1
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Sinha Roy A, Marohn JA, Freed JH. An analysis of double-quantum coherence ESR in an N-spin system: Analytical expressions and predictions. J Chem Phys 2024; 160:134105. [PMID: 38557852 PMCID: PMC11087869 DOI: 10.1063/5.0200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Electron spin resonance pulsed dipolar spectroscopy (PDS) has become popular in protein 3D structure analysis. PDS studies yield distance distributions between a pair or multiple pairs of spin probes attached to protein molecules, which can be used directly in structural studies or as constraints in theoretical predictions. Double-quantum coherence (DQC) is a highly sensitive and accurate PDS technique to study protein structures in the solid state and under physiologically relevant conditions. In this work, we have derived analytical expressions for the DQC signal for a system with N-dipolar coupled spin-1/2 particles in the solid state. The expressions are integrated over the relevant spatial parameters to obtain closed form DQC signal expressions. These expressions contain the concentration-dependent "instantaneous diffusion" and the background signal. For micromolar and lower concentrations, these effects are negligible. An approximate analysis is provided for cases of finite pulses. The expressions obtained in this work should improve the analysis of DQC experimental data significantly, and the analytical approach could be extended easily to a wide range of magnetic resonance phenomena.
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Affiliation(s)
| | - John A. Marohn
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
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2
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Ackermann K, Heubach CA, Schiemann O, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Distance Measurements at Low Nanomolar Concentrations: The Cu II-Trityl Case. J Phys Chem Lett 2024; 15:1455-1461. [PMID: 38294197 PMCID: PMC10860127 DOI: 10.1021/acs.jpclett.3c03311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Recent sensitivity enhancements in pulse dipolar electron paramagnetic resonance spectroscopy (PDS) have afforded distance measurements at submicromolar spin concentrations. This development opens the path for new science as more biomolecular systems can be investigated at their respective physiological concentrations. Here, we demonstrate that the combination of orthogonal spin-labeling using CuII ions and trityl yields a >3-fold increase in sensitivity compared to that of the established CuII-nitroxide labeling strategy. Application of the recently developed variable-time relaxation-induced dipolar modulation enhancement (RIDME) method yields a further ∼2.5-fold increase compared to the commonly used constant-time RIDME. This overall increase in sensitivity of almost an order of magnitude makes distance measurements in the range of 3 nm with protein concentrations as low as 10 nM feasible, >2 times lower than the previously reported concentration. We expect that experiments at single-digit nanomolar concentrations are imminent, which have the potential to transform biological PDS applications.
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
| | - Caspar A. Heubach
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Bela E. Bode
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
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3
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Heubach CA, Hasanbasri Z, Abdullin D, Reuter A, Korzekwa B, Saxena S, Schiemann O. Differentiating between Label and Protein Conformers in Pulsed Dipolar EPR Spectroscopy with the dHis-Cu 2+ (NTA) Motif. Chemistry 2023; 29:e202302541. [PMID: 37755452 DOI: 10.1002/chem.202302541] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 09/28/2023]
Abstract
Pulsed dipolar EPR spectroscopy (PDS) in combination with site-directed spin labeling is a powerful tool in structural biology. However, the commonly used spin labels are conjugated to biomolecules via rather long and flexible linkers, which hampers the translation of distance distributions into biomolecular conformations. In contrast, the spin label copper(II)-nitrilotriacetic acid [Cu2+ (NTA)] bound to two histidines (dHis) is rigid and yields narrow distance distributions, which can be more easily translated into biomolecular conformations. Here, we use this label on the 71 kDa Yersinia outer protein O (YopO) to decipher whether a previously experimentally observed bimodal distance distribution is due to two conformations of the biomolecule or of the flexible spin labels. Two different PDS experiments, that is, pulsed electron-electron double resonance (PELDOR aka DEER) and relaxation-induced dipolar modulation enhancement (RIDME), yield unimodal distance distribution with the dHis-Cu2+ (NTA) motif; this result suggests that the α-helical backbone of YopO adopts a single conformation in frozen solution. In addition, we show that the Cu2+ (NTA) label preferentially binds to the target double histidine (dHis) sites even in the presence of 22 competing native histidine residues. Our results therefore suggest that the generation of a His-null background is not required for this spin labeling methodology. Together these results highlight the value of the dHis-Cu2+ (NTA) motif in PDS experiments.
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Affiliation(s)
- Caspar A Heubach
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Zikri Hasanbasri
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Arne Reuter
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Benedict Korzekwa
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
- Leibniz-Center for Diabetes Research, University of Düsseldorf, Auf'm Hennekamp 65, 40225, Düsseldorf, Germany
| | - Sunil Saxena
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
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4
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Yang Z, Stein RA, Pink M, Madzelan P, Ngendahimana T, Rajca S, Wilson MA, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. J Am Chem Soc 2023; 145:25726-25736. [PMID: 37963181 PMCID: PMC10961179 DOI: 10.1021/jacs.3c09184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.
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Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Peter Madzelan
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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5
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Shu C, Yang Z, Rajca A. From Stable Radicals to Thermally Robust High-Spin Diradicals and Triradicals. Chem Rev 2023; 123:11954-12003. [PMID: 37831948 DOI: 10.1021/acs.chemrev.3c00406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Stable radicals and thermally robust high-spin di- and triradicals have emerged as important organic materials due to their promising applications in diverse fields. New fundamental properties, such as SOMO/HOMO inversion of orbital energies, are explored for the design of new stable radicals, including highly luminescent ones with good photostability. A relation with the singlet-triplet energy gap in the corresponding diradicals is proposed. Thermally robust high-spin di- and triradicals, with energy gaps that are comparable to or greater than a thermal energy at room temperature, are more challenging to synthesize but more rewarding. We summarize a number of high-spin di- and triradicals, based on nitronyl nitroxides that provide a relation between the experimental pairwise exchange coupling constant J/k in the high-spin species vs experimental hyperfine coupling constants in the corresponding monoradicals. This relation allows us to identify outliers, which may correspond to radicals where J/k is not measured with sufficient accuracy. Double helical high-spin diradicals, in which spin density is delocalized over the chiral π-system, have been barely explored, with the sole example of such high-spin diradical possessing alternant π-system with Kekulé resonance form. Finally, we discuss a high-spin diradical with electrical conductivity and derivatives of triangulene diradicals.
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Affiliation(s)
- Chan Shu
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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6
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Wang XW, Zhang X, Cui CY, Li B, Goldfarb D, Yang Y, Su XC. Stabilizing Nitroxide Spin Labels for Structural and Conformational Studies of Biomolecules by Maleimide Treatment. Chemistry 2023; 29:e202301350. [PMID: 37354082 DOI: 10.1002/chem.202301350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023]
Abstract
Nitroxide (NO) spin radicals are effective in characterizing structures, interactions and dynamics of biomolecules. The EPR applications in cell lysates or intracellular milieu require stable spin labels, but NO radicals are unstable in such conditions. We showed that the destabilization of NO radicals in cell lysates or even in cells is caused by NADPH/NADH related enzymes, but not by the commonly believed reducing reagents such as GSH. Maleimide stabilizes the NO radicals in the cell lysates by consumption of the NADPH/NADH that are essential for the enzymes involved in destabilizing NO radicals, instead of serving as the solo thiol scavenger. The maleimide treatment retains the crowding properties of the intracellular components and allows to perform long-time EPR measurements of NO labeled biomolecules close to the intracellular conditions. The strategy of maleimide treatment on cell lysates for the EPR applications has been demonstrated on double electron-electron resonance (DEER) measurements on a number of NO labeled protein samples. The method opens a broad application range for the NO labeled biomolecules by EPR in conditions that resemble the intracellular milieu.
