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Scott FJ, Dubroca T, Schurko RW, Hill S, Long JR, Mentink-Vigier F. Characterization of dielectric properties and their impact on MAS-DNP NMR applications. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107742. [PMID: 39116460 DOI: 10.1016/j.jmr.2024.107742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/17/2024] [Accepted: 07/13/2024] [Indexed: 08/10/2024]
Abstract
The dielectric properties of materials play a crucial role in the propagation and absorption of microwave beams employed in Magic Angle Spinning - Dynamic Nuclear Polarization (MAS-DNP) NMR experiments. Despite ongoing optimization efforts in sample preparation, routine MAS-DNP NMR applications often fall short of theoretical sensitivity limits. Offering a different perspective, we report the refractive indices and extinction coefficients of diverse materials used in MAS-DNP NMR experiments, spanning a frequency range from 70 to 960 GHz. Knowledge of their dielectric properties enables the accurate simulation of electron nutation frequencies, thereby guiding the design of more efficient hardware and sample preparation of biological or material samples. This is illustrated experimentally for four different rotor materials (sapphire, yttria-stabilized zirconia (YSZ), aluminum nitride (AlN), and SiAlON ceramics) used for DNP at 395 GHz/1H 600 MHz. Finally, electromagnetic simulations and state-of-the-art MAS-DNP numerical simulations provide a rational explanation for the observed magnetic field dependence of the enhancement when using nitroxide biradicals, offering insights that will improve MAS-DNP NMR at high magnetic fields.
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Affiliation(s)
- Faith J Scott
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Thierry Dubroca
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Robert W Schurko
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Joanna R Long
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA; Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA.
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA.
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2
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Endeward B, Bretschneider M, Trenkler P, Prisner TF. Implementation and applications of shaped pulses in EPR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 136-137:61-82. [PMID: 37716755 DOI: 10.1016/j.pnmrs.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 09/18/2023]
Abstract
In this review, we describe the application of shaped pulses for EPR spectroscopy. Pulses generated by fast arbitrary waveform generators are mostly used in the field of EPR spectroscopy for broadband (200 MHz-1 GHz) excitation of paramagnetic species. The implementation and optimization of such broadband pulses in existing EPR spectrometers, often designed and optimized for short rectangular microwave pulses, is demanding. Therefore, a major part of this review will describe in detail the implementation, testing and optimization of shaped pulses in existing EPR spectrometers. Additionally, we review applications using such pulses for broadband inversion of longitudinal magnetization as well as for the creation and manipulation of transverse magnetization in the field of dipolar and hyperfine EPR spectroscopy. They demonstrate the great potential of shaped pulses to improve the performance of pulsed EPR experiments. We give a brief theoretical description of shaped pulses and their limitations, especially for adiabatic pulses, most often used in EPR. We believe that this review can on the one hand be of practical use to EPR groups starting to work with such pulses, and on the other hand give readers an overview of the state of the art of shaped pulse applications in EPR spectroscopy.
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Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Matthias Bretschneider
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Paul Trenkler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany.
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3
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Wort JL, Ackermann K, Giannoulis A, Bode BE. Enhanced sensitivity for pulse dipolar EPR spectroscopy using variable-time RIDME. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107460. [PMID: 37167826 DOI: 10.1016/j.jmr.2023.107460] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/03/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Pulse dipolar EPR spectroscopy (PDS) measurements are an important complementary tool in structural biology and are increasingly applied to macromolecular assemblies implicated in human health and disease at physiological concentrations. This requires ever higher sensitivity, and recent advances have driven PDS measurements into the mid-nanomolar concentration regime, though optimization and acquisition of such measurements remains experimentally demanding and time expensive. One important consideration is that constant-time acquisition represents a hard limit for measurement sensitivity, depending on the maximum measured distance. Determining this distance a priori has been facilitated by machine-learning structure prediction (AlphaFold2 and RoseTTAFold) but is often confounded by non-representative behaviour in frozen solution that may mandate multiple rounds of optimization and acquisition. Herein, we endeavour to simultaneously enhance sensitivity and streamline PDS measurement optimization to one-step by benchmarking a variable-time acquisition RIDME experiment applied to CuII-nitroxide and CuII-CuII model systems. Results demonstrate marked sensitivity improvements of both 5- and 6-pulse variable-time RIDME of between 2- and 5-fold over the constant-time analogues.
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Affiliation(s)
- Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Angeliki Giannoulis
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland.
