1
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Ossadnik D, Kuzin S, Qi M, Yulikov M, Godt A. A Gd III-Based Spin Label at the Limits for Linewidth Reduction through Zero-Field Splitting Optimization. Inorg Chem 2023; 62:408-432. [PMID: 36525400 DOI: 10.1021/acs.inorgchem.2c03531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The remarkably narrow central line in the electron paramagnetic resonance spectrum and the very weak zero-field splitting (ZFS) make [GdIII(NO3Pic)] ([GdIII(TPATCN)]) an attractive starting point for the development of spin labels. For retaining the narrow line of this parent complex when modifying it with a substituent enabling bioconjugation, alkyl with a somehow remote functional group as a substituent at the picolinate moiety was found to be highly suitable because ZFS stayed weak, even if the threefold axial symmetry was broken. The ZFS is so weak that hyperfine coupling and/or g-value variations noticeably determine the linewidth in Q band and higher fields when the biomolecule is protonated, which is the standard situation, and in W band and higher fields for the protonated complex in a fully deuterated surrounding. Clearly, [NDSE-{GdIII(NO3Pic)}], a spin label targeting the cysteines in a peptide, is at a limit of linewidth narrowing through ZFS minimization. The labeling reaction is highly chemoselective and, applied to a polyproline with two cysteine units, it took no more than a minute at 7 °C and pH 7.8. Subsequent disulfide scrambling is very slow and can therefore be prevented. Double electron-electron resonance and relaxation-induced dipolar modulation enhancement applied to the spin-labeled polyproline proved the spin label useful for distance determination in peptides.
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Affiliation(s)
- Daniel Ossadnik
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Sergei Kuzin
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093Zurich, Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093Zurich, Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
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2
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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3
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Herath ID, Breen C, Hewitt SH, Berki TR, Kassir AF, Dodson C, Judd M, Jabar S, Cox N, Otting G, Butler SJ. A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time-Resolved Luminescence Studies. Chemistry 2021; 27:13009-13023. [PMID: 34152643 PMCID: PMC8518945 DOI: 10.1002/chem.202101143] [Citation(s) in RCA: 19] [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: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A lanthanide-binding tag site-specifically attached to a protein presents a tool to probe the protein by multiple spectroscopic techniques, including nuclear magnetic resonance, electron paramagnetic resonance and time-resolved luminescence spectroscopy. Here a new stable chiral LnIII tag, referred to as C12, is presented for spontaneous and quantitative reaction with a cysteine residue to generate a stable thioether bond. The synthetic protocol of the tag is relatively straightforward, and the tag is stable for storage and shipping. It displays greatly enhanced reactivity towards selenocysteine, opening a route towards selective tagging of selenocysteine in proteins containing cysteine residues. Loaded with TbIII or TmIII ions, the C12 tag readily generates pseudocontact shifts (PCS) in protein NMR spectra. It produces a relatively rigid tether between lanthanide and protein, which is beneficial for interpretation of the PCSs by single magnetic susceptibility anisotropy tensors, and it is suitable for measuring distance distributions in double electron-electron resonance experiments. Upon reaction with cysteine or other thiol compounds, the TbIII complex exhibits a 100-fold enhancement in luminescence quantum yield, affording a highly sensitive turn-on luminescence probe for time-resolved FRET assays and enzyme reaction monitoring.
