labeling allow in-cell EPR distance determination in E. coli.
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Affiliation(s)
- Pia Widder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| | - Julian Schuck
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB)
- University of Konstanz
- Konstanz
- Germany
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64
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Breitgoff FD, Keller K, Qi M, Klose D, Yulikov M, Godt A, Jeschke G. UWB DEER and RIDME distance measurements in Cu(II)-Cu(II) spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106560. [PMID: 31377151 DOI: 10.1016/j.jmr.2019.07.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Distance determination by Electron Paramagnetic Resonance (EPR) based on measurements of the dipolar coupling are technically challenging for electron spin systems with broad spectra due to comparatively narrow microwave pulse excitation bandwidths. With Na4[{CuII(PyMTA)}-(stiff spacer)-{CuII(PyMTA)}] as a model compound, we compared DEER and RIDME measurements and investigated the use of frequency-swept pulses. We found very large improvements in sensitivity when substituting the monochromatic pump pulse by a frequency-swept one in DEER experiments with monochromatic observer pulses. This effect was especially strong in X band, where nearly the whole spectrum can be included in the experiment. The RIDME experiment is characterised by a trade-off in signal intensity and modulation depth. Optimal parameters are further influenced by varying steepness of the background decay. A simple 2-point optimization experiment was found to serve as good estimate to identify the mixing time of highest sensitivity. Using frequency-swept pulses in the observer sequences resulted in lower SNR in both the RIDME and the DEER experiment. Orientation selectivity was found to vary in both experiments with the detection position as well as with the settings of the pump pulse in DEER. In RIDME, orientation selection by relaxation anisotropy of the inverted spin appeared to be negligible as form factors remain relatively constant with varying mixing time. This reduces the overall observed orientation selection to the one given by the detection position. Field-averaged data from RIDME and DEER with a shaped pump pulse resulted in the same dipolar spectrum. We found that both methods have their advantages and disadvantages for given instrumental limitations and sample properties. Thus the choice of method depends on the situation at hand and we discuss which parameters should be considered for optimization.
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Affiliation(s)
- Frauke D Breitgoff
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Katharina Keller
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Daniel Klose
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Maxim Yulikov
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Gunnar Jeschke
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
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65
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Kugele A, Silkenath B, Langer J, Wittmann V, Drescher M. Protein Spin Labeling with a Photocaged Nitroxide Using Diels-Alder Chemistry. Chembiochem 2019; 20:2479-2484. [PMID: 31090999 PMCID: PMC6790680 DOI: 10.1002/cbic.201900318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 12/31/2022]
Abstract
EPR spectroscopy of diamagnetic bio-macromolecules is based on site-directed spin labeling (SDSL). Herein, a novel labeling strategy for proteins is presented. A nitroxide-based spin label has been developed and synthesized that can be ligated to proteins by an inverse-electron-demand Diels-Alder (DAinv ) cycloaddition to genetically encoded noncanonical amino acids. The nitroxide moiety is shielded by a photoremovable protecting group with an attached tetra(ethylene glycol) unit to achieve water solubility. SDSL is demonstrated on two model proteins with the photoactivatable nitroxide for DAinv reaction (PaNDA) label. The strategy features high reaction rates, combined with high selectivity, and the possibility to deprotect the nitroxide in Escherichia coli lysate.
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Affiliation(s)
- Anandi Kugele
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Bjarne Silkenath
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Jakob Langer
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Valentin Wittmann
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Malte Drescher
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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66
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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67
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Golbek TW, Padmanarayana M, Roeters SJ, Weidner T, Johnson CP, Baio JE. Otoferlin C2F Domain-Induced Changes in Membrane Structure Observed by Sum Frequency Generation. Biophys J 2019; 117:1820-1830. [PMID: 31587832 DOI: 10.1016/j.bpj.2019.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/16/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022] Open
Abstract
Proteins that contain C2 domains are involved in a variety of biological processes, including encoding of sound, cell signaling, and cell membrane repair. Of particular importance is the interface activity of the C-terminal C2F domain of otoferlin due to the pathological mutations known to significantly disrupt the protein's lipid membrane interface binding activity, resulting in hearing loss. Therefore, there is a critical need to define the geometry and positions of functionally important sites and structures at the otoferlin-lipid membrane interface. Here, we describe the first in situ probe of the protein orientation of otoferlin's C2F domain interacting with a cell membrane surface. To identify this protein's orientation at the lipid interface, we applied sum frequency generation (SFG) vibrational spectroscopy and coupled it with simulated SFG spectra to observe and quantify the otoferlin C2F domain interacting with model lipid membranes. A model cell membrane was built with equal amounts of phosphatidylserine and phosphatidylcholine. SFG measurements of the lipids that make up the model membrane indicate a 62% increase in amplitude from the SFG signal near 2075 cm-1 upon protein interaction, suggesting domain-induced changes in the orientation of the lipids and possible membrane curvature. This increase is related to lipid ordering caused by the docking interaction of the otoferlin C2F domain. SFG spectra taken from the amide-I region contain features near 1630 and 1670 cm-1 related to the C2F domains beta-sandwich secondary structure, thus indicating that the domain binds in a specific orientation. By mapping the simulated SFG spectra to the experimentally collected SFG spectra, we found the C2F domain of otoferlin orients 22° normal to the lipid surface. This information allows us to map what portion of the domain directly interacts with the lipid membrane.
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Affiliation(s)
- Thaddeus W Golbek
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon; Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | | | - Tobias Weidner
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Colin P Johnson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon.
| | - Joe E Baio
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon.