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Affiliation(s)
- Xi-Wei Wang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xing Zhang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
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7
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Yang Z, Stein RA, Pink M, Madzelan P, Ngendahimana T, Rajca S, Wilson MA, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554361. [PMID: 37662277 PMCID: PMC10473685 DOI: 10.1101/2023.08.22.554361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least one order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase of the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of inter-spin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4 - 9, compared to the common spin label such as MTSL, which is not affected by CB-7. Inter-spin distances of 3-nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating undisturbed structure and conformation of the protein.
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Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Peter Madzelan
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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8
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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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9
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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10
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Abdullin D, Hett T, Fleck N, Kopp K, Cassidy S, Richert S, Schiemann O. Magneto-Structural Correlations in a Mixed Porphyrin(Cu 2+ )/Trityl Spin System: Magnitude, Sign, and Distribution of the Exchange Coupling Constant. Chemistry 2023; 29:e202203148. [PMID: 36519664 DOI: 10.1002/chem.202203148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Tetrathiatriarylmethyl radicals (TAM or trityl) are receiving increasing attention in various fields of magnetic resonance such as imaging, dynamic nuclear polarization, spin labeling, and, more recently, molecular magnetism and quantum information technology. Here, a trityl radical attached via a phenyl bridge to a copper(II)tetraphenylporphyrin was synthesized, and its magnetic properties studied by multi-frequency continuous-wave electron paramagnetic resonance (EPR) spectroscopy and magnetic measurements. EPR revealed that the electron spin-spin coupling constant J between the trityl and Cu2+ spin centers is ferromagnetic with a magnitude of -2.3 GHz (-0.077 cm-1 , + J S → 1 S → 2 ${+J{\vec{S}}_{1}{\vec{S}}_{2}}$ convention) and a distribution width of 1.2 GHz (0.040 cm-1 ). With the help of density functional theory (DFT) calculations, the obtained ferromagnetic exchange coupling, which is unusual for para-substituted phenyl-bridged biradicals, could be related to the almost perpendicular orientation of the phenyl linker with respect to the porphyrin and trityl ring planes in the energy minimum, while the J distribution was rationalized by the temperature weighted rotation of the phenyl bridge about the molecular axis connecting both spin centers. This study exemplifies the importance of molecular dynamics for the homogeneity (or heterogeneity) of the magnetic properties of trityl-based systems.
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Affiliation(s)
- Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Nico Fleck
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.,Merck KGaA, Q20/001, Frankfurterstr. 250, 64293, Darmstadt, Germany
| | - Kevin Kopp
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Simon Cassidy
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Sabine Richert
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.,Department of Chemical and Biological Physics, Weizmann Institute of Science, 761001, Rehovot, Israel
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11
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Hasanbasri Z, Poncelet M, Hunter H, Driesschaert B, Saxena S. A new 13C trityl-based spin label enables the use of DEER for distance measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 347:107363. [PMID: 36620971 PMCID: PMC9928843 DOI: 10.1016/j.jmr.2022.107363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Triarylmethyl (TAM)-based labels, while still underutilized, are a powerful class of labels for pulsed-Electron Spin Resonance (ESR) distance measurements. They feature slow relaxation rates for long-lasting signals, high stability for cellular experiments, and narrow spectral features for efficient excitation of the spins. However, the typical narrow line shape limits the available distance measurements to only single-frequency experiments, such as Double Quantum Coherence (DQC) and Relaxation Induced Dipolar Modulation Enhancement (RIDME), which can be complicated to perform or hard to process. Therefore, widespread usage of TAM labels can be enhanced by the use of Double Electron-Electron Resonance (DEER) distance measurements. In this work, we developed a new spin label, 13C1-mOX063-d24, with a 13C isotope as the radical center. Due to the resolved hyperfine splitting, the spectrum is sufficiently broadened to permit DEER-based experiments at Q-band spectrometers. Additionally, this new label can be incorporated orthogonally with Cu(II)-based protein label. The orthogonal labeling scheme enables DEER distance measurement at X-band frequencies. Overall, the new trityl label allows for DEER-based distance measurements that complement existing TAM-label DQC and RIDME experiments.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States
| | - Hannah Hunter
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States; C. Eugene Bennett Department of Chemistry West Virginia University, Morgantown, WV 26506, United States.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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12
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Vanas A, Soetbeer J, Breitgoff FD, Hintz H, Sajid M, Polyhach Y, Godt A, Jeschke G, Yulikov M, Klose D. Intermolecular contributions, filtration effects and signal composition of SIFTER (single-frequency technique for refocusing). MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:1-18. [PMID: 38269110 PMCID: PMC10807728 DOI: 10.5194/mr-4-1-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/14/2022] [Indexed: 01/26/2024]
Abstract
To characterize structure and molecular order in the nanometre range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, for the single-frequency technique for refocusing dipolar couplings (SIFTER), the buildup of dipolar modulation signal and intermolecular contributions is analysed for a uniform random distribution of monoradicals and biradicals in frozen glassy solvent by using the product operator formalism for electron spin S = 1 / 2 . A dipolar oscillation artefact appearing at both ends of the SIFTER time trace is predicted, which originates from the weak coherence transfer between biradicals. The relative intensity of this artefact is predicted to be temperature independent but to increase with the spin concentration in the sample. Different compositions of the intermolecular background are predicted in the case of biradicals and in the case of monoradicals. Our theoretical account suggests that the appropriate procedure of extracting the intramolecular dipolar contribution (form factor) requires fitting and subtracting the unmodulated part, followed by division by an intermolecular background function that is different in shape. This scheme differs from the previously used heuristic background division approach. We compare our theoretical derivations to experimental SIFTER traces for nitroxide and trityl monoradicals and biradicals. Our analysis demonstrates a good qualitative match with the proposed theoretical description. The resulting perspectives for a quantitative analysis of SIFTER data are discussed.