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Affiliation(s)
- Iresha D. Herath
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Colum Breen
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Sarah H. Hewitt
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Thomas R. Berki
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Ahmad F. Kassir
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Charlotte Dodson
- Department of Pharmacy & PharmacologyUniversity of Bath Claverton DownBathBA2 7AYUK
| | - Martyna Judd
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Shereen Jabar
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Nicholas Cox
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Gottfried Otting
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Stephen J. Butler
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
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4
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Heaven G, Hollas MA, Tabernero L, Fielding AJ. Spin Labeling of Surface Cysteines Using a Bromoacrylaldehyde Spin Label. APPLIED MAGNETIC RESONANCE 2021; 52:959-970. [PMID: 34776648 PMCID: PMC8550513 DOI: 10.1007/s00723-021-01350-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/28/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Structural investigations of proteins and their biological complexes are now frequently complemented by distance constraints between spin labeled cysteines generated using double electron-electron resonance (DEER) spectroscopy, via site directed spin labeling (SDSL). Methanethiosulfonate spin label (MTSSL), has become ubiquitous in the SDSL of proteins, however, has limitations owing to its high number of rotamers, and reducibility. In this article we introduce the use of bromoacrylaldehyde spin label (BASL) as a cysteine spin label, demonstrating an advantage over MTSSL due to its increased selectivity for surface cysteines, eliminating the need to 'knock out' superfluous cysteine residues. Applied to the multidomain protein, His domain protein tyrosine phosphatase (HD-PTP), we show that BASL can be easily added in excess with selective labeling, whereas MTSSL causes protein precipitation. Furthermore, using DEER, we were able to measure a single cysteine pair distance in a three cysteine domain within HD-PTP. The label has a further advantage of comprising a sulfide in a three-bond tether, making it a candidate for protein binding and in-cell studies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00723-021-01350-1.
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Affiliation(s)
- Graham Heaven
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL UK
| | - Michael A. Hollas
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL UK
| | - Lydia Tabernero
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PL UK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF UK
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5
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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6
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Welegedara AP, Maleckis A, Bandara R, Mahawaththa MC, Dilhani Herath I, Jiun Tan Y, Giannoulis A, Goldfarb D, Otting G, Huber T. Cell-Free Synthesis of Selenoproteins in High Yield and Purity for Selective Protein Tagging. Chembiochem 2021; 22:1480-1486. [PMID: 33319405 DOI: 10.1002/cbic.202000785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Indexed: 01/10/2023]
Abstract
The selenol group of selenocysteine is much more nucleophilic than the thiol group of cysteine. Selenocysteine residues in proteins thus offer reactive points for rapid post-translational modification. Herein, we show that selenoproteins can be expressed in high yield and purity by cell-free protein synthesis by global substitution of cysteine by selenocysteine. Complete alkylation of solvent-exposed selenocysteine residues was achieved in 10 minutes with 4-chloromethylene dipicolinic acid (4Cl-MDPA) under conditions that left cysteine residues unchanged even after overnight incubation. GdIII -GdIII distances measured by double electron-electron resonance (DEER) experiments of maltose binding protein (MBP) containing two selenocysteine residues tagged with 4Cl-MDPA-GdIII were indistinguishable from GdIII -GdIII distances measured of MBP containing cysteine reacted with 4Br-MDPA tags.
