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Abdullin D, Rauh Corro P, Hett T, Schiemann O. PDSFit: PDS data analysis in the presence of orientation selectivity, g-anisotropy, and exchange coupling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:37-60. [PMID: 38130168 DOI: 10.1002/mrc.5415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS), encompassing techniques such as pulsed electron-electron double resonance (PELDOR or DEER) and relaxation-induced dipolar modulation enhancement (RIDME), is a valuable method in structural biology and materials science for obtaining nanometer-scale distance distributions between electron spin centers. An important aspect of PDS is the extraction of distance distributions from the measured time traces. Most software used for this PDS data analysis relies on simplifying assumptions, such as assuming isotropic g-factors of ~2 and neglecting orientation selectivity and exchange coupling. Here, the program PDSFit is introduced, which enables the analysis of PELDOR and RIDME time traces with or without orientation selectivity. It can be applied to spin systems consisting of up to two spin centers with anisotropic g-factors and to spin systems with exchange coupling. It employs a model-based fitting of the time traces using parametrized distance and angular distributions, and parametrized PDS background functions. The fitting procedure is followed by an error analysis for the optimized parameters of the distributions and backgrounds. Using five different experimental data sets published previously, the performance of PDSFit is tested and found to provide reliable solutions.
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Affiliation(s)
- Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Pablo Rauh Corro
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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2
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Rogers CJ, Asthana D, Brookfield A, Chiesa A, Timco GA, Collison D, Natrajan LS, Carretta S, Winpenny REP, Bowen AM. Modelling Conformational Flexibility in a Spectrally Addressable Molecular Multi‐Qubit Model System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ciarán J. Rogers
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Deepak Asthana
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
- Department of Chemistry Ashoka University Sonipat Haryana India
| | - Adam Brookfield
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Alessandro Chiesa
- Dipartimento di Scienze Matematiche Fisiche e Informatiche Università di Parma 43124 Parma Italy
- INFN–Sezione di Milano-Bicocca Gruppo Collegato di Parma I-43124 Parma Italy
- UdR Parma INSTM I-43124 Parma Italy
| | - Grigore A. Timco
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - David Collison
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Louise S. Natrajan
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Stefano Carretta
- Dipartimento di Scienze Matematiche Fisiche e Informatiche Università di Parma 43124 Parma Italy
- INFN–Sezione di Milano-Bicocca Gruppo Collegato di Parma I-43124 Parma Italy
- UdR Parma INSTM I-43124 Parma Italy
| | - Richard E. P. Winpenny
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Alice M. Bowen
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
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3
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Rogers CJ, Asthana D, Brookfield A, Chiesa A, Timco GA, Collison D, Natrajan LS, Carretta S, Winpenny REP, Bowen AM. Modelling Conformational Flexibility in a Spectrally Addressable Molecular Multi-Qubit Model System. Angew Chem Int Ed Engl 2022; 61:e202207947. [PMID: 36222278 PMCID: PMC9828767 DOI: 10.1002/anie.202207947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/11/2022]
Abstract
Dipolar coupled multi-spin systems have the potential to be used as molecular qubits. Herein we report the synthesis of a molecular multi-qubit model system with three individually addressable, weakly interacting, spin1 / 2 ${{ 1/2 }}$ centres of differing g-values. We use pulsed Electron Paramagnetic Resonance (EPR) techniques to characterise and separately address the individual electron spin qubits; CuII , Cr7 Ni ring and a nitroxide, to determine the strength of the inter-qubit dipolar interaction. Orientation selective Relaxation-Induced Dipolar Modulation Enhancement (os-RIDME) detecting across the CuII spectrum revealed a strongly correlated CuII -Cr7 Ni ring relationship; detecting on the nitroxide resonance measured both the nitroxide and CuII or nitroxide and Cr7 Ni ring correlations, with switchability of the interaction based on differing relaxation dynamics, indicating a handle for implementing EPR-based quantum information processing (QIP) algorithms.