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Affiliation(s)
- Agathe Vanas
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Frauke Diana Breitgoff
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Henrik Hintz
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Muhammad Sajid
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Department of Chemistry, Bielefeld University, Universitätsstrasse
25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg
2, 8093 Zurich, Switzerland
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13
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Ossadnik D, Kuzin S, Qi M, Yulikov M, Godt A. A Gd III-Based Spin Label at the Limits for Linewidth Reduction through Zero-Field Splitting Optimization. Inorg Chem 2023; 62:408-432. [PMID: 36525400 DOI: 10.1021/acs.inorgchem.2c03531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The remarkably narrow central line in the electron paramagnetic resonance spectrum and the very weak zero-field splitting (ZFS) make [GdIII(NO3Pic)] ([GdIII(TPATCN)]) an attractive starting point for the development of spin labels. For retaining the narrow line of this parent complex when modifying it with a substituent enabling bioconjugation, alkyl with a somehow remote functional group as a substituent at the picolinate moiety was found to be highly suitable because ZFS stayed weak, even if the threefold axial symmetry was broken. The ZFS is so weak that hyperfine coupling and/or g-value variations noticeably determine the linewidth in Q band and higher fields when the biomolecule is protonated, which is the standard situation, and in W band and higher fields for the protonated complex in a fully deuterated surrounding. Clearly, [NDSE-{GdIII(NO3Pic)}], a spin label targeting the cysteines in a peptide, is at a limit of linewidth narrowing through ZFS minimization. The labeling reaction is highly chemoselective and, applied to a polyproline with two cysteine units, it took no more than a minute at 7 °C and pH 7.8. Subsequent disulfide scrambling is very slow and can therefore be prevented. Double electron-electron resonance and relaxation-induced dipolar modulation enhancement applied to the spin-labeled polyproline proved the spin label useful for distance determination in peptides.
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Affiliation(s)
- Daniel Ossadnik
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Sergei Kuzin
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093Zurich, Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093Zurich, Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615Bielefeld, Germany
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14
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Ketter S, Joseph B. Gd 3+-Trityl-Nitroxide Triple Labeling and Distance Measurements in the Heterooligomeric Cobalamin Transport Complex in the Native Lipid Bilayers. J Am Chem Soc 2023; 145:960-966. [PMID: 36599418 PMCID: PMC9853854 DOI: 10.1021/jacs.2c10080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Increased efforts are being made for observing proteins in their native environments. Pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) is a powerful tool for this purpose. Conventionally, PELDOR employs an identical spin pair, which limits the output to a single distance for monomeric samples. Here, we show that the Gd3+-trityl-nitroxide (NO) three-spin system is a versatile tool to study heterooligomeric membrane protein complexes, even within their native membrane. This allowed for an independent determination of four different distances (Gd3+-trityl, Gd3+-NO, trityl-NO, and Gd3+-Gd3+) within the same sample. We demonstrate the feasibility of this approach by observing sequential ligand binding and the dynamics of complex formation in the cobalamin transport system involving four components (cobalamin, BtuB, TonB, and BtuF). Our results reveal that TonB binding alone is sufficient to release cobalamin from BtuB in the native asymmetric bilayers. This approach provides a potential tool for the structural and quantitative analysis of dynamic protein-protein interactions in oligomeric complexes, even within their native surroundings.
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15
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Poncelet M, Ngendahimana T, Gluth TD, Hoblitzell EH, Eubank TD, Eaton GR, Eaton SS, Driesschaert B. Synthesis and characterization of a biocompatible 13C 1 isotopologue of trityl radical OX071 for in vivo EPR viscometry. Analyst 2022; 147:5643-5648. [PMID: 36373434 PMCID: PMC9729415 DOI: 10.1039/d2an01527g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
We describe the synthesis, characterization, and application of an isotopologue of the trityl radical OX071, labeled with 13C at the central carbon (13C1). This spin probe features large anisotropy of the hyperfine coupling with the 13C1 (I = 1/2), leading to an EPR spectrum highly sensitive to molecular tumbling. The high biocompatibility and lack of interaction with blood albumin allow for systemic delivery and in vivo measurement of tissue microviscosity by EPR.
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Affiliation(s)
- Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Teresa D Gluth
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
| | - Emily H Hoblitzell
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, School of Medicine, Morgantown, WV, 26506, USA
| | - Timothy D Eubank
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, School of Medicine, Morgantown, WV, 26506, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, 26506, USA
- In Vivo Multifunctional Magnetic Resonance center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
- Eugene Bennett Department of Chemistry, West Virginia University, WV, 26506, USA
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16
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Seal M, Feintuch A, Goldfarb D. The effect of spin-lattice relaxation on DEER background decay. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 345:107327. [PMID: 36410061 DOI: 10.1016/j.jmr.2022.107327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
The common approach to background removal in double electron-electron resonance (DEER) measurements on frozen solutions with a three-dimensional homogeneous distribution of doubly labeled biomolecules is to fit the background to an exponential decay function. Excluded volume effects or distribution in a dimension lower than three, such as proteins in a membrane, can lead to a stretched exponential decay. In this work, we show that in cases of spin labels with short spin-lattice relaxation time, up to an order of magnitude longer than the DEER trace length, relevant for metal-based spin labels, spin flips that take place during the DEER evolution time affect the background decay shape. This was demonstrated using a series of temperature-dependent DEER measurements on frozen solutions of a nitroxide radical, a Gd(III) complex, Cu(II) ions, and a bis-Gd(III) model complex. As expected, the background decay was exponential for the nitroxide, whereas deviations were noted for Gd(III) and Cu(II). Based on the theoretical approach of Keller et al. (Phys. Chem. Chem. Phys. 21 (2019) 8228-8245), which addresses the effect of spin-lattice relaxation-induced spin flips during the evolution time, we show that the background decay can be fitted to an exponent including a linear and quadratic term in t, which is the position of the pump pulse. Analysis of the data in terms of the probability of spontaneous spin flips induced by spin-lattice relaxation showed that this approach worked well for the high temperature range studied for Gd(III) and Cu(II). At the low temperature range, the spin flips that occured during the DEER evolution time for Gd(III) exceeded the measured spin-lattice relaxation rate and include contributions from spin flips due to another mechanisms, most likely nuclear spin diffusion.
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Affiliation(s)
- Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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17
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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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18
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Goldfarb D. Exploring protein conformations in vitro and in cell with EPR distance measurements. Curr Opin Struct Biol 2022; 75:102398. [PMID: 35667279 DOI: 10.1016/j.sbi.2022.102398] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022]
Abstract
The electron-electron double resonance (DEER) method, which provides distance distributions between two spin labels, attached site specifically to biomolecules (proteins and nucleic acids), is currently a well-recognized biophysical tool in structural biology. The most commonly used spin labels are based on nitroxide stable radicals, conjugated to the proteins primarily via native or engineered cysteine residues. However, in recent years, new spin labels, along with different labeling chemistries, have been introduced, driven in part by the desire to study structural and dynamical properties of biomolecules in their native environment, the cell. This mini-review focuses on these new spin labels, which allow for DEER on orthogonal spin labels, and on the state of the art methods for in-cell DEER distance measurements.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 761001, Israel
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19
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Liu W, Tao O, Chen L, Ling Y, Zeng M, Jin H, Jiang D. Synthesis and characterization of a Cu(ii) coordination-containing TAM radical as a nitroxyl probe. RSC Adv 2022; 12:15980-15985. [PMID: 35733682 PMCID: PMC9138401 DOI: 10.1039/d1ra07511j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Nitroxyl (HNO) has been identified as an important signaling molecule in biological systems, and it plays critical roles in many physiological processes. However, its detection remains challenging because of the limited sensitivity and/or specificity of existing detection methods. Low-frequency electron paramagnetic resonance (EPR) spectroscopy and imaging, coupled with the use of exogenous paramagnetic probes, have been indispensable techniques for the in vivo measurement of various physiological parameters owing to their specificity, noninvasiveness and good depth of magnetic field penetration in animal tissues. However, the in vivo detection of HNO levels by EPR spectroscopy and imaging is limited due to the need for improved probes. We report the first "turn on-response" EPR probe for HNO utilizing a Cu(ii) coordination-containing TAM radical (denoted as CuII[TD1]). Upon reaction with HNO, CuII[TD1] shows a 16.1-fold turn-on in EPR signal with a low detection limit of 1.95 μM. Moreover, low-temperature EPR spectroscopic and ESI-MS studies showed that the sensing mechanism relies on the reduction of Cu(ii) by HNO. Lastly, CuII[TD1] is selective for HNO over other reactive nitrogen and oxygen species except for some reductants (Cys and Asc). This new Cu(ii) coordination-containing TAM radical shows great potential for in vivo EPR HNO applications in the absence of reducing agents and provides insights into developing improved and targeted EPR HNO probes for biomedical applications.