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Affiliation(s)
- Adarshi P Welegedara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.,Department of Chemistry, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, 1006, Riga, Latvia
| | - Ruchira Bandara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Iresha Dilhani Herath
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Yi Jiun Tan
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Angeliki Giannoulis
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
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7
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Gamble Jarvi A, Sargun A, Bogetti X, Wang J, Achim C, Saxena S. Development of Cu 2+-Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations. J Phys Chem B 2020; 124:7544-7556. [PMID: 32790374 DOI: 10.1021/acs.jpcb.0c05509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Peptide nucleic acids (PNAs) are a promising group of synthetic analogues of DNA and RNA that offer several distinct advantages over the naturally occurring nucleic acids for applications in biosensing, drug delivery, and nanoelectronics. Because of its structural differences from DNA/RNA, methods to analyze and assess the structure, conformations, and dynamics are needed. In this work, we develop synergistic techniques for the study of the PNA conformation. We use CuQ2, a Cu2+ complex with 8-hydroxyquinoline (HQ), as an alternative base pair and as a spin label in electron paramagnetic resonance (EPR) distance methods. We use molecular dynamics (MD) simulations with newly developed force field parameters for the spin labels to interpret the distance constraints determined by EPR. We complement these methods by UV-vis and circular dichroism measurements and assess the efficacy of the Cu2+ label on a PNA duplex whose backbone is based on aminoethylglycine and a duplex with a hydroxymethyl backbone modification. We show that the Cu2+ label functions efficiently within the standard PNA and the hydroxymethyl-modified PNA and that the MD parameters may be used to accurately reproduce our EPR findings. Through the combination of EPR and MD, we gain new insights into the PNA structure and conformations as well as into the mechanism of orientational selectivity in Cu2+ EPR at X-band. These results present for the first time a rigid Cu2+ spin label used for EPR distance measurements in PNA and the accompanying MD force fields for the spin label. Our studies also reveal that the spin labels have a low impact on the structure of the PNA duplexes. The combined MD and EPR approach represents an important new tool for the characterization of the PNA duplex structure and provides valuable information to aid in the rational application of PNA at large.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Artur Sargun
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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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: 1.4] [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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9
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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: 2.7] [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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10
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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: 4.7] [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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11
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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: 22] [Impact Index Per Article: 3.7] [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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12
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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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13
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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: 4.0] [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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14
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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: 31] [Impact Index Per Article: 5.2] [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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15
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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: 4.8] [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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16
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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: 2.3] [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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17
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Gamble Jarvi A, Ranguelova K, Ghosh S, Weber RT, Saxena S. On the Use of Q-Band Double Electron–Electron Resonance To Resolve the Relative Orientations of Two Double Histidine-Bound Cu2+ Ions in a Protein. J Phys Chem B 2018; 122:10669-10677. [DOI: 10.1021/acs.jpcb.8b07727] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kalina Ranguelova
- Bruker BioSpin, Inc., EPR Division, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ralph T. Weber
- Bruker BioSpin, Inc., EPR Division, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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18
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Weickert S, Seitz T, Myers WK, Timmel CR, Drescher M, Wittmann V. Conformationally Unambiguous Spin Label for Exploring the Binding Site Topology of Multivalent Systems. J Phys Chem Lett 2018; 9:6131-6135. [PMID: 30284834 DOI: 10.1021/acs.jpclett.8b02243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multivalent carbohydrate-lectin interactions are a key concept in biological processes mediating, for example, signaling and adhesion. Binding affinities of multivalent ligands often increase by orders of magnitude compared to a monovalent binding situation. Thus, the design of multivalent ligands as potent inhibitors is a highly active field of research, where knowledge about the binding site topology is crucial. Here, we report a general strategy for precise distance measurements between the binding sites of multivalent target proteins using monovalent ligands. We designed and synthesized Monovalent, conformationally Unambiguously Spin-labeled LIgands (MUeSLI). Distances between the binding sites of the multivalent model lectin wheat germ agglutinin in complex with a GlcNAc-derived MUeSLI were determined using pulsed electron paramagnetic resonance spectroscopy. This approach is an efficient method for exploring multivalent systems with monovalent ligands, and it is readily transferable to other target proteins, allowing the targeted design of multivalent ligands without structural information available.
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Affiliation(s)
- Sabrina Weickert
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , 78457 Konstanz , Germany
| | - Torben Seitz
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , 78457 Konstanz , Germany
| | - William K Myers
- Department of Chemistry and Centre for Advanced Electron Spin Resonance (CAESR) , University of Oxford , South Parks Road , Oxford OX1 3QR , United Kingdom
| | - Christiane R Timmel
- Department of Chemistry and Centre for Advanced Electron Spin Resonance (CAESR) , University of Oxford , South Parks Road , Oxford OX1 3QR , United Kingdom
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , 78457 Konstanz , Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , 78457 Konstanz , Germany
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19
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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: 7.7] [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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20
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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: 3.4] [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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21
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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: 3.0] [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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22
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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: 9.9] [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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23
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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: 2.9] [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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24
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Mahawaththa MC, Lee MD, Giannoulis A, Adams LA, Feintuch A, Swarbrick JD, Graham B, Nitsche C, Goldfarb D, Otting G. Small neutral Gd(iii) tags for distance measurements in proteins by double electron–electron resonance experiments. Phys Chem Chem Phys 2018; 20:23535-23545. [DOI: 10.1039/c8cp03532f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small Gd(iii) tags based on DO3A deliver narrow and readily predictable distances by double electron–electron resonance (DEER) measurements.