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68
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Teucher M, Zhang H, Bader V, Winklhofer KF, García-Sáez AJ, Rajca A, Bleicken S, Bordignon E. A new perspective on membrane-embedded Bax oligomers using DEER and bioresistant orthogonal spin labels. Sci Rep 2019; 9:13013. [PMID: 31506457 PMCID: PMC6737250 DOI: 10.1038/s41598-019-49370-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/20/2019] [Indexed: 12/23/2022] Open
Abstract
Bax is a Bcl-2 protein crucial for apoptosis initiation and execution, whose active conformation is only partially understood. Dipolar EPR spectroscopy has proven to be a valuable tool to determine coarse-grained models of membrane-embedded Bcl-2 proteins. Here we show how the combination of spectroscopically distinguishable nitroxide and gadolinium spin labels and Double Electron-Electron Resonance can help to gain new insights into the quaternary structure of active, membrane-embedded Bax oligomers. We show that attaching labels bulkier than the conventional MTSL may affect Bax fold and activity, depending on the protein/label combination. However, we identified a suitable pair of spectroscopically distinguishable labels, which allows to study complex distance networks in the oligomers that could not be disentangled before. Additionally, we compared the stability of the different spin-labeled protein variants in E. coli and HeLa cell extracts. We found that the gem-diethyl nitroxide-labeled Bax variants were reasonably stable in HeLa cell extracts. However, when transferred into human cells, Bax was found to be mislocalized, thus preventing its characterization in a physiological environment. The successful use of spectroscopically distinguishable labels on membrane-embedded Bax-oligomers opens an exciting new path towards structure determination of membrane-embedded homo- or hetero-oligomeric Bcl-2 proteins via EPR.
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Affiliation(s)
- Markus Teucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska, USA
| | - Verian Bader
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska, USA
| | - Stephanie Bleicken
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany.
- ZEMOS, Ruhr University Bochum, Bochum, Germany.
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany.
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69
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Goldfarb D. Pulse EPR in biological systems - Beyond the expert's courtyard. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:102-108. [PMID: 31337564 DOI: 10.1016/j.jmr.2019.07.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 07/08/2019] [Indexed: 05/14/2023]
Abstract
Application of EPR to biological systems includes many techniques and applications. In this short perspective, which dares to look into the future, I focus on pulse EPR, which is my field of expertise. Generally, pulse EPR techniques can be divided into two main groups: (1) hyperfine spectroscopy, which explores electron-nuclear interactions, and (2) pulse-dipolar (PD) EPR spectroscopy, which is based on electron-electron spin interactions. Here I focus on PD-EPR because it has a better chance of becoming a widely applied, easy-to-use table-top method to study the structural and dynamic aspects of bio-molecules. I will briefly introduce this technique, its current state of the art, the challenges it is facing, and finally I will describe futuristic scenarios of low-cost PD-EPR approaches that can cross the diffusion barrier from the core of experts to the bulk of the scientific community.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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70
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Siegal G, Selenko P. Cells, drugs and NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:202-212. [PMID: 31358370 DOI: 10.1016/j.jmr.2019.07.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/08/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for investigating cellular structures and their compositions. While in vivo and whole-cell NMR have a long tradition in cell-based approaches, high-resolution in-cell NMR spectroscopy is a new addition to these methods. In recent years, technological advancements in multiple areas provided converging benefits for cellular MR applications, especially in terms of robustness, reproducibility and physiological relevance. Here, we review the use of cellular NMR methods for drug discovery purposes in academia and industry. Specifically, we discuss how developments in NMR technologies such as miniaturized bioreactors and flow-probe perfusion systems have helped to consolidate NMR's role in cell-based drug discovery efforts.
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Affiliation(s)
- Gregg Siegal
- ZoBio B.V., BioPartner 2 Building, J.H. Oortweg 19, 2333 Leiden, the Netherlands
| | - Philipp Selenko
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000 Rehovot, Israel.
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71
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Yardeni EH, Bahrenberg T, Stein RA, Mishra S, Zomot E, Graham B, Tuck KL, Huber T, Bibi E, Mchaourab HS, Goldfarb D. Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels. Sci Rep 2019; 9:12528. [PMID: 31467343 PMCID: PMC6715713 DOI: 10.1038/s41598-019-48694-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/08/2019] [Indexed: 11/09/2022] Open
Abstract
Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E. coli. Our results identify highly flexible regions of MdfA, which may play an important role in its functional dynamics. Comparison of distance distribution of spin label pairs on the periplasm with those calculated using inward- and outward-facing crystal structures of MdfA, show that in detergent micelles, the protein adopts a predominantly outward-facing conformation, although more closed than the crystal structure. The cytoplasmic pairs suggest a small preference to the outward-facing crystal structure, with a somewhat more open conformation than the crystal structure. Parallel DEER measurements with the two types of labels led to similar distance distributions, demonstrating the feasibility of using W-band spectroscopy with a Gd(III) label for investigation of the structural dynamics of membrane proteins.
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Affiliation(s)
- Eliane H Yardeni
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Elia Zomot
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Thomas Huber
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Eitan Bibi
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel.
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel.