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Affiliation(s)
- Wenbo Liu
- School of Pharmacy and Life Sciences, Jiujiang University Jiujiang 332000 China
| | - Ouyang Tao
- School of Pharmacy and Life Sciences, Jiujiang University Jiujiang 332000 China
| | - Li Chen
- School of Public Health, TianJin Medical University China
| | - Yun Ling
- School of Pharmacy and Life Sciences, Jiujiang University Jiujiang 332000 China
| | - Ming Zeng
- School of Pharmacy and Life Sciences, Jiujiang University Jiujiang 332000 China
| | - Hongguang Jin
- School of Pharmacy and Life Sciences, Jiujiang University Jiujiang 332000 China
| | - Dengzhao Jiang
- School of Pharmacy and Life Sciences, Jiujiang University Jiujiang 332000 China
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20
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Moore W, Huffman JL, Driesschaert B, Eaton SS, Eaton GR. Impact of Chlorine Substitution on Electron Spin Relaxation of a Trityl Radical. APPLIED MAGNETIC RESONANCE 2022; 53:797-808. [PMID: 35601029 PMCID: PMC9122340 DOI: 10.1007/s00723-021-01405-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A perchlorotriarylmethyl tricarboxylic acid radical 99% enriched in 13C at the central carbon (13C1-PTMTC) was characterized in phosphate buffered saline solution (pH = 7.2) (PBS) at ambient temperature. Samples immobilized in 1:1 PBS:glycerol or in 9:1 trehalose:sucrose were studied as a function of temperature. Isotope enrichment at C1 creates a trityl that can be used to accurately measure microscopic viscosity. Understanding of the impact of the 13C hyperfine interaction on electron spin relaxation is important for application of this trityl in oximetry and distance measurements. The anisotropic 13C1 hyperfine couplings (Ax = Ay = 24 ± 2 MHz, Az = 200 ± 1 MHz) are larger than for the related 13C1-perdeuterated Finland trityl (13C1-dFT) and the g anisotropy (gx = 2.0013, gy = 2.0016, gz = 2.0042) is slightly larger than for 13C1-dFT. The tumbling correlation times (τR) for 13C1-PTMTC are 0.20 ± 0.02 ns in PBS and 0.40 ± 0.05 ns in 3:1 PBS:glycerol, which are shorter than for 13C1-dFT in the same solutions. T1 for 13C1-PTMTC is 3.5 ± 0.5 μs in PBS and 5.3 ± 0.4 μs in 3:1 PBS:glycerol, which are shorter than for 13C1-dFT due to faster tumbling, larger anisotropy of the 13C1 hyperfine, and about 30% larger contribution from the local mode. In immobilized samples T1 for 13C1-PTMTC is similar to that for 13C1-dFT and other trityls without chlorine or 13C1 substituents, indicating that the 13C1 and Cl substituents on the phenyl rings have little impact on T1. The temperature dependence of T1 was modeled with contributions from the direct, Raman, and local mode processes. Broadening of CW linewidths of about 0.6 G in fluid solution and about 2 G in rigid lattice is attributed to unresolved 35,37Cl hyperfine couplings.
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Affiliation(s)
- Whylder Moore
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Justin L. Huffman
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
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21
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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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22
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Biondi B, Syryamina VN, Rocchio G, Barbon A, Formaggio F, Toniolo C, Raap J, Dzuba SA. Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides? ACS OMEGA 2022; 7:5154-5165. [PMID: 35187331 PMCID: PMC8851612 DOI: 10.1021/acsomega.1c06227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.
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Affiliation(s)
- Barbara Biondi
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Victoria N. Syryamina
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Gabriele Rocchio
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Antonio Barbon
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jan Raap
- Leiden
Institute of Chemistry, Gorlaeus Laboratories,
Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
- Department
of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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23
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24
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Tracking protein domain movements by EPR distance determination and multilateration. Methods Enzymol 2022; 666:121-144. [DOI: 10.1016/bs.mie.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Vicino MF, Wuebben C, Kerzhner M, Famulok M, Schiemann O. Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation. Methods Mol Biol 2022; 2439:205-221. [PMID: 35226324 DOI: 10.1007/978-1-0716-2047-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance (EPR) is a spectroscopic method for investigating structures, conformational changes, and dynamics of biomacromolecules, for example, oligonucleotides. In order to be applicable, the oligonucleotide has to be labeled site-specifically with paramagnetic tags, the so-called spin labels. Here, we provide a protocol for spin labeling of long oligonucleotides with nitroxides. In the first step, a short and commercially available RNA strand is labeled with a nitroxide via a copper-(I)-catalyzed azide-alkyne cycloaddition (CuAAC), also referred to as "click" reaction. In the second step, the labeled RNA strand is fused to another RNA sequence by means of enzymatic ligation to obtain the labeled full-length construct. The protocol is robust and has been shown experimentally to deliver high yields for RNA sequences up to 81 nucleotides, but longer strands are in principle also feasible. Moreover, it sets the path to label, for example, long riboswitches, ribozymes, and DNAzymes for coarse-grained structure determination and enables to investigate mechanistical features of these systems.
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Affiliation(s)
- Maria Francesca Vicino
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany
| | - Mark Kerzhner
- Life & Medical Sciences Institute (LIMES), Chemische Biologie, c/o Kekulé-Institut für organische Chemie, Bonn, Germany
| | - Michael Famulok
- Life & Medical Sciences Institute (LIMES), Chemische Biologie, c/o Kekulé-Institut für organische Chemie, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany.