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Affiliation(s)
- Ciarán J. Rogers
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Deepak Asthana
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
- Department of ChemistryAshoka UniversitySonipatHaryanaIndia
| | - Adam Brookfield
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Alessandro Chiesa
- Dipartimento di Scienze Matematiche Fisiche e InformaticheUniversità di Parma43124ParmaItaly
- INFN–Sezione di Milano-BicoccaGruppo Collegato di ParmaI-43124ParmaItaly
- UdR ParmaINSTMI-43124ParmaItaly
| | - Grigore A. Timco
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - David Collison
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Louise S. Natrajan
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Stefano Carretta
- Dipartimento di Scienze Matematiche Fisiche e InformaticheUniversità di Parma43124ParmaItaly
- INFN–Sezione di Milano-BicoccaGruppo Collegato di ParmaI-43124ParmaItaly
- UdR ParmaINSTMI-43124ParmaItaly
| | - Richard E. P. Winpenny
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Alice M. Bowen
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
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4
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Keller K, Ritsch I, Hintz H, Hülsmann M, Qi M, Breitgoff FD, Klose D, Polyhach Y, Yulikov M, Godt A, Jeschke G. Accessing distributions of exchange and dipolar couplings in stiff molecular rulers with Cu(ii) centres. Phys Chem Chem Phys 2020; 22:21707-21730. [DOI: 10.1039/d0cp03105d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel approaches to quantitatively analyse distributed exchange couplings are described and tested on experimental data sets for stiff synthetic molecules.
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5
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Abdullin D, Brehm P, Fleck N, Spicher S, Grimme S, Schiemann O. Pulsed EPR Dipolar Spectroscopy on Spin Pairs with one Highly Anisotropic Spin Center: The Low-Spin Fe III Case. Chemistry 2019; 25:14388-14398. [PMID: 31386227 PMCID: PMC6900076 DOI: 10.1002/chem.201902908] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/05/2019] [Indexed: 02/01/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling constants and thus the distance between electron spin centers. Up to now, PDS measurements have been mostly applied to spin centers whose g-anisotropies are moderate and therefore have a negligible effect on the dipolar coupling constants. In contrast, spin centers with large g-anisotropy yield dipolar coupling constants that depend on the g-values. In this case, the usual methods of extracting distances from the raw PDS data cannot be applied. Here, the effect of the g-anisotropy on PDS data is studied in detail on the example of the low-spin Fe3+ ion. First, this effect is described theoretically, using the work of Bedilo and Maryasov (Appl. Magn. Reson. 2006, 30, 683-702) as a basis. Then, two known Fe3+ /nitroxide compounds and one new Fe3+ /trityl compound were synthesized and PDS measurements were carried out on them using a method called relaxation induced dipolar modulation enhancement (RIDME). Based on the theoretical results, a RIDME data analysis procedure was developed, which facilitated the extraction of the inter-spin distance and the orientation of the inter-spin vector relative to the Fe3+ g-tensor frame from the RIDME data. The accuracy of the determined distances and orientations was confirmed by comparison with MD simulations. This method can thus be applied to the highly relevant class of metalloproteins with, for example, low-spin Fe3+ ions.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Philipp Brehm
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
- Current address: Institute of Inorganic ChemistryUniversity of Bonn53115BonnGermany
| | - Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Sebastian Spicher
- Mulliken Center for Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
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6
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Srivastava M, Freed JH. Singular Value Decomposition Method To Determine Distance Distributions in Pulsed Dipolar Electron Spin Resonance: II. Estimating Uncertainty. J Phys Chem A 2018; 123:359-370. [PMID: 30525624 DOI: 10.1021/acs.jpca.8b07673] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper is a continuation of the method introduced by Srivastava and Freed (2017) that is a new method based on truncated singular value decomposition (TSVD) for obtaining physical results from experimental signals without any need for Tikhonov regularization or other similar methods that require a regularization parameter. We show here how to estimate the uncertainty in the SVD-generated solutions. The uncertainty in the solution may be obtained by finding the minimum and maximum values over which the solution remains converged. These are obtained from the optimum range of singular value contributions, where the width of this region depends on the solution point location (e.g., distance) and the signal-to-noise ratio (SNR) of the signal. The uncertainty levels typically found are very small with substantial SNR of the (denoised) signal, emphasizing the reliability of the method. With poorer SNR, the method is still satisfactory but with greater uncertainty, as expected. Pulsed dipolar electron spin resonance spectroscopy experiments are used as an example, but this TSVD approach is general and thus applicable to any similar experimental method wherein singular matrix inversion is needed to obtain the physically relevant result. We show that the Srivastava-Freed TSVD method along with the estimate of uncertainty can be effectively applied to pulsed dipolar electron spin resonance signals with SNR > 30, and even for a weak signal (e.g., SNR ≈ 3) reliable results are obtained by this method, provided the signal is first denoised using wavelet transforms (WavPDS).