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72
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Bleicken S, Assafa TE, Zhang H, Elsner C, Ritsch I, Pink M, Rajca S, Jeschke G, Rajca A, Bordignon E. gem-Diethyl Pyrroline Nitroxide Spin Labels: Synthesis, EPR Characterization, Rotamer Libraries and Biocompatibility. ChemistryOpen 2019; 8:1057-1065. [PMID: 31463171 PMCID: PMC6709561 DOI: 10.1002/open.201900119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Indexed: 12/29/2022] Open
Abstract
The availability of bioresistant spin labels is crucial for the optimization of site-directed spin labeling protocols for EPR structural studies of biomolecules in a cellular context. As labeling can affect proteins' fold and/or function, having the possibility to choose between different spin labels will increase the probability to produce spin-labeled functional proteins. Here, we report the synthesis and characterization of iodoacetamide- and maleimide-functionalized spin labels based on the gem-diethyl pyrroline structure. The two nitroxide labels are compared to conventional gem-dimethyl analogs by site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy, using two water soluble proteins: T4 lysozyme and Bid. To foster their use for structural studies, we also present rotamer libraries for these labels, compatible with the MMM software. Finally, we investigate the "true" biocompatibility of the gem-diethyl probes comparing the resistance towards chemical reduction of the NO group in ascorbate solutions and E. coli cytosol at different spin concentrations.
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Affiliation(s)
- Stephanie Bleicken
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
- ZEMOSRuhr University BochumUniversitaetsstrasse 150, 44801BochumGermany
| | - Tufa E. Assafa
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
| | - Hui Zhang
- Department of ChemistryUniversity of Nebraska, LincolnNebraska68588-0304USA
| | - Christina Elsner
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
| | - Irina Ritsch
- ETH ZurichLaboratory of Physical ChemistryVladimir-Prelog-Weg 2CH-8093ZurichSwitzerland.
| | - Maren Pink
- IUMSC, Department of ChemistryIndiana UniversityBloomington, Indiana47405-7102USA
| | - Suchada Rajca
- Department of ChemistryUniversity of Nebraska, LincolnNebraska68588-0304USA
| | - Gunnar Jeschke
- ETH ZurichLaboratory of Physical ChemistryVladimir-Prelog-Weg 2CH-8093ZurichSwitzerland.
| | - Andrzej Rajca
- Department of ChemistryUniversity of Nebraska, LincolnNebraska68588-0304USA
| | - Enrica Bordignon
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
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73
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Joseph B, Jaumann EA, Sikora A, Barth K, Prisner TF, Cafiso DS. In situ observation of conformational dynamics and protein ligand-substrate interactions in outer-membrane proteins with DEER/PELDOR spectroscopy. Nat Protoc 2019; 14:2344-2369. [PMID: 31278399 PMCID: PMC6886689 DOI: 10.1038/s41596-019-0182-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/18/2019] [Indexed: 12/01/2022]
Abstract
Observing structure and conformational dynamics of membrane proteins at high-resolution in their native environments is challenging because of the lack of suitable techniques. We have developed an approach for high-precision distance measurements in the nanometer range for outer membrane proteins (OMPs) in intact E. coli and native membranes. OMPs in Gram-negative bacteria rarely have reactive cysteines. This enables in-situ labeling of engineered cysteines with a methanethiosulfonate functionalized nitroxide spin label (MTSL) with minimal background signals. Following overexpression of the target protein, spin labeling is performed with E. coli or isolated outer membranes (OM) under selective conditions. The interspin distances are measured in-situ using pulsed electron-electron double resonance spectroscopy (PELDOR or DEER). The residual background signals, which are problematic for in-situ structural biology, contributes specifically to the intermolecular part of the signal and can be selectively removed to extract the desired interspin distance distribution. The initial cloning stage can take 5–7 d and the subsequent protein expression, OM isolation, spin labeling, PELDOR experiment, and the data analysis typically take 4–5 d. The described protocol provides a general strategy for observing protein-ligand/substrate interactions, oligomerization, and conformational dynamics of OMPs in the native OM and intact E. coli. EDITORIAL SUMMARY This protocol describes how to label bacterial outer membrane proteins with spin labels to study conformational changes and their interaction with ligands and substrates in native membranes and cells using Pulsed Electron-Electron Double Resonance (PELDOR or DEER) spectroscopy. TWEET A new protocol for studying conformational changes and ligand/substrate interactions of bacterial outer membrane proteins in-situ. COVER TEASER Studying membrane protein conformations in-situ
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Affiliation(s)
- Benesh Joseph
- Institute of Biophysics, Department of Physics, University of Frankfurt, Frankfurt am Main, Germany. .,Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany.
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Arthur Sikora
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
| | - Katja Barth
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
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74
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Dalaloyan A, Martorana A, Barak Y, Gataulin D, Reuveny E, Howe A, Elbaum M, Albeck S, Unger T, Frydman V, Abdelkader EH, Otting G, Goldfarb D. Tracking Conformational Changes in Calmodulin in vitro, in Cell Extract, and in Cells by Electron Paramagnetic Resonance Distance Measurements. Chemphyschem 2019; 20:1860-1868. [PMID: 31054266 DOI: 10.1002/cphc.201900341] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Indexed: 12/12/2022]
Abstract
It is an open question whether the conformations of proteins sampled in dilute solutions are the same as in the cellular environment. Here we address this question by double electron-electron resonance (DEER) distance measurements with Gd(III) spin labels to probe the conformations of calmodulin (CaM) in vitro, in cell extract, and in human HeLa cells. Using the CaM mutants N53C/T110C and T34C/T117C labeled with maleimide-DOTA-Gd(III) in the N- and C-terminal domains, we observed broad and varied interdomain distance distributions. The in vitro distance distributions of apo-CaM and holo-CaM in the presence and absence of the IQ target peptide can be described by combinations of closed, open, and collapsed conformations. In cell extract, apo- and holo-CaM bind to target proteins in a similar way as apo- and holo-CaM bind to IQ peptide in vitro. In HeLa cells, however, in the presence or absence of elevated in-cell Ca2+ levels CaM unexpectedly produced more open conformations and very broad distance distributions indicative of many different interactions with in-cell components. These results show-case the importance of in-cell analyses of protein structures.