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26
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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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27
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Chen L, Wu L, Tan X, Rockenbauer A, Song Y, Liu Y. Synthesis and Redox Properties of Water-Soluble Asymmetric Trityl Radicals. J Org Chem 2021; 86:8351-8364. [PMID: 34043350 DOI: 10.1021/acs.joc.1c00766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tetrathiatriarylmethyl (trityl) radicals have been recently shown to react with biological oxidoreductants including glutathione (GSH), ascorbic acid (Asc), and superoxide anion radical (O2•-). However, how the substituents affect the reactivity of trityl radicals is still unknown. In this work, five asymmetric trityl radicals were synthesized and their reactivities with GSH, Asc, and O2•- investigated. Under aerobic conditions, GSH induces fast decays for the thioether- (TSA) and N-methyleneglycine-substituted (TGA) derivatives and slow decay for the 4-carboxyphenyl-containing one (TPA). Under anaerobic conditions, the direct reduction of these radicals by GSH also occurs with rate constants (kGSH) from 1.8 × 10-4 M-1 s-1 for TPA to 1.0 × 10-2 M-1 s-1 for TGA. Moreover, these radicals can also react with O2•- with rate constants (kSO) from 1.2 × 103 M-1 s-1 for ET-01 to 1.6 × 104 M-1 s-1 for TGA. Surprisingly, these radicals are completely inert to Asc in both aerobic and anaerobic conditions. Additionally, the substituents exert an important effect on redox potentials of these trityl radicals. This work demonstrates that the redox properties of the trityl radicals strongly depend on their substituents, and TPA with high stability toward GSH shows great potential for intracellular applications.
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Affiliation(s)
- Li Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Lanlan Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary.,Department of Physics, Budapest University of Technology and Economics, Budafoki ut 8, 1111 Budapest, Hungary
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Medicinal Chemistry, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
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28
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Gualandi L, Franchi P, Mezzina E, Goldup SM, Lucarini M. Spin-labelled mechanically interlocked molecules as models for the interpretation of biradical EPR spectra. Chem Sci 2021; 12:8385-8393. [PMID: 34221319 PMCID: PMC8221063 DOI: 10.1039/d1sc01462e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022] Open
Abstract
Biradical spin probes can provide detailed information about the distances between molecules/regions of molecules because the through-space coupling of radical centres, characterised by J, is strongly distance dependent. However, if the system can adopt multiple configurations, as is common in supramolecular complexes, the shape of the EPR spectrum is influenced not only by J but also the rate of exchange between different states. In practice, it is often hard to separate these variables and as a result, the effect of the latter is sometimes overlooked. To demonstrate this challenge unequivocally we synthesised rotaxane biradicals containing nitronyl nitroxide units at the termini of their axles. The rotaxanes exchange between the available biradical conformations more slowly than the corresponding non-interlocked axles but, despite this, in some cases, the EPR spectra of the axle and rotaxane remain remarkably similar. Detailed analysis allowed us to demonstrate that the similar EPR spectral shapes result from different combinations of J and rates of conformational interconversion, a phenomenon suggested theoretically more than 50 years ago. This work reinforces the idea that thorough analysis must be performed when interpreting the spectra of biradicals employed as spin probes in solution.
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Affiliation(s)
- Lorenzo Gualandi
- Department of Chemistry "Giacomo Ciamician", University of Bologna Via San Giacomo 11 Bologna Italy
| | - Paola Franchi
- Department of Chemistry "Giacomo Ciamician", University of Bologna Via San Giacomo 11 Bologna Italy
| | - Elisabetta Mezzina
- Department of Chemistry "Giacomo Ciamician", University of Bologna Via San Giacomo 11 Bologna Italy
| | - Stephen M Goldup
- Department of Chemistry, University of Southampton University Road, Highfield Southampton UK
| | - Marco Lucarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna Via San Giacomo 11 Bologna Italy
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29
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Hasanbasri Z, Singewald K, Gluth TD, Driesschaert B, Saxena S. Cleavage-Resistant Protein Labeling With Hydrophilic Trityl Enables Distance Measurements In-Cell. J Phys Chem B 2021; 125:5265-5274. [PMID: 33983738 DOI: 10.1021/acs.jpcb.1c02371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensitive in-cell distance measurements in proteins using pulsed-electron spin resonance (ESR) require reduction-resistant and cleavage-resistant spin labels. Among the reduction-resistant moieties, the hydrophilic trityl core known as OX063 is promising due to its long phase-memory relaxation time (Tm). This property leads to a sufficiently intense ESR signal for reliable distance measurements. Furthermore, the Tm of OX063 remains sufficiently long at higher temperatures, opening the possibility for measurements at temperatures above 50 K. In this work, we synthesized deuterated OX063 with a maleimide linker (mOX063-d24). We show that the combination of the hydrophilicity of the label and the maleimide linker enables high protein labeling that is cleavage-resistant in-cells. Distance measurements performed at 150 K using this label are more sensitive than the measurements at 80 K. The sensitivity gain is due to the significantly short longitudinal relaxation time (T1) at higher temperatures, which enables more data collection per unit of time. In addition to in vitro experiments, we perform distance measurements in Xenopus laevis oocytes. Interestingly, the Tm of mOX063-d24 is sufficiently long even in the crowded environment of the cell, leading to signals of appreciable intensity. Overall, mOX063-d24 provides highly sensitive distance measurements both in vitro and in-cells.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Teresa D Gluth
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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30
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Vicino MF, Hett T, Schiemann O. Spin Labeling of RNA Using "Click" Chemistry for Coarse-grained Structure Determination via Pulsed Electron-electron Double Resonance Spectroscopy. Bio Protoc 2021; 11:e4004. [PMID: 34150941 PMCID: PMC8187847 DOI: 10.21769/bioprotoc.4004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 11/02/2022] Open
Abstract
Understanding the function of oligonucleotides on a molecular level requires methods for studying their structure, conformational changes, and internal dynamics. Various biophysical methods exist to achieve this, including the whole toolbox of Electron Paramagnetic Resonance (EPR or ESR) spectroscopy. An EPR method widely used in this regard is Pulsed Electron-Electron Double Resonance (PELDOR or DEER), which provides distances in the nanometer range between electron spins in biomolecules with Angstrom precision, without restriction to the size of the biomolecule, and in solution. Since oligonucleotides inherently do not contain unpaired electrons, these have to be introduced in the form of so-called spin labels. Firstly, this protocol describes how nitroxide spin labels can be site-specifically attached to oligonucleotides using "Click" chemistry. The reaction provides little byproducts, high yields, and is conveniently performed in aqueous solution. Secondly, the protocol details how to run the PELDOR experiment, analyze the data, and derive a coarse-grained structure. Here, emphasis is placed on the pitfalls, requirements for a good dataset, and limits of interpretation; thus, the protocol gives the user a guideline for the whole experiment i.e., from spin labeling, via the PELDOR measurement and data analysis, to the final coarse-grained structure. Graphical abstract: Schematic overview of the workflow described in this protocol: First, the spin-labeling of RNA is described, which is performed as a "Click"-reaction between the alkyne-functionalized RNA strand and the azide group of the spin label. Next, step-by-step instructions are given for setting up PELDOR/DEER distance measurements on the labeled RNA, and for data analysis. Finally, guidelines are provided for building a structural model from the previously analyzed data.