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7
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CW EPR and DEER Methods to Determine BCL-2 Family Protein Structure and Interactions: Application of Site-Directed Spin Labeling to BAK Apoptotic Pores. Methods Mol Biol 2018. [PMID: 30536012 DOI: 10.1007/978-1-4939-8861-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The continuous wave (CW) and pulse electron paramagnetic resonance (EPR) methods enable the measurement of distances between spin-labeled residues in biopolymers including proteins, providing structural information. Here we describe the CW EPR deconvolution/convolution method and the four-pulse double electron-electron resonance (DEER) approach for distance determination, which were applied to elucidate the organization of the BAK apoptotic pores formed in the lipid bilayers.
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8
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Milikisiyants S, Voinov MA, Smirnov AI. Refocused Out-Of-Phase (ROOPh) DEER: A pulse scheme for suppressing an unmodulated background in double electron-electron resonance experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:9-18. [PMID: 29800786 DOI: 10.1016/j.jmr.2018.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/12/2018] [Accepted: 05/14/2018] [Indexed: 05/24/2023]
Abstract
EPR pulsed dipolar spectroscopy (PDS) is indispensable for measurements of nm-scale distances between electronic spins in biological and other systems. While several useful modifications and pulse sequences for PDS have been developed in recent years, DEER experiments utilizing pump and observer pulses at two different frequencies remain the most popular for practical applications. One of the major drawbacks of all the available DEER approaches is the presence of a significant unmodulated fraction in the detected signal that arises from an incomplete inversion of the coupled spins by the pump pulse. The latter fraction is perceived as one of the major sources of error for the reconstructed distance distributions. We describe an alternative detection scheme - a Refocused Out-Of-Phase DEER (ROOPh-DEER) - to acquire only the modulated fraction of the dipolar DEER signal. When Zeeman splitting is small compared to the temperature, the out-of-phase magnetization components cancel each other and are not observed in 4-pulse DEER experiment. In ROOPh-DEER these components are refocused by an additional pump pulse while the in-phase component containing an unmodulated background is filtered out by a pulse at the observed frequency applied right at the position of the refocused echo. Experimental implementation of the ROOPh-DEER detection scheme requires at least three additional pulses as was demonstrated on an example of a 7-pulse sequence. The application of 7-pulse ROOPh-DEER sequence to a model biradical yielded the interspin distance of 1.94 ± 0.07 nm identical to the one obtained with the conventional 4-pulse DEER, however, without the unmodulated background present as a dominant fraction in the latter signal.
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Affiliation(s)
- Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695, USA
| | - Maxim A Voinov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695, USA
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695, USA.
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9
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Sahu ID, Lorigan GA. Site-Directed Spin Labeling EPR for Studying Membrane Proteins. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3248289. [PMID: 29607317 PMCID: PMC5828257 DOI: 10.1155/2018/3248289] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/21/2017] [Indexed: 01/13/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a rapidly expanding powerful biophysical technique to study the structural and dynamic properties of membrane proteins in a native environment. Membrane proteins are responsible for performing important functions in a wide variety of complicated biological systems that are responsible for the survival of living organisms. In this review, a brief introduction of the most popular SDSL EPR techniques and illustrations of recent applications for studying pertinent structural and dynamic properties on membrane proteins will be discussed.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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10
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Giannoulis A, Motion CL, Oranges M, Bühl M, Smith GM, Bode BE. Orientation selection in high-field RIDME and PELDOR experiments involving low-spin CoII ions. Phys Chem Chem Phys 2018; 20:2151-2154. [DOI: 10.1039/c7cp07248a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orientation selective pulse dipolar electron paramagnetic resonance unravels relative geometries of spin centres from RIDME and PELDOR data.
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Affiliation(s)
- Angeliki Giannoulis
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
| | | | - Maria Oranges
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
| | - Michael Bühl
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
| | - Graham M. Smith
- SUPA, School of Physics & Astronomy, University of St Andrews
- UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
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11
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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: 3.2] [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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12
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Meyer A, Jassoy JJ, Spicher S, Berndhäuser A, Schiemann O. Performance of PELDOR, RIDME, SIFTER, and DQC in measuring distances in trityl based bi- and triradicals: exchange coupling, pseudosecular coupling and multi-spin effects. Phys Chem Chem Phys 2018; 20:13858-13869. [DOI: 10.1039/c8cp01276h] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The performance of pulsed EPR methods for distance measurements is evaluated on three different trityl model systems.