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4
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Ackermann K, Wort JL, Bode BE. Pulse dipolar EPR for determining nanomolar binding affinities. Chem Commun (Camb) 2022; 58:8790-8793. [PMID: 35837993 PMCID: PMC9350988 DOI: 10.1039/d2cc02360a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein interaction studies often require very low concentrations and highly sensitive biophysical methods. Here, we demonstrate that pulse dipolar electron paramagnetic resonance spectroscopy allows measuring dissociation constants in the nanomolar range. This approach is appealing for concentration-limited biomolecular systems and medium-to-high-affinity binding studies, demonstrated here at 50 nanomolar protein concentration. CuII-nitroxide RIDME measurements at 100 nM protein concentration allow reliable extraction of dissociation constants and distances, while measurements at 50 nM protein concentration allow reliable extraction of dissociation constants only.![]()
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
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Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
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Ackermann K, Wort JL, Bode BE. Nanomolar Pulse Dipolar EPR Spectroscopy in Proteins: Cu II-Cu II and Nitroxide-Nitroxide Cases. J Phys Chem B 2021; 125:5358-5364. [PMID: 33998795 PMCID: PMC7611071 DOI: 10.1021/acs.jpcb.1c03666] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The study of ever more complex biomolecular assemblies implicated in human health and disease is facilitated by a suite of complementary biophysical methods. Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is a powerful tool that provides highly precise geometric constraints in frozen solutions; however, the drive toward PDS at physiologically relevant sub-μM concentrations is limited by the currently achievable concentration sensitivity. Recently, PDS using a combination of nitroxide- and CuII-based spin labels allowed measuring a 500 nM concentration of a model protein. Using commercial instrumentation and spin labels, we demonstrate CuII-CuII and nitroxide-nitroxide PDS measurements at protein concentrations below previous examples reaching 500 and 100 nM, respectively. These results demonstrate the general feasibility of sub-μM PDS measurements at short to intermediate distances (∼1.5 to 3.5 nm), and are of particular relevance for applications where the achievable concentration is limiting.
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EL Mkami H, Hunter R, Cruickshank P, Taylor M, Lovett J, Feintuch A, Qi M, Godt A, Smith G. High-sensitivity Gd 3+-Gd 3+ EPR distance measurements that eliminate artefacts seen at short distances. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:301-313. [PMID: 37904818 PMCID: PMC10500690 DOI: 10.5194/mr-1-301-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/18/2020] [Indexed: 11/01/2023]
Abstract
Gadolinium complexes are attracting increasing attention as spin labels for EPR dipolar distance measurements in biomolecules and particularly for in-cell measurements. It has been shown that flip-flop transitions within the central transition of the high-spin Gd3 + ion can introduce artefacts in dipolar distance measurements, particularly when measuring distances less than 3 nm. Previous work has shown some reduction of these artefacts through increasing the frequency separation between the two frequencies required for the double electron-electron resonance (DEER) experiment. Here we use a high-power (1 kW), wideband, non-resonant system operating at 94 GHz to evaluate DEER measurement protocols using two stiff Gd(III) rulers, consisting of two b i s -Gd3 + -PyMTA complexes, with separations of 2.1 nm and 6.0 nm, respectively. We show that by avoiding the - 1 2 → 1 2 central transition completely, and placing both the pump and the observer pulses on either side of the central transition, we can now observe apparently artefact-free spectra and narrow distance distributions, even for a Gd-Gd distance of 2.1 nm. Importantly we still maintain excellent signal-to-noise ratio and relatively high modulation depths. These results have implications for in-cell EPR measurements at naturally occurring biomolecule concentrations.
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Affiliation(s)
- Hassane EL Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Paul A. S. Cruickshank
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Michael J. Taylor
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science,
Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
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8
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Potapov A. Application of spherical harmonics for DEER data analysis in systems with a conformational distribution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 316:106769. [PMID: 32574865 DOI: 10.1016/j.jmr.2020.106769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Double electron-electron resonance (DEER) and other pulse electron paramagnetic resonance (EPR) techniques are valuable tools for determining distances between paramagnetic centres. DEER theory is well developed for a scenario where relative orientations of paramagnetic centres do not affect the DEER data. In particular, such theory enables a number of approaches for extracting distance distributions. However, in a more general case, when orientation selection effects become substantial, the analytical theory of DEER is less well developed, therefore quite commonly researchers rely on a comparison of some model-based simulations with experimental data. This work elaborates the theory of DEER with orientation selection effects, focusing on a scenario of a moderate conformational disorder, leading to an orientation distribution in a pair of paramagnetic centres. The analytical treatment based on expansions into spherical harmonics, provides important insights into the structure of DEER data. As follows from this treatment, DEER spectra with orientation selection can be represented as a linear combination of modified Pake pattern (MPP) components. The conformational disorder has a filtering effect on the weights of MPP components, specifically by significantly suppressing MPP components of higher degrees. The developed theory provides a pathway for model-based simulations of DEER data where orientation distribution is defined by analytical functions with parameters. The theory based on spherical harmonics expansions was also applied to develop an iterative processing algorithm based on Tikhonov regularization, which disentangles the distance and orientation information in a model-free manner. As an input, this procedure takes several DEER datasets measured at various positions of an EPR line, and outputs a distance distribution and orientation distribution information encoded in a set of coefficients related to the weights of MPP components. The model-based and model-free approaches based on the developed theory were validated for a nitroxide biradical and a spin-labelled protein.