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Affiliation(s)
| | | | | | | | | | - Andrew Howe
- Department of Chemical and Biological Physics
| | | | - Shira Albeck
- Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Elwy H Abdelkader
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, Australia
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75
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Su XC, Chen JL. Site-Specific Tagging of Proteins with Paramagnetic Ions for Determination of Protein Structures in Solution and in Cells. Acc Chem Res 2019; 52:1675-1686. [PMID: 31150202 DOI: 10.1021/acs.accounts.9b00132] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-resolution NMR spectroscopy is sensitive to local structural variations and subtle dynamics of biomolecules and is an important technique for studying the structures, dynamics, and interactions of these molecules. Small-molecule probes, including paramagnetic tags, have been developed for this purpose. Paramagnetic effects manifested in magnetic resonance spectra have long been recognized as valuable tools for chemical analysis of small molecules, and these effects were later applied in the fields of chemical biology and structural biology. However, such applications require the installation of a paramagnetic center in the biomolecules of interest. Paramagnetic metal ions and stable free radicals are the most widely used paramagnetic probes for biological magnetic resonance spectroscopy, and therefore mild, high-yielding approaches for chemically attaching paramagnetic tags to biomolecules are in high demand. In this Account, we begin by discussing paramagnetic species, especially transition metal ions and lanthanide ions, that are suitable for NMR and EPR studies, particularly for in-cell applications. Thereafter, we describe approaches for site-specific tagging of proteins with paramagnetic ions and discuss considerations involved in designing high-quality paramagnetic tags, including the strength of the binding between the metal-chelating moiety and the paramagnetic ion, the chemical stability, and the flexibility of the tether between the paramagnetic tag and the target protein. The flexibility of a tag correlates strongly with the averaging of paramagnetic effects observed in NMR spectra, and we describe methods for increasing tag rigidity and applications of such tags in biological systems. We also describe specific applications of established site-specific tagging approaches and newly developed paramagnetic tags for the elucidation of protein structures and dynamics at atomic resolution both in solution and in cells. First, we describe the determination of the 3D structure of a short-lived, low-abundance enzyme intermediate complex in real time by using pseudocontact shifts as structural restraints. Second, we demonstrate the utility of stable paramagnetic tags for determining 3D structures of proteins in live cells, and pseudocontact shifts are shown to be valuable structural restraints for in-cell protein analysis. Third, we show that a NMR optimized paramagnetic tag allows one to determine distance restraints on proteins by double electron-electron resonance (DEER) measurements with high spatial resolution both in vitro and in cells. Finally, we summarize recent advances in site-specific tagging of proteins to achieve atomic-resolution information about structural changes of proteins, and the advantages and challenges of magnetic resonance spectroscopy in biological systems.
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Affiliation(s)
- Xun-Cheng Su
- 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
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76
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Azarkh M, Bieber A, Qi M, Fischer JW, Yulikov M, Godt A, Drescher M. Gd(III)-Gd(III) Relaxation-Induced Dipolar Modulation Enhancement for In-Cell Electron Paramagnetic Resonance Distance Determination. J Phys Chem Lett 2019; 10:1477-1481. [PMID: 30864799 PMCID: PMC6625747 DOI: 10.1021/acs.jpclett.9b00340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/13/2019] [Indexed: 05/26/2023]
Abstract
In-cell distance determination by electron paramagnetic resonance (EPR) spectroscopy reveals essential structural information about biomacromolecules under native conditions. We demonstrate that the pulsed EPR technique RIDME (relaxation induced dipolar modulation enhancement) can be utilized for such distance determination. The performance of in-cell RIDME has been assessed at Q-band using stiff molecular rulers labeled with Gd(III)-PyMTA and microinjected into Xenopus laevis oocytes. The overtone coefficients are determined to be the same for protonated aqueous solutions and inside cells. As compared to in-cell DEER (double electron-electron resonance, also abbreviated as PELDOR), in-cell RIDME features approximately 5 times larger modulation depth and does not show artificial broadening in the distance distributions due to the effect of pseudosecular terms.
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Affiliation(s)
- Mykhailo Azarkh
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Anna Bieber
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Mian Qi
- Faculty
of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Jörg W.
A. Fischer
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Maxim Yulikov
- 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 (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Malte Drescher
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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77
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Abstract
The DEER (double electron-electron resonance, also called PELDOR) experiment, which probes the dipolar interaction between two spins and thus reveals distance information, is an important tool for structural studies. In recent years, shaped pump pulses have become a valuable addition to the DEER experiment. Shaped pulses offer an increased excitation bandwidth and the possibility to precisely adjust pulse parameters, which is beneficial especially for demanding biological samples. We have noticed that on our home built W-band spectrometer, the dead-time free 4-pulse DEER sequence with chirped pump pulses suffers from distortions at the end of the DEER trace. Although minor, these are crucial for Gd(III)-Gd(III) DEER where the modulation depth is on the order of a few percent. Here we present a modified DEER sequence—referred to as reversed DEER (rDEER)—that circumvents the coherence pathway which gives rise to the distortion. We compare the rDEER (with two chirped pump pulses) performance values to regular 4-pulse DEER with one monochromatic as well as two chirped pulses and investigate the source of the distortion. We demonstrate the applicability and effectivity of rDEER on three systems, ubiquitin labeled with Gd(III)-DOTA-maleimide (DOTA, 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid) or with Gd(III)-DO3A (DO3A, 1,4,7,10-Tetraazacyclododecane-1,4,7-triyl) triacetic acid) and the multidrug transporter MdfA, labeled with a Gd(III)-C2 tag, and report an increase in the signal-to-noise ratio in the range of 3 to 7 when comparing the rDEER with two chirped pump pulses to standard 4-pulse DEER.