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Affiliation(s)
- Andreas Meyer
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Jean Jacques Jassoy
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Andreas Berndhäuser
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
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13
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Constructive quantum interference in a bis-copper six-porphyrin nanoring. Nat Commun 2017; 8:14842. [PMID: 28327654 PMCID: PMC5364408 DOI: 10.1038/ncomms14842] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/03/2017] [Indexed: 12/14/2022] Open
Abstract
The exchange interaction, J, between two spin centres is a convenient measure of through bond electronic communication. Here, we investigate quantum interference phenomena in a bis-copper six-porphyrin nanoring by electron paramagnetic resonance spectroscopy via measurement of the exchange coupling between the copper centres. Using an analytical expression accounting for both dipolar and exchange coupling to simulate the time traces obtained in a double electron electron resonance experiment, we demonstrate that J can be quantified to high precision even in the presence of significant through-space coupling. We show that the exchange coupling between two spin centres is increased by a factor of 4.5 in the ring structure with two parallel coupling paths as compared to an otherwise identical system with just one coupling path, which is a clear signature of constructive quantum interference. Quantum interference in charge transport is attracting interest with applications in nanoelectronics and quantum computing. Here, the authors present a method for quantifying electronic transmission through molecules, and demonstrate constructive quantum interference in a molecule with two identical, parallel coupling paths.
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14
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Srivastava M, Georgieva ER, Freed JH. A New Wavelet Denoising Method for Experimental Time-Domain Signals: Pulsed Dipolar Electron Spin Resonance. J Phys Chem A 2017; 121:2452-2465. [PMID: 28257206 DOI: 10.1021/acs.jpca.7b00183] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We adapt a new wavelet-transform-based method of denoising experimental signals to pulse-dipolar electron-spin resonance spectroscopy (PDS). We show that signal averaging times of the time-domain signals can be reduced by as much as 2 orders of magnitude, while retaining the fidelity of the underlying signals, in comparison with noiseless reference signals. We have achieved excellent signal recovery when the initial noisy signal has an SNR ≳ 3. This approach is robust and is expected to be applicable to other time-domain spectroscopies. In PDS, these time-domain signals representing the dipolar interaction between two electron spin labels are converted into their distance distribution functions P(r), usually by regularization methods such as Tikhonov regularization. The significant improvements achieved by using denoised signals for this regularization are described. We show that they yield P(r)'s with more accurate detail and yield clearer separations of respective distances, which is especially important when the P(r)'s are complex. Also, longer distance P(r)'s, requiring longer dipolar evolution times, become accessible after denoising. In comparison to standard wavelet denoising approaches, it is clearly shown that the new method (WavPDS) is superior.
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Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Elka R Georgieva
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Jack H Freed
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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15
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Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications. Biochem Soc Trans 2016; 43:1023-32. [PMID: 26517918 DOI: 10.1042/bst20150138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented.
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16
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Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics. Biochem Soc Trans 2016; 44:905-15. [DOI: 10.1042/bst20160024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/19/2022]
Abstract
During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated.
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17
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Song L, Liu Z, Kaur P, Esquiaqui JM, Hunter RI, Hill S, Smith GM, Fanucci GE. Toward increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:188-196. [PMID: 26923151 DOI: 10.1016/j.jmr.2016.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
High-field, high-frequency electron paramagnetic resonance (EPR) spectroscopy at W-(∼94 GHz) and D-band (∼140 GHz) is important for investigating the conformational dynamics of flexible biological macromolecules because this frequency range has increased spectral sensitivity to nitroxide motion over the 100 ps to 2 ns regime. However, low concentration sensitivity remains a roadblock for studying aqueous samples at high magnetic fields. Here, we examine the sensitivity of a non-resonant thin-layer cylindrical sample holder, coupled to a quasi-optical induction-mode W-band EPR spectrometer (HiPER), for continuous wave (CW) EPR analyses of: (i) the aqueous nitroxide standard, TEMPO; (ii) the unstructured to α-helical transition of a model IDP protein; and (iii) the base-stacking transition in a kink-turn motif of a large 232 nt RNA. For sample volumes of ∼50 μL, concentration sensitivities of 2-20 μM were achieved, representing a ∼10-fold enhancement compared to a cylindrical TE011 resonator on a commercial Bruker W-band spectrometer. These results therefore highlight the sensitivity of the thin-layer sample holders employed in HiPER for spin-labeling studies of biological macromolecules at high fields, where applications can extend to other systems that are facilitated by the modest sample volumes and ease of sample loading and geometry.