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Affiliation(s)
- Alexey Potapov
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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9
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Jeschke G. Quo vadis EPR? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:36-41. [PMID: 31345773 DOI: 10.1016/j.jmr.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/21/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Complexity of paramagnetic catalysts and materials increases, and the same applies to systems targeted by integrative structural biology. Hence, EPR spectroscopists must find ways to enhance information content of their data. I argue that a third major wave of method development in EPR spectroscopy, which is triggered by recent advances in digital electronics and computing, can achieve this. Transfer of NMR methods to EPR will go on, but part of the new EPR methodology will depend on completely new concepts.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zurich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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10
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Shah A, Roux A, Starck M, Mosely JA, Stevens M, Norman DG, Hunter RI, El Mkami H, Smith GM, Parker D, Lovett JE. A Gadolinium Spin Label with Both a Narrow Central Transition and Short Tether for Use in Double Electron Electron Resonance Distance Measurements. Inorg Chem 2019; 58:3015-3025. [DOI: 10.1021/acs.inorgchem.8b02892] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anokhi Shah
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
| | - Amandine Roux
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Matthieu Starck
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jackie A. Mosely
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Michael Stevens
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David G. Norman
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Hassane El Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - David Parker
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
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11
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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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12
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Band A, Donohue MP, Epel B, Madhu S, Szalai VA. Integration of a versatile bridge concept in a 34 GHz pulsed/CW EPR spectrometer. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 288:28-36. [PMID: 29414061 PMCID: PMC5837943 DOI: 10.1016/j.jmr.2018.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
We present a 34 GHz continuous wave (CW)/pulsed electron paramagnetic resonance (EPR) spectrometer capable of pulse-shaping that is based on a versatile microwave bridge design. The bridge radio frequency (RF)-in/RF-out design (500 MHz to 1 GHz input/output passband, 500 MHz instantaneous input/output bandwidth) creates a flexible platform with which to compare a variety of excitation and detection methods utilizing commercially available equipment external to the bridge. We use three sources of RF input to implement typical functions associated with CW and pulse EPR spectroscopic measurements. The bridge output is processed via high speed digitizer and an in-phase/quadrature (I/Q) demodulator for pulsed work or sent to a wideband, high dynamic range log detector for CW. Combining this bridge with additional commercial hardware and new acquisition and control electronics, we have designed and constructed an adaptable EPR spectrometer that builds upon previous work in the literature and is functionally comparable to other available systems.
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Affiliation(s)
- Alan Band
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Matthew P Donohue
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States; Maryland NanoCenter, University of Maryland, College Park, MD 20742, United States
| | - Boris Epel
- Center for EPR Imaging in Vivo Physiology, University of Chicago Medical Center, Chicago, IL 60637, United States
| | - Shraeya Madhu
- Poolesville High School, Poolesville, MD 20837, United States
| | - Veronika A Szalai
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States.
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13
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Bahrenberg T, Rosenski Y, Carmieli R, Zibzener K, Qi M, Frydman V, Godt A, Goldfarb D, Feintuch A. Improved sensitivity for W-band Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements with shaped pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 283:1-13. [PMID: 28834777 DOI: 10.1016/j.jmr.2017.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Chirp and shaped pulses have been recently shown to be highly advantageous for improving sensitivity in DEER (double electron-electron resonance, also called PELDOR) measurements due to their large excitation bandwidth. The implementation of such pulses for pulse EPR has become feasible due to the availability of arbitrary waveform generators (AWG) with high sampling rates to support pulse shaping for pulses with tens of nanoseconds duration. Here we present a setup for obtaining chirp pulses on our home-built W-band (95GHz) spectrometer and demonstrate its performance on Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements. We carried out an extensive optimization procedure on two model systems, Gd(III)-PyMTA-spacer-Gd(III)-PyMTA (Gd-PyMTA ruler; zero-field splitting parameter (ZFS) D∼1150MHz) as well as nitroxide-spacer-nitroxide (nitroxide ruler) to evaluate the applicability of shaped pulses to Gd(III) complexes and nitroxides, which are two important classes of spin labels used in modern DEER/EPR experiments. We applied our findings to ubiquitin, doubly labeled with Gd-DOTA-monoamide (D∼550MHz) asa model for a system with a small ZFS. Our experiments were focused on the questions (i) what are the best conditions for positioning of the detection frequency, (ii) which pump pulse parameters (bandwidth, positioning in the spectrum, length) yield the best signal-to-noise ratio (SNR) improvements when compared to classical DEER, and (iii) how do the sample's spectral parameters influence the experiment. For the nitroxide ruler, we report an improvement of up to 1.9 in total SNR, while for the Gd-PyMTA ruler the improvement was 3.1-3.4 and for Gd-DOTA-monoamide labeled ubiquitin it was a factor of 1.8. Whereas for the Gd-PyMTA ruler the two setups pump on maximum and observe on maximum gave about the same improvement, for Gd-DOTA-monoamide a significant difference was found. In general the choice of the best set of parameters depends on the D parameter of the Gd(III) complex.
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Affiliation(s)
- Thorsten Bahrenberg
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Yael Rosenski
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Raanan Carmieli
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Koby Zibzener
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, 33615 Bielefeld, Germany
| | - Veronica Frydman
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, 33615 Bielefeld, Germany
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel.
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