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78
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Shah A, Roux A, Starck M, Mosely JA, Stevens M, Norman DG, Hunter RI, El Mkami H, Smith GM, Parker D, Lovett JE. A Gadolinium Spin Label with Both a Narrow Central Transition and Short Tether for Use in Double Electron Electron Resonance Distance Measurements. Inorg Chem 2019; 58:3015-3025. [DOI: 10.1021/acs.inorgchem.8b02892] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anokhi Shah
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
| | - Amandine Roux
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Matthieu Starck
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jackie A. Mosely
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Michael Stevens
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David G. Norman
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Hassane El Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - David Parker
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
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79
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Singewald K, Lawless MJ, Saxena S. Increasing nitroxide lifetime in cells to enable in-cell protein structure and dynamics measurements by electron spin resonance spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 299:21-27. [PMID: 30550988 DOI: 10.1016/j.jmr.2018.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/19/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
There is increasing evidence that the stability, structure, dynamics, and function of many proteins differ in cells versus in vitro. The determination of protein structure and dynamics within the native cellular environment may lead to better understanding of protein behavior. Electron spin resonance (ESR) has emerged as a technique that can report on protein structure and dynamics within cells. Nitroxide based spin labels are capable of reporting on protein dynamics, structure, and backbone flexibility but are limited due to nitroxide reduction occurring in cells. In order to overcome this limitation, we used the oxidizing agent potassium ferricyanide (K3Fe(CN)6) as well as the cleavage resistant spin label 3-malemido-PROXYL (5-MSL). Furthermore, we hypothesized that injection concentration is an important parameter regarding nitroxide reduction kinetics. By increasing the injection concentration of doubly 5-MSL labeled protein into Xenopus laevis oocytes, we found an increased nitroxide lifetime. Our work demonstrates unprecedented incubation times of 3-h in-cell and 5-h in-cytosol for double electron-electron resonance (DEER) experiments using nitroxide spin labels. This allows for more meaningful measurements of larger protein systems which may require longer incubation times for equilibration in the cellular milieu. Even longer incubation times are possible by combining our approach with more shielded nitroxides and Q-band.
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Affiliation(s)
- Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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80
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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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81
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Yang Y, Yang F, Li XY, Su XC, Goldfarb D. In-Cell EPR Distance Measurements on Ubiquitin Labeled with a Rigid PyMTA-Gd(III) Tag. J Phys Chem B 2019; 123:1050-1059. [DOI: 10.1021/acs.jpcb.8b11442] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yin Yang
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 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 (Tianjin), 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 (Tianjin), Nankai University, Tianjin 300071, China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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82
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Bordignon E, Kucher S, Polyhach Y. EPR Techniques to Probe Insertion and Conformation of Spin-Labeled Proteins in Lipid Bilayers. Methods Mol Biol 2019; 2003:493-528. [PMID: 31218631 DOI: 10.1007/978-1-4939-9512-7_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy of spin-labeled membrane proteins is a valuable biophysical technique to study structural details and conformational transitions of proteins close to their physiological environment, for example, in liposomes, membrane bilayers, and nanodiscs. Unlike in nuclear magnetic resonance (NMR) spectroscopy, having only one or few specific side chains labeled at a time with paramagnetic probes makes the size of the object under investigation irrelevant in terms of technique sensitivity. As a drawback, extensive site-directed mutagenesis is required in order to analyze the properties of the protein under investigation. EPR can provide detailed information on side chain dynamics of large membrane proteins or protein complexes embedded in membranes with an exquisite sensitivity for flexible regions and on water accessibility profiles across the membrane bilayer. Moreover, distances between the two spin-labeled side chains in membrane proteins can be detected with high precision at cryogenic temperatures. The application of EPR to membrane proteins still presents some challenges in terms of sample preparation, sensitivity and data interpretation, thus it is difficult to give ready-to-go methodological recipes. However, new technological developments (arbitrary waveform generators) and new spin labels spectroscopically orthogonal to nitroxides increased the range of applicability from in vitro toward in-cell EPR experiments. This chapter is an updated version of the one published in the first edition of the book and describes the state of the art in the application of nitroxide-based site-directed spin labeling EPR to membrane proteins, addressing new tools such as arbitrary waveform generators and spectroscopically orthogonal labels, such as Gd(III)-based labels. We will present challenges in sample preparation and data analysis for functional and structural membrane protein studies using site-directed spin labeling techniques and give experimental details on EPR techniques providing information on side chain dynamics and water accessibility using nitroxide probes. An updated optimal Q-band DEER setup for nitroxide probes will be described, and its extension to gadolinium-containing samples will be addressed.