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Affiliation(s)
- Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Pavanjeet Kaur
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Robert I Hunter
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Graham M Smith
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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18
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Stevens MA, McKay JE, Robinson JLS, El Mkami H, Smith GM, Norman DG. The use of the Rx spin label in orientation measurement on proteins, by EPR. Phys Chem Chem Phys 2016; 18:5799-806. [PMID: 26426572 PMCID: PMC4756314 DOI: 10.1039/c5cp04753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/25/2015] [Indexed: 12/15/2022]
Abstract
The bipedal spin label Rx is more restricted in its conformation and dynamics than its monopodal counterpart R1. To systematically investigate the utility of the Rx label, we have attempted to comprehensively survey the attachment of Rx to protein secondary structures. We have examined the formation, structure and dynamics of the spin label in relation to the underlying protein in order to determine feasibility and optimum conditions for distance and orientation measurement by pulsed EPR. The labeled proteins have been studied using molecular dynamics, CW EPR, pulsed EPR distance measurement at X-band and orientation measurement at W-band. The utility of different modes and positions of attachment have been compared and contrasted.
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Affiliation(s)
- M A Stevens
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - J E McKay
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - J L S Robinson
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - H El Mkami
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - G M Smith
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - D G Norman
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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19
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Collauto A, Feintuch A, Qi M, Godt A, Meade T, Goldfarb D. Gd(III) complexes as paramagnetic tags: Evaluation of the spin delocalization over the nuclei of the ligand. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 263:156-163. [PMID: 26802219 DOI: 10.1016/j.jmr.2015.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 05/15/2023]
Abstract
Complexes of the Gd(III) ion are currently being established as spin labels for distance determination in biomolecules by pulse dipolar spectroscopy. Because Gd(III) is an f ion, one expects electron spin density to be localized on the Gd(III) ion - an important feature for the mentioned application. Most of the complex ligands have nitrogens as Gd(III) coordinating atoms. Therefore, measurement of the (14)N hyperfine coupling gives access to information on the localization of the electron spin on the Gd(III) ion. We carried out W-band, 1D and 2D (14)N and (1)H ENDOR measurements on the Gd(III) complexes Gd-DOTA, Gd-538, Gd-595, and Gd-PyMTA that serve as spin labels for Gd-Gd distance measurements. The obtained (14)N spectra are particularly well resolved, revealing both the hyperfine and nuclear quadrupole splittings, which were assigned using 2D Mims ENDOR experiments. Additionally, the spectral contributions of the two different types of nitrogen atoms of Gd-PyMTA, the aliphatic N atom and the pyridine N atom, were distinguishable. The (14)N hyperfine interaction was found to have a very small isotropic hyperfine component of -0.25 to -0.37MHz. Furthermore, the anisotropic hyperfine interactions with the (14)N nuclei and with the non-exchangeable protons of the ligands are well described by the point-dipole approximation using distances derived from the crystal structures. We therefore conclude that the spin density is fully localized on the Gd(III) ion and that the spin density distribution over the nuclei of the ligands is rightfully ignored when analyzing distance measurements.
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Affiliation(s)
- A Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - A Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - M Qi
- University Bielefeld, Faculty of Chemistry and Center for Molecular Materials, D-33615 Bielefeld, Germany
| | - A Godt
- University Bielefeld, Faculty of Chemistry and Center for Molecular Materials, D-33615 Bielefeld, Germany
| | - T Meade
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - D Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel.
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20
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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: 3.0] [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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21
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Abstract
Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
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22
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Prisner TF, Marko A, Sigurdsson ST. Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:187-98. [PMID: 25701439 DOI: 10.1016/j.jmr.2014.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 05/22/2023]
Abstract
Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.
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Affiliation(s)
- T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - S Th Sigurdsson
- Science Institute, University of Iceland, Reykjavik, Iceland
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23
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Dalaloyan A, Qi M, Ruthstein S, Vega S, Godt A, Feintuch A, Goldfarb D. Gd(iii)–Gd(iii) EPR distance measurements – the range of accessible distances and the impact of zero field splitting. Phys Chem Chem Phys 2015; 17:18464-76. [DOI: 10.1039/c5cp02602d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gd rulers were designed in the 2–8 nm range for in-depth evaluation of Gd(iii) complexes as spin labels for EPR distance measurements.