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Affiliation(s)
- Maria F. Vicino
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Tobias Hett
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
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31
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Hett T, Zbik T, Mukherjee S, Matsuoka H, Bönigk W, Klose D, Rouillon C, Brenner N, Peuker S, Klement R, Steinhoff HJ, Grubmüller H, Seifert R, Schiemann O, Kaupp UB. Spatiotemporal Resolution of Conformational Changes in Biomolecules by Combining Pulsed Electron-Electron Double Resonance Spectroscopy with Microsecond Freeze-Hyperquenching. J Am Chem Soc 2021; 143:6981-6989. [PMID: 33905249 DOI: 10.1021/jacs.1c01081] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The function of proteins is linked to their conformations that can be resolved with several high-resolution methods. However, only a few methods can provide the temporal order of intermediates and conformational changes, with each having its limitations. Here, we combine pulsed electron-electron double resonance spectroscopy with a microsecond freeze-hyperquenching setup to achieve spatiotemporal resolution in the angstrom range and lower microsecond time scale. We show that the conformational change of the Cα-helix in the cyclic nucleotide-binding domain of the Mesorhizobium loti potassium channel occurs within about 150 μs and can be resolved with angstrom precision. Thus, this approach holds great promise for obtaining 4D landscapes of conformational changes in biomolecules.
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Affiliation(s)
- Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Tobias Zbik
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Shatanik Mukherjee
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Klose
- Fachbereich Physik, Universität Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany
| | - Christophe Rouillon
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Norbert Brenner
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Sebastian Peuker
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Reinhard Klement
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,Life & Medical Sciences Institute (LIMES), University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
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32
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Bahrenberg T, Jahn SM, Feintuch A, Stoll S, Goldfarb D. The decay of the refocused Hahn echo in double electron-electron resonance (DEER) experiments. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:161-173. [PMID: 37904783 PMCID: PMC10539729 DOI: 10.5194/mr-2-161-2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/13/2021] [Indexed: 11/01/2023]
Abstract
Double electron-electron resonance (DEER) is a pulse electron paramagnetic resonance (EPR) technique that measures distances between paramagnetic centres. It utilizes a four-pulse sequence based on the refocused Hahn spin echo. The echo decays with increasing pulse sequence length 2 ( τ 1 + τ 2 ) , where τ 1 and τ 2 are the two time delays. In DEER, the value of τ 2 is determined by the longest inter-spin distance that needs to be resolved, and τ 1 is adjusted to maximize the echo amplitude and, thus, sensitivity. We show experimentally that, for typical spin centres (nitroxyl, trityl, and Gd(III)) diluted in frozen protonated solvents, the largest refocused echo amplitude for a given τ 2 is obtained neither at very short τ 1 (which minimizes the pulse sequence length) nor at τ 1 = τ 2 (which maximizes dynamic decoupling for a given total sequence length) but rather at τ 1 values smaller than τ 2 . Large-scale spin dynamics simulations based on the coupled cluster expansion (CCE), including the electron spin and several hundred neighbouring protons, reproduce the experimentally observed behaviour almost quantitatively. They show that electron spin dephasing is driven by solvent protons via the flip-flop coupling among themselves and their hyperfine couplings to the electron spin.
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Affiliation(s)
- Thorsten Bahrenberg
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Samuel M. Jahn
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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33
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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34
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Fleck N, Heubach C, Hett T, Spicher S, Grimme S, Schiemann O. Ox-SLIM: Synthesis of and Site-Specific Labelling with a Highly Hydrophilic Trityl Spin Label. Chemistry 2021; 27:5292-5297. [PMID: 33404074 PMCID: PMC8048664 DOI: 10.1002/chem.202100013] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Indexed: 01/04/2023]
Abstract
The combination of pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) with site-directed spin labelling is a powerful tool in structural biology. Rational design of trityl-based spin labels has enabled studying biomolecular structures at room temperature and within cells. However, most current trityl spin labels suffer either from aggregation with proteins due to their hydrophobicity, or from bioconjugation groups not suitable for in-cell measurements. Therefore, we introduce here the highly hydrophilic trityl spin label Ox-SLIM. Engineered as a short-linked maleimide, it combines the most recent developments in one single molecule, as it does not aggregate with proteins, exhibits high resistance under in-cell conditions, provides a short linker, and allows for selective and efficient spin labelling via cysteines. Beyond establishing synthetic access to Ox-SLIM, its suitability as a spin label is illustrated and ultimately, highly sensitive PDS measurements are presented down to protein concentrations as low as 45 nm resolving interspin distances of up to 5.5 nm.
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Affiliation(s)
- Nico Fleck
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
| | - Caspar Heubach
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
| | - Tobias Hett
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
| | - Sebastian Spicher
- University of BonnInstitute of Physical and Theoretical ChemistryBeringstr. 453115BonnGermany
| | - Stefan Grimme
- University of BonnInstitute of Physical and Theoretical ChemistryBeringstr. 453115BonnGermany
| | - Olav Schiemann
- University of BonnInstitute of Physical and Theoretical ChemistryWegelerstr. 1253115BonnGermany
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35
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Emerging applications of site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) to study food protein structure, dynamics, and interaction. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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36
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Ketter S, Gopinath A, Rogozhnikova O, Trukhin D, Tormyshev VM, Bagryanskaya EG, Joseph B. In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels. Chemistry 2021; 27:2299-2304. [PMID: 33197077 PMCID: PMC7898545 DOI: 10.1002/chem.202004606] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Indexed: 01/03/2023]
Abstract
In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM ) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.
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Affiliation(s)
- Sophie Ketter
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Olga Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Dmitrii Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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37
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Georgieva ER. Protein Conformational Dynamics upon Association with the Surfaces of Lipid Membranes and Engineered Nanoparticles: Insights from Electron Paramagnetic Resonance Spectroscopy. Molecules 2020; 25:E5393. [PMID: 33218036 PMCID: PMC7698768 DOI: 10.3390/molecules25225393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning from a solution environment to the states in which they are associated with the surfaces of biological membranes or engineered nanoobjects. In the former case these structural transitions generally underlie functional protein states. The latter case is mostly relevant to the application of protein immobilization in biotechnological industries, developing methods for protein purification, etc. Therefore, evaluating the stability of the protein functional state is particularly important. EPR spectroscopy in the form of continuous-wave EPR or pulse EPR distance measurements in conjunction with protein spin labeling provides highly versatile and sensitive tools to characterize the changes in protein local dynamics as well as large conformational rearrangements. The technique can be widely utilized in studies of both protein-membrane and engineered nanoobject-protein complexes.
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Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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38
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Demay-Drouhard P, Ching HYV, Decroos C, Guillot R, Li Y, Tabares LC, Policar C, Bertrand HC, Un S. Understanding the g-tensors of perchlorotriphenylmethyl and Finland-type trityl radicals. Phys Chem Chem Phys 2020; 22:20792-20800. [PMID: 32909565 DOI: 10.1039/d0cp03626a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 285 GHz EPR spectra of perchlorotriphenylmethyl and tetrathiatriarylmethyl radicals in frozen solution have been accurately measured. The relationship between their molecular structures and their g-tensors has been investigated with the aid of DFT calculations, revealing that the degree of spin density delocalization away from the central methylene carbon is an important determining factor of the g-anisotropy. In particular, the small amount of spin densities on the Cl or S heteroatoms at the 2 and 6 positions with respect to the central carbon have the strongest influence. Furthermore, the amount of spin densities on these heteroatoms and thus the anisotropy can be modulated by the protonation (esterification) state of the carboxylate groups at the 4 position. These results provide unique insights into the g-anisotropy of persistent trityl radicals and how it can be tuned.