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Affiliation(s)
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Angeliki Giannoulis
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Luke A. Adams
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Christoph Nitsche
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Gottfried Otting
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
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25
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Ghosh S, Lawless MJ, Rule GS, Saxena S. The Cu 2+-nitrilotriacetic acid complex improves loading of α-helical double histidine site for precise distance measurements by pulsed ESR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:163-171. [PMID: 29272745 DOI: 10.1016/j.jmr.2017.12.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 05/09/2023]
Abstract
Site-directed spin labeling using two strategically placed natural histidine residues allows for the rigid attachment of paramagnetic Cu2+. This double histidine (dHis) motif enables extremely precise, narrow distance distributions resolved by Cu2+-based pulsed ESR. Furthermore, the distance measurements are easily relatable to the protein backbone-structure. The Cu2+ ion has, till now, been introduced as a complex with the chelating agent iminodiacetic acid (IDA) to prevent unspecific binding. Recently, this method was found to have two limiting concerns that include poor selectivity towards α-helices and incomplete Cu2+-IDA complexation. Herein, we introduce an alternative method of dHis-Cu2+ loading using the nitrilotriacetic acid (NTA)-Cu2+ complex. We find that the Cu2+-NTA complex shows a four-fold increase in selectivity toward α-helical dHis sites. Furthermore, we show that 100% Cu2+-NTA complexation is achievable, enabling precise dHis loading and resulting in no free Cu2+ in solution. We analyze the optimum dHis loading conditions using both continuous wave and pulsed ESR. We implement these findings to show increased sensitivity of the Double Electron-Electron Resonance (DEER) experiment in two different protein systems. The DEER signal is increased within the immunoglobulin binding domain of protein G (called GB1). We measure distances between a dHis site on an α-helix and dHis site either on a mid-strand or a non-hydrogen bonded edge-strand β-sheet. Finally, the DEER signal is increased twofold within two α-helix dHis sites in the enzymatic dimer glutathione S-transferase exemplifying the enhanced α-helical selectivity of Cu2+-NTA.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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26
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Gmeiner C, Klose D, Mileo E, Belle V, Marque SRA, Dorn G, Allain FHT, Guigliarelli B, Jeschke G, Yulikov M. Orthogonal Tyrosine and Cysteine Site-Directed Spin Labeling for Dipolar Pulse EPR Spectroscopy on Proteins. J Phys Chem Lett 2017; 8:4852-4857. [PMID: 28933855 DOI: 10.1021/acs.jpclett.7b02220] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Site-directed spin labeling of native tyrosine residues in isolated domains of the protein PTBP1, using a Mannich-type reaction, was combined with conventional spin labeling of cysteine residues. Double electron-electron resonance (DEER) EPR measurements were performed for both the nitroxide-nitroxide and Gd(III)-nitroxide label combinations within the same protein molecule. For the prediction of distance distributions from a structure model, rotamer libraries were generated for the two linker forms of the tyrosine-reactive isoindoline-based nitroxide radical Nox. Only moderate differences exist between the spatial spin distributions for the two linker forms of Nox. This strongly simplifies DEER data analysis, in particular, if only mean distances need to be predicted.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Elisabetta Mileo
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Valérie Belle
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Sylvain R A Marque
- Aix Marseille Univ , CNRS, ICR, Institut de Chimie Radicalaire, Marseille 13397, France
- N. N. Vorozhtsov Novosibirsk Insititute of Organic Chemistry , 630090 Novosibirsk, Russia
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Bruno Guigliarelli
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
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27
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Welegedara AP, Yang Y, Lee MD, Swarbrick JD, Huber T, Graham B, Goldfarb D, Otting G. Double‐Arm Lanthanide Tags Deliver Narrow Gd