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Affiliation(s)
- Arina Dalaloyan
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Mian Qi
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Sharon Ruthstein
- Department of Chemistry
- Faculty of Exact Sciences
- Bar-Ilan University
- Ramat Gan
- Israel
| | - Shimon Vega
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Adelheid Godt
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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24
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25
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Valera S, Bode BE. Strategies for the synthesis of yardsticks and abaci for nanometre distance measurements by pulsed EPR. Molecules 2014; 19:20227-56. [PMID: 25479188 PMCID: PMC6271543 DOI: 10.3390/molecules191220227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/19/2014] [Accepted: 11/27/2014] [Indexed: 01/18/2023] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) techniques have been found to be efficient tools for the elucidation of structure in complex biological systems as they give access to distances in the nanometre range. These measurements can provide additional structural information such as relative orientations, structural flexibility or aggregation states. A wide variety of model systems for calibration and optimisation of pulsed experiments has been synthesised. Their design is based on mimicking biological systems or materials in specific properties such as the distances themselves and the distance distributions. Here, we review selected approaches to the synthesis of chemical systems bearing two or more spin centres, such as nitroxide or trityl radicals, metal ions or combinations thereof and outline their application in pulsed EPR distance measurements.
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Affiliation(s)
- Silvia Valera
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, KY16 9ST Fife, UK.
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26
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Yin XX, Hadjiloucas S, Zhang Y. Complex extreme learning machine applications in terahertz pulsed signals feature sets. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014; 117:387-403. [PMID: 25037827 DOI: 10.1016/j.cmpb.2014.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/16/2014] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
This paper presents a novel approach to the automatic classification of very large data sets composed of terahertz pulse transient signals, highlighting their potential use in biochemical, biomedical, pharmaceutical and security applications. Two different types of THz spectra are considered in the classification process. Firstly a binary classification study of poly-A and poly-C ribonucleic acid samples is performed. This is then contrasted with a difficult multi-class classification problem of spectra from six different powder samples that although have fairly indistinguishable features in the optical spectrum, they also possess a few discernable spectral features in the terahertz part of the spectrum. Classification is performed using a complex-valued extreme learning machine algorithm that takes into account features in both the amplitude as well as the phase of the recorded spectra. Classification speed and accuracy are contrasted with that achieved using a support vector machine classifier. The study systematically compares the classifier performance achieved after adopting different Gaussian kernels when separating amplitude and phase signatures. The two signatures are presented as feature vectors for both training and testing purposes. The study confirms the utility of complex-valued extreme learning machine algorithms for classification of the very large data sets generated with current terahertz imaging spectrometers. The classifier can take into consideration heterogeneous layers within an object as would be required within a tomographic setting and is sufficiently robust to detect patterns hidden inside noisy terahertz data sets. The proposed study opens up the opportunity for the establishment of complex-valued extreme learning machine algorithms as new chemometric tools that will assist the wider proliferation of terahertz sensing technology for chemical sensing, quality control, security screening and clinic diagnosis. Furthermore, the proposed algorithm should also be very useful in other applications requiring the classification of very large datasets.
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Affiliation(s)
- X-X Yin
- Center for Applied Informatics and College of Enginering and Science, Victoria University, Footscray, VIC3011, Australia.