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Affiliation(s)
- Paul Demay-Drouhard
- Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - H Y Vincent Ching
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Christophe Decroos
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Sud, CNRS UMR 8182, Université Paris-Saclay, 91405 Orsay, France
| | - Yun Li
- Laboratoire de Chimie des Processus Biologiques, CNRS UMR 8229, Collège de France, PSL University, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Leandro C Tabares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Clotilde Policar
- Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Helene C Bertrand
- Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Sun Un
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Moore W, McPeak JE, Poncelet M, Driesschaert B, Eaton SS, Eaton GR. 13C isotope enrichment of the central trityl carbon decreases fluid solution electron spin relaxation times. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106797. [PMID: 32769018 PMCID: PMC7492462 DOI: 10.1016/j.jmr.2020.106797] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 05/19/2023]
Abstract
Electron spin relaxation times for perdeuterated Finland trityl 99% enriched in 13C at the central carbon (13C1-dFT) were measured in phosphate buffered saline (pH = 7.2) (PBS) solution at X-band. The anisotropic 13C1 hyperfine (Ax = Ay = 18 ± 2, Az = 162 ± 1 MHz) and g values (2.0033, 2.0032, 2.00275) in a 9:1 trehalose:sucrose glass at 293 K and in 1:1 PBS:glycerol at 160 K were determined by simulation of spectra at X-band and Q-band. In PBS at room temperature the tumbling correlation time, τR, is 0.29 ± 0.02 ns. The linewidths are broadened by incomplete motional averaging of the hyperfine anisotropy and T2 is 0.13 ± 0.02 µs, which is shorter than the T2 ~ 3.8 µs for natural abundance dFT at low concentration in PBS. T1 for 13C1-dFT in deoxygenated PBS is 5.9 ± 0.5 µs, which is shorter than for natural abundance dFT in PBS (16 µs) but much longer than in air-saturated solution (0.48 ± 0.04 µs). The tumbling dependence of T1 in PBS, 3:1 PBS:glycerol (τR = 0.80 ± 0.05 ns, T1 = 9.7 ± 0.7 µs) and 1:1 PBS:glycerol (τR = 3.4 ± 0.3 ns, T1 = 12.0 ± 1.0 µs) was modeled with contributions to the relaxation predominantly from modulation of hyperfine anisotropy and a local mode. The 1/T1 rate for the 1% 12C1-dFT in the predominantly 13C labeled sample is about a factor of 6 more strongly concentration dependent than for natural abundance 12C1-trityl, which reflects the importance of Heisenberg exchange with molecules with different resonance frequencies and faster relaxation rates. In glassy matrices at 160 K, T1 and Tm for 13C1-dFT are in good agreement with previously reported values for 12C1-dFT consistent with the expectation that modulation of nuclear hyperfine does not contribute to electron spin relaxation in a rigid lattice.
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Affiliation(s)
- Whylder Moore
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Joseph E McPeak
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance Center, West Virginia University, Morgantown, WV 26506, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA.
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40
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Kopp K, Schiemann O, Fleck N. Improved, Odorless Access to Benzo[1,2-d;4,5-d']- bis[1,3]dithioles and Tert-butyl Arylsulfides via C-S Cross Coupling. Molecules 2020; 25:molecules25163666. [PMID: 32806560 PMCID: PMC7464442 DOI: 10.3390/molecules25163666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 11/26/2022] Open
Abstract
Benzo[1,2-d;4,5-d′]bis[1,3]dithioles are important building blocks within a range of functional materials such as fluorescent dyes, conjugated polymers, and stable trityl radicals. Access to these is usually gained via tert-butyl aryl sulfides, the synthesis of which requires the use of highly malodorous tert-butyl thiol and relies on SNAr-chemistry requiring harsh reaction conditions, while giving low yields. In the present work, S-tert-butyl isothiouronium bromide is successfully applied as an odorless surrogate for tert-butyl thiol. The C-S bond formation is carried out under palladium catalysis with the thiolate formed in situ resulting in high yields of tert-butyl aryl sulfides. The subsequent formation of benzo[1,2-d;4,5-d′]bis[1,3]dithioles is here achieved with scandium(III)triflate, a less harmful reagent than the usually used Lewis acids, e.g., boron trifluoride or tetrafluoroboric acid. This enables a convenient and environmentally more compliant access to high yields of benzo[1,2-d;4,5-d′]bis[1,3]dithioles.
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41
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Sanzhaeva U, Poncelet M, Tseytlin O, Tseytlin M, Gencheva M, Eubank TD, Khramtsov VV, Driesschaert B. Synthesis, Characterization, and Application of a Highly Hydrophilic Triarylmethyl Radical for Biomedical EPR. J Org Chem 2020; 85:10388-10398. [PMID: 32698583 DOI: 10.1021/acs.joc.0c00557] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stable tetrathiatriarylmethyl radicals have significantly contributed to the recent progress in biomedical electron paramagnetic resonance (EPR) due to their unmatched stability in biological media and long relaxation times. However, the lipophilic core of the most commonly used structure (Finland trityl) is responsible for its interaction with plasma biomacromolecules, such as albumin, and self-aggregation at high concentrations and/or low pH. While Finland trityl is generally considered inert toward many reactive radical species, we report that sulfite anion radical efficiently substitutes the three carboxyl moieties of Finland trityl with a high rate constant of 3.53 × 108 M-1 s-1, leading to a trisulfonated Finland trityl radical. This newly synthesized highly hydrophilic trityl radical shows an ultranarrow linewidth (ΔBpp = 24 mG), a lower affinity for albumin than Finland trityl, and a high aqueous solubility even at acidic pH. Therefore, this new tetrathiatriarylmethyl radical can be considered as a superior spin probe in comparison to the widely used Finland trityl. One of its potential applications was demonstrated by in vivo mapping oxygen in a mouse model of breast cancer. Moreover, we showed that one of the three sulfo groups can be easily substituted with S-, N-, and P-nucleophiles, opening access to various monofunctionalized sulfonated trityl radicals.