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Affiliation(s)
- Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany.
| | - Svetlana Kucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
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83
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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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84
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Keller K, Qi M, Gmeiner C, Ritsch I, Godt A, Jeschke G, Savitsky A, Yulikov M. Intermolecular background decay in RIDME experiments. Phys Chem Chem Phys 2019; 21:8228-8245. [DOI: 10.1039/c8cp07815g] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Theoretical and experimental studies of the RIDME background reveal electron and nuclear spectral diffusion contributions.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Irina Ritsch
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Anton Savitsky
- Physics Department
- Technical University Dortmund
- Dortmund
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
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85
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Gigli L, Andrałojć W, Dalaloyan A, Parigi G, Ravera E, Goldfarb D, Luchinat C. Assessing protein conformational landscapes: integration of DEER data in Maximum Occurrence analysis. Phys Chem Chem Phys 2018; 20:27429-27438. [PMID: 30357188 DOI: 10.1039/c8cp06195e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The properties of the conformational landscape of a biomolecule are of capital importance to understand its function. It is widely accepted that a statistical ensemble is far more representative than a single structure, especially for proteins with disordered regions. While experimental data provide the most important handle on the conformational variability that the system is experiencing, they usually report on either time or ensemble averages. Since the available conformations largely outnumber the (independent) available experimental data, the latter can be equally well reproduced by a variety of ensembles. We have proposed the Maximum Occurrence (MaxOcc) approach to provide an upper bound of the statistical weight of each conformation. This method is expected to converge towards the true statistical weights by increasing the number of independent experimental datasets. In this paper we explore the ability of DEER (Double Electron Electron Resonance) data, which report on the distance distribution between two spin labels attached to a biomolecule, to restrain the MaxOcc values and its complementarity to previously introduced experimental techniques such as NMR and Small-Angle X-ray Scattering. We here present the case of Ca2+ bound calmodulin (CaM) as a test case and show that DEER data impose a sizeable reduction of the conformational space described by high MaxOcc conformations.
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Affiliation(s)
- Lucia Gigli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.
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86
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Yang Y, Yang F, Gong YJ, Bahrenberg T, Feintuch A, Su XC, Goldfarb D. High Sensitivity In-Cell EPR Distance Measurements on Proteins using an Optimized Gd(III) Spin Label. J Phys Chem Lett 2018; 9:6119-6123. [PMID: 30277780 DOI: 10.1021/acs.jpclett.8b02663] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Distance measurements by electron-electron double resonance (DEER) carried out on spin-labeled proteins delivered into cells provide new insights into the conformational states of proteins in their native environment. Such measurements depend on spin labels that exhibit high redox stability and high DEER sensitivity. Here we present a new Gd(III)-based spin label, BrPSPy-DO3A-Gd(III), which was derived from an earlier label, BrPSPy-DO3MA-Gd(III), by removing the methyl group from the methyl acetate pending arms. The small chemical modification led to a reduction in the zero-field splitting and to a significant increase in the phase memory time, which together culminated in a remarkable improvement of in-cell DEER sensitivity, while maintaining the high distance resolution. The excellent performance of BrPSPy-DO3A-Gd(III) in in-cell DEER measurements was demonstrated on doubly labeled ubiquitin and GB1 delivered into HeLa cells by electroporation.
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Affiliation(s)
- Yin Yang
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , China
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin 300071 , China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
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87
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Reichel K, Stelzl LS, Köfinger J, Hummer G. Precision DEER Distances from Spin-Label Ensemble Refinement. J Phys Chem Lett 2018; 9:5748-5752. [PMID: 30212206 DOI: 10.1021/acs.jpclett.8b02439] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Double electron-electron resonance (DEER) experiments probe nanometer-scale distances in spin-labeled proteins and nucleic acids. Rotamer libraries of the covalently attached spin-labels help reduce position uncertainties. Here we show that rotamer reweighting is essential for precision distance measurements, making it possible to resolve Ångstrom-scale domain motions. We analyze extensive DEER measurements on the three N-terminal polypeptide transport-associated (POTRA) domains of the outer membrane protein Omp85. Using the "Bayesian inference of ensembles" maximum-entropy method, we extract rotamer weights from the DEER measurements. Small weight changes suffice to eliminate otherwise significant discrepancies between experiments and model and unmask 1-3 Å domain motions relative to the crystal structure. Rotamer-weight refinement is a simple yet powerful tool for precision distance measurements that should be broadly applicable to label-based measurements including DEER, paramagnetic relaxation enhancement, and fluorescence resonance energy transfer (FRET).
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Affiliation(s)
- Katrin Reichel
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
- Institute of Biophysics , Goethe University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany
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88
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 406] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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89
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Wilson CB, Aronson S, Clayton JA, Glaser SJ, Han S, Sherwin MS. Multi-step phase-cycling in a free-electron laser-powered pulsed electron paramagnetic resonance spectrometer. Phys Chem Chem Phys 2018; 20:18097-18109. [PMID: 29938285 DOI: 10.1039/c8cp01876f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) is a powerful tool for research in chemistry, biology, physics and materials science, which can benefit significantly from moving to frequencies above 100 GHz. In pulsed EPR spectrometers driven by powerful sub-THz oscillators, such as the free electron laser (FEL)-powered EPR spectrometer at UCSB, control of the duration, power and relative phases of the pulses in a sequence must be performed at the frequency and power level of the oscillator. Here we report on the implementation of an all-quasioptical four-step phase cycling procedure carried out directly at the kW power level of the 240 GHz pulses used in the FEL-powered EPR spectrometer. Phase shifts are introduced by modifying the optical path length of a 240 GHz pulse with precision-machined dielectric plates in a procedure we call phase cycling with optomechanical phase shifters (POPS), while numerical receiver phase cycling is implemented in post-processing. The POPS scheme was successfully used to reduce experimental dead times, enabling pulsed EPR of fast-relaxing spin systems such as gadolinium complexes at temperatures above 190 K. Coherence transfer pathway selection with POPS was used to perform spin echo relaxation experiments to measure the phase memory time of P1 centers in diamond in the presence of a strong unwanted FID signal in the background. The large excitation bandwidth of FEL-EPR, together with phase cycling, enabled the quantitative measurement of instantaneous electron spectral diffusion, from which the P1 center concentration was estimated to within 10%. Finally, phase cycling enabled saturation-recovery measurements of T1 in a trityl-water solution at room temperature - the first FEL-EPR measurement of electron T1.