| | - S Hadjiloucas
- School of Systems Engineering, University of Reading, Reading RG6 6AY, UK
| | - Y Zhang
- Center for Applied Informatics and College of Enginering and Science, Victoria University, Footscray, VIC3011, Australia
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27
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Edwards D, Huber T, Hussain S, Stone K, Kinnebrew M, Kaminker I, Matalon E, Sherwin M, Goldfarb D, Han S. Determining the Oligomeric Structure of Proteorhodopsin by Gd3+-Based Pulsed Dipolar Spectroscopy of Multiple Distances. Structure 2014; 22:1677-86. [DOI: 10.1016/j.str.2014.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/15/2014] [Accepted: 09/04/2014] [Indexed: 12/30/2022]
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28
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Abdullin D, Hagelueken G, Hunter RI, Smith GM, Schiemann O. Geometric model-based fitting algorithm for orientation-selective PELDOR data. Mol Phys 2014. [DOI: 10.1080/00268976.2014.960494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | | | | | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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29
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Mateo-Alonso A. Pyrene-fused pyrazaacenes: from small molecules to nanoribbons. Chem Soc Rev 2014; 43:6311-24. [DOI: 10.1039/c4cs00119b] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Goldfarb D. Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy. Phys Chem Chem Phys 2014; 16:9685-99. [DOI: 10.1039/c3cp53822b] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Kunjir NC, Reginsson GW, Schiemann O, Sigurdsson ST. Measurements of short distances between trityl spin labels with CW EPR, DQC and PELDOR. Phys Chem Chem Phys 2013; 15:19673-85. [PMID: 24135783 DOI: 10.1039/c3cp52789a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trityl based spin labels are emerging as a complement to nitroxides in nanometer distance measurements using EPR methods. The narrow spectral width of the trityl radicals prompts us to ask the question at which distance between these spin centers, the pseudo-secular part of the dipolar coupling and spin density delocalization have to be taken into account. For this, two trityl-trityl and one trityl-nitroxide model compounds were synthesized with well-defined interspin distances. Continuous wave (CW) EPR, double quantum coherence (DQC) and pulsed electron-electron double resonance (PELDOR) spectra were acquired from these compounds at commercial X-band frequencies. The data analysis shows that two of the compounds, with distances of up to 25 Å, fall into the strong coupling regime and that precise distances can only be obtained if both the spin density delocalization and the pseudo-secular part of the dipolar coupling are included in the analysis.
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Affiliation(s)
- Nitin C Kunjir
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavík, Iceland.
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32
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Tsvetkov YD. Nitroxyls and PELDOR: Nitroxyl radicals in pulsed electron-electron double resonance spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Lovett JE, Abbott RJM, Roversi P, Johnson S, Caesar JJE, Doria M, Jeschke G, Timmel CR, Lea SM. Investigating the structure of the factor B vWF-A domain/CD55 protein-protein complex using DEER spectroscopy: successes and pitfalls. Mol Phys 2013; 111:2865-2872. [PMID: 24954957 PMCID: PMC4056885 DOI: 10.1080/00268976.2013.827754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/05/2013] [Indexed: 01/03/2023]
Abstract
The electron paramagnetic resonance technique of double electron-electron resonance (DEER) was used to measure nanometre-scale distances between nitroxide spin labels attached to the complement regulatory protein CD55 (also known as decay accelerating factor) and the von Willebrand factor A (vWF-A) domain of factor B. Following a thorough assessment of the quality of the data, distances obtained from good-quality measurements are compared to predicted distances from a previously hypothesised model for the complex and are found to be incompatible. The success of using these distances as restraints in multi-body docking routines is presented critically.
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Affiliation(s)
- Janet E Lovett
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK ; EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Rachel J M Abbott
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pietro Roversi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK ; Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Marianna Doria
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK ; Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Gunnar Jeschke
- Laboratory for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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34
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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35
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Hubbell WL, López CJ, Altenbach C, Yang Z. Technological advances in site-directed spin labeling of proteins. Curr Opin Struct Biol 2013; 23:725-33. [PMID: 23850140 DOI: 10.1016/j.sbi.2013.06.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/12/2013] [Indexed: 12/23/2022]
Abstract
Molecular flexibility over a wide time range is of central importance to the function of many proteins, both soluble and membrane. Revealing the modes of flexibility, their amplitudes, and time scales under physiological conditions is the challenge for spectroscopic methods, one of which is site-directed spin labeling EPR (SDSL-EPR). Here we provide an overview of some recent technological advances in SDSL-EPR related to investigation of structure, structural heterogeneity, and dynamics of proteins. These include new classes of spin labels, advances in measurement of long range distances and distance distributions, methods for identifying backbone and conformational fluctuations, and new strategies for determining the kinetics of protein motion.
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Affiliation(s)
- Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
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36
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Yap YS, Yamamoto H, Tabuchi Y, Negoro M, Kagawa A, Kitagawa M. Strongly driven electron spins using a K(u) band stripline electron paramagnetic resonance resonator. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 232:62-67. [PMID: 23703225 DOI: 10.1016/j.jmr.2013.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 06/02/2023]
Abstract
This article details our work to obtain strong excitation for electron paramagnetic resonance (EPR) experiments by improving the resonator's efficiency. The advantages and application of strong excitation are discussed. Two 17 GHz transmission-type, stripline resonators were designed, simulated and fabricated. Scattering parameter measurements were carried out and quality factor were measured to be around 160 and 85. Simulation results of the microwave's magnetic field distribution are also presented. To determine the excitation field at the sample, nutation experiments were carried out and power dependence were measured using two organic samples at room temperature. The highest recorded Rabi frequency was rated at 210 MHz with an input power of about 1 W, which corresponds to a π/2 pulse of about 1.2 ns.