3+
–Gd
3+
Distance Distributions in Double Electron–Electron Resonance (DEER) Measurements. Chemistry 2017; 23:11694-11702. [DOI: 10.1002/chem.201702521] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Adarshi P. Welegedara
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Yin Yang
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Thomas Huber
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences Monash University Parkville VIC 3052 Australia
| | - Daniella Goldfarb
- Department of Chemical Physics Weizmann Institute of Science Rehovot 7610001 Israel
| | - Gottfried Otting
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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28
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Manukovsky N, Feintuch A, Kuprov I, Goldfarb D. Time domain simulation of Gd3+–Gd3+ distance measurements by EPR. J Chem Phys 2017; 147:044201. [DOI: 10.1063/1.4994084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nurit Manukovsky
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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29
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Wu Z, Lee MD, Carruthers TJ, Szabo M, Dennis ML, Swarbrick JD, Graham B, Otting G. New Lanthanide Tag for the Generation of Pseudocontact Shifts in DNA by Site-Specific Ligation to a Phosphorothioate Group. Bioconjug Chem 2017; 28:1741-1748. [PMID: 28485576 DOI: 10.1021/acs.bioconjchem.7b00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudocontact shifts (PCS) generated by paramagnetic lanthanides provide a rich source of long-range structural restraints that can readily be measured by nuclear magnetic resonance (NMR) spectroscopy. Many different lanthanide-binding tags have been designed for site-specific tagging of proteins, but established routes for tagging DNA with a single metal ion rely on difficult chemical synthesis. Here we present a simple and practical strategy for site-specific tagging of inexpensive phosphorothioate (PT) oligonucleotides. Commercially available PT oligonucleotides are diastereomers with S and R stereoconfiguration at the backbone PT site. The respective SP and RP diastereomers can readily be separated by HPLC. A new alkylating lanthanide-binding tag, C10, was synthesized that delivered quantitative tagging yields with both diastereomers. PCSs were observed following ligation with the complementary DNA strand to form double-stranded DNA duplexes. The PCSs were larger for the SP than the RP oligonucleotide and good correlation between back-calculated and experimental PCSs was observed. The C10 tag can also be attached to cysteine residues in proteins, where it generates a stable thioether bond. Ligated to the A28C mutant of ubiquitin, the tag produced excellent fits of magnetic susceptibility anisotropy (Δχ) tensors, with larger tensors than for the tagged PT oligonucleotides, indicating that the tag is not completely immobilized after ligation with a PT group.
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Affiliation(s)
- Zuyan Wu
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Michael D Lee
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Thomas J Carruthers
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
| | - Monika Szabo
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Matthew L Dennis
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - James D Swarbrick
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Bim Graham
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University , Canberra, ACT 2601, Australia
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30
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Nitsche C, Otting G. Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 98-99:20-49. [PMID: 28283085 DOI: 10.1016/j.pnmrs.2016.11.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Christoph Nitsche
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia. http://www.rsc.anu.edu.au/~go/index.html
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31
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Yang Y, Gong YJ, Litvinov A, Liu HK, Yang F, Su XC, Goldfarb D. Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins. Phys Chem Chem Phys 2017; 19:26944-26956. [DOI: 10.1039/c7cp04311b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The coordination mode of the metal ion in the spin label affects the distance distribution determined by DEER distance measurements.