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Affiliation(s)
- C Blake Wilson
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, USA.
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90
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Luchinat E, Banci L. In-Cell NMR in Human Cells: Direct Protein Expression Allows Structural Studies of Protein Folding and Maturation. Acc Chem Res 2018; 51:1550-1557. [PMID: 29869502 DOI: 10.1021/acs.accounts.8b00147] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cellular structural biology methods are needed to characterize biological processes at atomic resolution in the physiological environment of the cell. Toward this goal, solution in-cell NMR is a powerful approach because it provides structural and dynamic data on macromolecules inside living cells. Several approaches have been developed for in-cell NMR in cultured human cells, which are needed to study processes related to human diseases that rely on the delivery of exogenous macromolecules to the cells. Such strategies, however, may not be applicable to proteins that are sensitive to the external environment or prone to aggregate and can introduce artifacts during protein purification or delivery. As a complementary approach, direct protein expression for in-cell NMR in human cells was developed. This strategy is especially useful when studying processes like protein folding, maturation, and post-translational modification, starting right after protein synthesis. Compared with the protein expression techniques in mammalian cells commonly used in cellular biology, the low sensitivity of NMR requires higher protein levels. Among the cell lines used for high-yield protein expression, the HEK293T cell line was chosen, as it can be efficiently transfected with a cost-effective reagent. A vector originally designed for secreted proteins allows high-level cytosolic protein expression. For isotopic labeling, commercially available or homemade labeled media are employed. Uniform or amino acid type-selective labeling strategies are possible. Protein expression can be targeted to specific organelles (e.g., mitochondria), allowing for in organello NMR applications. A variant of the approach was developed that allows the sequential expression of two or more proteins, with only one selectively labeled. Protein expression in HEK293T cells was applied to recapitulate the maturation steps of intracellular superoxide dismutase 1 (SOD1) and to study the effect of mutations linked to familial amyotrophic lateral sclerosis (fALS) by in-cell NMR. Intracellular wild-type SOD1 spontaneously binds zinc, while it needs the copper chaperone for superoxide dismutase (CCS) for copper delivery and disulfide bond formation. Some fALS-linked mutations impair zinc binding and cause SOD1 to irreversibly unfold, likely forming the precursor of cytotoxic aggregates. The SOD-like domain of CCS acts as a molecular chaperone toward mutant SOD1, stabilizing its folding and allowing zinc binding and correct maturation. Changes in protein redox state distributions can also be investigated by in-cell NMR. Mitochondrial proteins require the redox-regulating partners glutaredoxin 1 (Grx1) and thioredoxin (Trx) to remain in the reduced, import-competent state in the cytosol, whereas SOD1 requires CCS for disulfide bond formation. In both cases, the proteins do not equilibrate with the cytosolic redox pool. Cysteine oxidation in response to oxidative stress can also be monitored. In the near future, in-cell NMR in human cells will likely benefit from technological advancements in NMR hardware, the development of bioreactor systems for increased sample lifetime, the application of paramagnetic NMR to obtain structural restraints, and advanced tools for genome engineering and should be increasingly integrated with advanced cellular imaging techniques.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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91
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Glasbrenner M, Vogler S, Ochsenfeld C. Gauge-origin dependence in electronic g-tensor calculations. J Chem Phys 2018; 148:214101. [DOI: 10.1063/1.5028454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael Glasbrenner
- Chair of Theoretical Chemistry and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, 81377 Munich, Germany
| | - Sigurd Vogler
- Chair of Theoretical Chemistry and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, 81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, 81377 Munich, Germany
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92
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Prokopiou G, Lee MD, Collauto A, Abdelkader EH, Bahrenberg T, Feintuch A, Ramirez-Cohen M, Clayton J, Swarbrick JD, Graham B, Otting G, Goldfarb D. Small Gd(III) Tags for Gd(III)–Gd(III) Distance Measurements in Proteins by EPR Spectroscopy. Inorg Chem 2018; 57:5048-5059. [DOI: 10.1021/acs.inorgchem.8b00133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia Prokopiou
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Thorsten Bahrenberg
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marie Ramirez-Cohen
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jessica Clayton
- Department of Physics, University of California, Santa Barbara, California 93106-9530, United States
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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93
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John L, Drescher M. Xenopus laevis Oocytes Preparation for in-Cell EPR Spectroscopy. Bio Protoc 2018; 8:e2798. [PMID: 34286018 DOI: 10.21769/bioprotoc.2798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 12/14/2022] Open
Abstract
One of the most exciting perspectives for studying bio-macromolecules comes from the emerging field of in-cell spectroscopy, which enables to determine the structure and dynamics of bio-macromolecules in the cell. In-cell electron paramagnetic resonance (EPR) spectroscopy in combination with micro-injection of bio-macromolecules into Xenopus laevis oocytes is ideally suited for this purpose. Xenopus laevis oocytes are a commonly used eukaryotic cell model in different fields of biology, such as cell- and development-biology. For in-cell EPR, the bio-macromolecules of interest are microinjected into the Xenopus laevis oocytes upon site-directed spin labeling. The sample solution is filled into a thin glass capillary by means of Nanoliter Injector and after that microinjected into the dark animal part of the Xenopus laevis oocytes by puncturing the membrane cautiously. Afterwards, three or five microinjected Xenopus laevis oocytes, depending on the kind of the final in-cell EPR experiment, are loaded into a Q-band EPR sample tube followed by optional shock-freezing (for experiment in frozen solution) and measurement (either at cryogenic or physiological temperatures) after the desired incubation time. The incubation time is limited due to cytotoxic effects of the microinjected samples and the stability of the paramagnetic spin label in the reducing cellular environment. Both aspects are quantified by monitoring cell morphology and reduction kinetics.