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Affiliation(s)
- Yung Szen Yap
- Graduate School of Engineering Science, Osaka University, Japan.
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37
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38
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Tkach I, Pornsuwan S, Höbartner C, Wachowius F, Sigurdsson ST, Baranova TY, Diederichsen U, Sicoli G, Bennati M. Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation. Phys Chem Chem Phys 2013; 15:3433-7. [PMID: 23381580 DOI: 10.1039/c3cp44415e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pulsed electron-electron double resonance (PELDOR, also known as DEER) has become a method of choice to measure distances in biomolecules. In this work we show how the performance of the method can be improved at high EPR frequencies (94 GHz) using variable dual frequency irradiation in a dual mode cavity in order to obtain enhanced resolution toward orientation selection. Dipolar evolution traces of a representative RNA duplex and an α-helical peptide were analysed in terms of possible bi-radical structures by considering the inherent ambiguity of symmetry-related solutions.
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Affiliation(s)
- Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Kaminker I, Tkach I, Manukovsky N, Huber T, Yagi H, Otting G, Bennati M, Goldfarb D. W-band orientation selective DEER measurements on a Gd3+/nitroxide mixed-labeled protein dimer with a dual mode cavity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 227:66-71. [PMID: 23314001 DOI: 10.1016/j.jmr.2012.11.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 06/01/2023]
Abstract
Double electron-electron resonance (DEER) at W-band (95 GHz) was applied to measure the distance between a pair of nitroxide and Gd(3+) chelate spin labels, about 6 nm apart, in a homodimer of the protein ERp29. While high-field DEER measurements on systems with such mixed labels can be highly attractive in terms of sensitivity and the potential to access long distances, a major difficulty arises from the large frequency spacing (about 700 MHz) between the narrow, intense signal of the Gd(3+) central transition and the nitroxide signal. This is particularly problematic when using standard single-mode cavities. Here we show that a novel dual-mode cavity that matches this large frequency separation dramatically increases the sensitivity of DEER measurements, allowing evolution times as long as 12 μs in a protein. This opens the possibility of accessing distances of 8 nm and longer. In addition, orientation selection can be resolved and analyzed, thus providing additional structural information. In the case of W-band DEER on a Gd(3+)-nitroxide pair, only two angles and their distributions have to be determined, which is a much simpler problem to solve than the five angles and their distributions associated with two nitroxide spin labels.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
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40
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Borbat PP, Freed JH. Pulse Dipolar Electron Spin Resonance: Distance Measurements. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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Marko A, Prisner TF. An algorithm to analyze PELDOR data of rigid spin label pairs. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp42942j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Eaton SS, Eaton GR. The world as viewed by and with unpaired electrons. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:151-63. [PMID: 22975244 PMCID: PMC3496796 DOI: 10.1016/j.jmr.2012.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 06/01/2023]
Abstract
Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models.
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Affiliation(s)
- Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA
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43
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Reginsson GW, Kunjir NC, Sigurdsson ST, Schiemann O. Trityl radicals: spin labels for nanometer-distance measurements. Chemistry 2012; 18:13580-4. [PMID: 22996284 DOI: 10.1002/chem.201203014] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Indexed: 12/11/2022]
Abstract
Spin labelling with trityls: to gather information about the structure and dynamics of trityl radicals, spin-labelled polymers were measured with pulsed electron-electron double resonance (PELDOR) and double-quantum coherence (DQC). This study demonstrates that trityl radicals have great potential as spin labels that eliminate some limitations of nitroxide spin labels.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, St. Andrews, UK
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44
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Reginsson GW, Shelke SA, Rouillon C, White MF, Sigurdsson ST, Schiemann O. Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR. Nucleic Acids Res 2012; 41:e11. [PMID: 22941643 PMCID: PMC3592447 DOI: 10.1093/nar/gks817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Site-directed spin labeling and pulsed electron-electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
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45
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Structural Information from Oligonucleotides. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2012. [DOI: 10.1007/430_2012_76] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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46
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Polyhach Y, Bordignon E, Tschaggelar R, Gandra S, Godt A, Jeschke G. High sensitivity and versatility of the DEER experiment on nitroxide radical pairs at Q-band frequencies. Phys Chem Chem Phys 2012; 14:10762-73. [DOI: 10.1039/c2cp41520h] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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