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Affiliation(s)
- Yin Yang
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Aleksei Litvinov
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Hong-Kai Liu
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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32
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Lawless MJ, Ghosh S, Cunningham TF, Shimshi A, Saxena S. On the use of the Cu2+–iminodiacetic acid complex for double histidine based distance measurements by pulsed ESR. Phys Chem Chem Phys 2017; 19:20959-20967. [DOI: 10.1039/c7cp02564e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Cu2+-based DEER signal of the double histidine motif was increased by a factor of two by understanding optimal loading conditions.
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Affiliation(s)
- M. J. Lawless
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - S. Ghosh
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - T. F. Cunningham
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - A. Shimshi
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - S. Saxena
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
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33
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Meyer A, Schiemann O. PELDOR and RIDME Measurements on a High-Spin Manganese(II) Bisnitroxide Model Complex. J Phys Chem A 2016; 120:3463-72. [DOI: 10.1021/acs.jpca.6b00716] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andreas Meyer
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
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34
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Demay-Drouhard P, Ching HYV, Akhmetzyanov D, Guillot R, Tabares LC, Bertrand HC, Policar C. A Bis-Manganese(II)-DOTA Complex for Pulsed Dipolar Spectroscopy. Chemphyschem 2016; 17:2066-78. [DOI: 10.1002/cphc.201600234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
| | - H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC); Department of Biochemistry, Biophysics and Structural Biology; Université Paris-Saclay, CEA, CNRS UMR 9198; Gif-sur-Yvette F-91198 France
| | - Dmitry Akhmetzyanov
- Goethe-University Frankfurt am Main; Institute of Physical and Theoretical Chemistry and; Center for Biomolecular Magnetic Resonance; Max von Laue Str. 7 60438 Frankfurt am Main Germany
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux O'Orsay; Université Paris-Sud, UMR CNRS 8182, Université Paris-Saclay; 91405 Orsay France
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC); Department of Biochemistry, Biophysics and Structural Biology; Université Paris-Saclay, CEA, CNRS UMR 9198; Gif-sur-Yvette F-91198 France
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University; Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06; CNRS UMR 7203 LBM; 24 rue Lhomond 75005 Paris France
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35
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Cunningham TF, Pornsuwan S, Horne WS, Saxena S. Rotameric preferences of a protein spin label at edge-strand β-sheet sites. Protein Sci 2016; 25:1049-60. [PMID: 26948069 DOI: 10.1002/pro.2918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022]
Abstract
Protein spin labeling to yield the nitroxide-based R1 side chain is a powerful method to measure protein dynamics and structure by electron spin resonance. However, R1 measurements are complicated by the flexibility of the side chain. While analysis approaches for solvent-exposed α-helical environment have been developed to partially account for flexibility, similar work in β-sheets is lacking. The goal of this study is to provide the first essential steps for understanding the conformational preferences of R1 within edge β-strands using X-ray crystallography and double electron electron resonance (DEER) distance measurements. Crystal structures yielded seven rotamers for a non-hydrogen-bonded site and three rotamers for a hydrogen-bonded site. The observed rotamers indicate contextual differences in R1 conformational preferences compared to other solvent-exposed environments. For the DEER measurements, each strand site was paired with the same α-helical site elsewhere on the protein. The most probable distance observed by DEER is rationalized based on the rotamers observed in the crystal structure. Additionally, the appropriateness of common molecular modeling methods that account for R1 conformational preferences are assessed for the β-sheet environment. These results show that interpretation of R1 behavior in β-sheets is difficult and indicate further development is needed for these computational methods to correctly relate DEER distances to protein structure at edge β-strand sites.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Soraya Pornsuwan
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
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36
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Collauto A, Frydman V, Lee MD, Abdelkader EH, Feintuch A, Swarbrick JD, Graham B, Otting G, Goldfarb D. RIDME distance measurements using Gd(iii) tags with a narrow central transition. Phys Chem Chem Phys 2016; 18:19037-49. [DOI: 10.1039/c6cp03299k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methods based on pulse electron paramagnetic resonance allow measurement of the electron–electron dipolar coupling between two high-spin labels.