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Affiliation(s)
- Laura John
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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94
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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] [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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95
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Cattani J, Subramaniam V, Drescher M. Room-temperature in-cell EPR spectroscopy: alpha-Synuclein disease variants remain intrinsically disordered in the cell. Phys Chem Chem Phys 2018; 19:18147-18151. [PMID: 28696461 DOI: 10.1039/c7cp03432f] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human alpha-Synuclein (aS), implicated in Parkinson's disease, adopts a rich variety of different conformations depending on the macromolecular context. In order to unravel its pathophysiological role, monitoring its intracellular conformational state and identifying differences for the disease variants is crucial. Here, we present an intracellular spectroscopy approach based on a systematic spin-labeling site-scan in combination with intracellular electron paramagnetic resonance spectroscopy determining conformations on a molecular scale. A quantitative and model-based data analysis revealed that the vast majority of aS, be it wild-type or disease variants A30P or A53T, exists in the monomeric intrinsically disordered form in the cell.
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Affiliation(s)
- Julia Cattani
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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96
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Gmeiner C, Dorn G, Allain FHT, Jeschke G, Yulikov M. Spin labelling for integrative structure modelling: a case study of the polypyrimidine-tract binding protein 1 domains in complexes with short RNAs. Phys Chem Chem Phys 2018; 19:28360-28380. [PMID: 29034946 DOI: 10.1039/c7cp05822e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A combined method, employing NMR and EPR spectroscopies, has demonstrated its strength in solving structures of protein/RNA and other types of biomolecular complexes. This method works particularly well when the large biomolecular complex consists of a limited number of rigid building blocks, such as RNA-binding protein domains (RBDs). A variety of spin labels is available for such studies, allowing for conventional as well as spectroscopically orthogonal double electron-electron resonance (DEER) measurements in EPR. In this work, we compare different types of nitroxide-based and Gd(iii)-based spin labels attached to isolated RBDs of the polypyrimidine-tract binding protein 1 (PTBP1) and to short RNA fragments. In particular, we demonstrate experiments on spectroscopically orthogonal labelled RBD/RNA complexes. For all experiments we analyse spin labelling, DEER method performance, resulting distance distributions, and their consistency with the predictions from the spin label rotamers analysis. This work provides a set of intra-domain calibration DEER data, which can serve as a basis to start structure determination of the full length PTBP1 complex with an RNA derived from encephalomycarditis virus (EMCV) internal ribosomal entry site (IRES). For a series of tested labelling sites, we discuss their particular advantages and drawbacks in such a structure determination approach.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland.
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97
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Chen JL, Zhao Y, Gong YJ, Pan BB, Wang X, Su XC. Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2018; 70:77-92. [PMID: 29224182 DOI: 10.1007/s10858-017-0160-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu Zhao
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin-Bin Pan
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China.
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98
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Pan BB, Yang F, Ye Y, Wu Q, Li C, Huber T, Su XC. 3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy. Chem Commun (Camb) 2018; 52:10237-40. [PMID: 27470136 DOI: 10.1039/c6cc05490k] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determining the three-dimensional structure of a protein in living cells remains particularly challenging. We demonstrated that the integration of site-specific tagging proteins and GPS-Rosetta calculations provides a fast and effective way of determining the structures of proteins in living cells, and in principle the interactions and dynamics of protein-ligand complexes.
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Affiliation(s)
- Bin-Bin Pan
- State Key Laboratory and Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China.
| | - Feng Yang
- State Key Laboratory and Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China.
| | - Yansheng Ye
- 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 Institute of Physics and Mathematics, 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 Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, 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 Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
| | - Xun-Cheng Su
- State Key Laboratory and Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China.
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99
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Karthikeyan G, Bonucci A, Casano G, Gerbaud G, Abel S, Thomé V, Kodjabachian L, Magalon A, Guigliarelli B, Belle V, Ouari O, Mileo E. A Bioresistant Nitroxide Spin Label for In-Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies. Angew Chem Int Ed Engl 2018; 57:1366-1370. [DOI: 10.1002/anie.201710184] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/07/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB; Laboratoire de Chimie Bactérienne; Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
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100
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Karthikeyan G, Bonucci A, Casano G, Gerbaud G, Abel S, Thomé V, Kodjabachian L, Magalon A, Guigliarelli B, Belle V, Ouari O, Mileo E. A Bioresistant Nitroxide Spin Label for In-Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710184] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB; Laboratoire de Chimie Bactérienne; Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
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