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Affiliation(s)
- A. Collauto
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - V. Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - M. D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - E. H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - A. Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - J. D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - B. Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - G. Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - D. Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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37
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Roser P, Schmidt MJ, Drescher M, Summerer D. Site-directed spin labeling of proteins for distance measurements in vitro and in cells. Org Biomol Chem 2016; 14:5468-76. [DOI: 10.1039/c6ob00473c] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We here review strategies for site-directed spin labeling (SDSL) of proteins and discuss their potential for EPR distance measurements to study protein function in vitro and in cells.
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Affiliation(s)
- P. Roser
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - M. J. Schmidt
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - M. Drescher
- Department of Chemistry
- Zukunftskolleg
- and Konstanz Research School Chemical Biology
- University of Konstanz
- 78457 Konstanz
| | - D. Summerer
- Department of Chemistry and Chemical Biology
- Technical University of Dortmund
- 44227 Dortmund
- Germany
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38
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Keller K, Zalibera M, Qi M, Koch V, Wegner J, Hintz H, Godt A, Jeschke G, Savitsky A, Yulikov M. EPR characterization of Mn(ii) complexes for distance determination with pulsed dipolar spectroscopy. Phys Chem Chem Phys 2016; 18:25120-25135. [DOI: 10.1039/c6cp04884f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
EPR properties of four Mn(ii) complexes and Tikhonov regularization-based analysis of RIDME data containing dipolar overtones are presented.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Michal Zalibera
- Max Planck Institut for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
- Institute of Physical Chemistry and Chemical Physics
- Slovak University of Technology in Bratislava
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Vanessa Koch
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Julia Wegner
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - 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 Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Anton Savitsky
- Max Planck Institut for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
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39
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Cohen MR, Frydman V, Milko P, Iron MA, Abdelkader EH, Lee MD, Swarbrick JD, Raitsimring A, Otting G, Graham B, Feintuch A, Goldfarb D. Overcoming artificial broadening in Gd3+–Gd3+ distance distributions arising from dipolar pseudo-secular terms in DEER experiments. Phys Chem Chem Phys 2016; 18:12847-59. [DOI: 10.1039/c6cp00829a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double electron–electron resonance (DEER) is used to probe structure of Gd3+-tagged biomolecules by determining Gd3+–Gd3+ distances.
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Affiliation(s)
- Marie Ramirez Cohen
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Veronica Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Petr Milko
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Mark A. Iron
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | | | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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40
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Abdelkader EH, Yao X, Feintuch A, Adams LA, Aurelio L, Graham B, Goldfarb D, Otting G. Pulse EPR-enabled interpretation of scarce pseudocontact shifts induced by lanthanide binding tags. JOURNAL OF BIOMOLECULAR NMR 2016; 64:39-51. [PMID: 26597990 DOI: 10.1007/s10858-015-0003-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor to the 3D structure of the protein in an 8-parameter fit, which requires a large set of PCSs to be reliable. In an alternative approach, we used multiple Gd(3+)-Gd(3+) distances measured by double electron-electron resonance (DEER) experiments to define the metal position, allowing Δχ-tensor determinations from more robust 5-parameter fits that can be performed with a relatively sparse set of PCSs. Using this approach with the 32 kDa E. coli aspartate/glutamate binding protein (DEBP), we demonstrate a structural transition between substrate-bound and substrate-free DEBP, supported by PCSs generated by C3-Tm(3+) and C3-Tb(3+) tags attached to a genetically encoded p-azidophenylalanine residue. The significance of small PCSs was magnified by considering the difference between the chemical shifts measured with Tb(3+) and Tm(3+) rather than involving a diamagnetic reference. The integrative sparse data approach developed in this work makes poorly soluble proteins of limited stability amenable to structural studies in solution, without having to rely on cysteine mutations for tag attachment.
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Affiliation(s)
- Elwy H Abdelkader
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Xuejun Yao
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Luke A Adams
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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