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Affiliation(s)
- Urikhan Sanzhaeva
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, West Virginia 26506, United States
| | - Martin Poncelet
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Pharmaceutical Sciences, West Virginia University, School of Pharmacy, Morgantown, West Virginia 26506, United States
| | - Oxana Tseytlin
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, West Virginia 26506, United States
| | - Mark Tseytlin
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, West Virginia 26506, United States
| | - Marieta Gencheva
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Microbiology, Immunology, and Cell Biology, West Virginia University, School of Medicine, Morgantown, West Virginia 26506, United States
| | - Timothy D Eubank
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Microbiology, Immunology, and Cell Biology, West Virginia University, School of Medicine, Morgantown, West Virginia 26506, United States
| | - Valery V Khramtsov
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Biochemistry, West Virginia University, School of Medicine, Morgantown, West Virginia 26506, United States
| | - Benoit Driesschaert
- In Vivo Multifunctional Magnetic Resonance Center, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States.,Department of Pharmaceutical Sciences, West Virginia University, School of Pharmacy, Morgantown, West Virginia 26506, United States
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42
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Bretschneider M, Spindler PE, Rogozhnikova OY, Trukhin DV, Endeward B, Kuzhelev AA, Bagryanskaya E, Tormyshev VM, Prisner TF. Multiquantum Counting of Trityl Radicals. J Phys Chem Lett 2020; 11:6286-6290. [PMID: 32667797 DOI: 10.1021/acs.jpclett.0c01615] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We demonstrate a series of multitrityl radical compounds where accurate spin-counting by pulsed electron paramagnetic resonance (EPR) can be achieved at X-band (9 GHz) frequencies, even for molecules with very short and flexible linkers. Multiquantum filter experiments, well-known from NMR, were used to count the number of coupled electron spins in these compounds. The six pulse double quantum filter sequence used in EPR for distance determinations in biradicals was used. Precise phase settings to separate higher quantum coherences were achieved by an arbitrary waveform generator. The trityl radicals have narrow spectral width so that homogeneous excitation of all spins by the pulses is possible. The transversal relaxation times of higher quantum coherences of trityl radicals are sufficiently long to allow their detection. Our results on model compounds show the potential of this approach to determine oligomeric states in protein complexes in their native environment using functionalized trityl spin labels.
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Affiliation(s)
- Matthias Bretschneider
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
| | - Phillip E Spindler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
| | - Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Elena Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
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43
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Wang X, Peng C, He K, Ji K, Tan X, Han G, Liu Y, Liu Y, Song Y. Intracellular delivery of liposome-encapsulated Finland trityl radicals for EPR oximetry. Analyst 2020; 145:4964-4971. [PMID: 32510063 DOI: 10.1039/d0an00108b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tetrathiatriarylmethyl (TAM, trityl) radicals have found wide applications in electron paramagnetic resonance (EPR) oximetry. However, the biomedical applications of TAM radicals were exclusively limited to an extracellular region owing to their negatively charged nature. The intracellular delivery of TAM radicals still remains a challenge. In the present work, we report a liposome-based method to encapsulate the water-soluble Finland trityl radical CT-03 for its intracellular delivery. Using the thin lipid film hydration method, CT-03-loaded liposomes were prepared from DSPC/cholesterol/DOTAP with a mean size of 167.5 ± 2.4 nm and a zeta potential of 27.8 ± 0.8 mV. EPR results showed that CT-03 was entrapped into the liposomes and still exhibited good oxygen (O2) sensitivity. Moreover, CT-03 was successfully delivered into HepG2 cells and HUVECs using the CT-03-loaded liposomes. Importantly, the combination of the liposome-encapsulated radical CT-03 and the other TAM radical CT02-H enabled simultaneous measurements of the intracellular and extracellular O2 concentrations and O2 consumption rates in HepG2 cells. Our present study provides a new approach for intracellular delivery of TAM radicals and could significantly expand their biomedical applications.
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Affiliation(s)
- Xing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China.
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44
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short-Linked, Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020; 59:9767-9772. [PMID: 32329172 PMCID: PMC7318235 DOI: 10.1002/anie.202004452] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/15/2022]
Abstract
The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site-directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in-cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide-functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm, and shows high stability against reduction. Using this label, the guanine-nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.
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Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
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45
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EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility. Arch Biochem Biophys 2020; 684:108323. [DOI: 10.1016/j.abb.2020.108323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
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46
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short‐Linked, Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004452] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Römerstr. 164 53117 Bonn Germany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Römerstr. 164 53117 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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47
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Braun TS, Widder P, Osswald U, Groß L, Williams L, Schmidt M, Helmle I, Summerer D, Drescher M. Isoindoline-Based Nitroxides as Bioresistant Spin Labels for Protein Labeling through Cysteines and Alkyne-Bearing Noncanonical Amino Acids. Chembiochem 2020; 21:958-962. [PMID: 31657498 PMCID: PMC7187341 DOI: 10.1002/cbic.201900537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/18/2019] [Indexed: 12/15/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful tool in protein structural research. Nitroxides are highly suitable spin labeling reagents, but suffer from limited stability, particularly in the cellular environment. Herein we present the synthesis of a maleimide- and an azide-modified tetraethyl-shielded isoindoline-based nitroxide (M- and Az-TEIO) for labeling of cysteines or the noncanonical amino acid para-ethynyl-l-phenylalanine (pENF). We demonstrate the high stability of TEIO site-specifically attached to the protein thioredoxin (TRX) against reduction in prokaryotic and eukaryotic environments, and conduct double electron-electron resonance (DEER) measurements. We further generate a rotamer library for the new residue pENF-Az-TEIO that affords a distance distribution that is in agreement with the measured distribution.
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Affiliation(s)
- Theresa Sophie Braun
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Pia Widder
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Uwe Osswald
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Lina Groß
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Lara Williams
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Moritz Schmidt
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Irina Helmle
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Present address: Faculty of ScienceDepartment of Pharmaceutical BiologyUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical BiologyTU DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Malte Drescher
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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48
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Abdullin D, Schiemann O. Pulsed Dipolar EPR Spectroscopy and Metal Ions: Methodology and Biological Applications. Chempluschem 2020; 85:353-372. [DOI: 10.1002/cplu.201900705] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/16/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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49
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Yang Y, Pan BB, Tan X, Yang F, Liu Y, Su XC, Goldfarb D. In-Cell Trityl-Trityl Distance Measurements on Proteins. J Phys Chem Lett 2020; 11:1141-1147. [PMID: 31951412 PMCID: PMC7307952 DOI: 10.1021/acs.jpclett.9b03208] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Double-electron electron resonance (DEER) can be used to track the structural dynamics of proteins in their native environment, the cell. This method provides the distance distribution between two spin labels attached at specific, well-defined positions in a protein. For the method to be viable under in-cell conditions, the spin label and its attachment to the protein should exhibit high chemical stability in the cell. Here we present low-temperature, trityl-trityl DEER distance measurements on two model proteins, PpiB (prolyl cis-trans isomerase from E. coli) and GB1 (immunoglobulin G-binding protein), doubly labeled with the trityl spin label, CT02MA. Both proteins gave in-cell distance distributions similar to those observed in vitro, with maxima at 4.5-5 nm, and the data were further compared with in-cell Gd(III)-Gd(III) DEER obtained for PpiB labeled with BrPSPy-DO3A-Gd(III) at the same positions. These results highlight the challenges of designing trityl tags suitable for in-cell distance determination at ambient temperatures on live cells.
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Affiliation(s)
- Yin Yang
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Bin-Bin Pan
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xiaoli Tan
- Tianjin
Key Laboratory on Technologies Enabling Development of Clinical Therapeutics
and Diagnostics, School of Pharmacy, Tianjin
Medical University, Tianjin 300070, China
| | - Feng Yang
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Yangping Liu
- Tianjin
Key Laboratory on Technologies Enabling Development of Clinical Therapeutics
and Diagnostics, School of Pharmacy, Tianjin
Medical University, Tianjin 300070, China
| | - Xun-Cheng Su
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Daniella Goldfarb
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
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50
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Tormyshev VM, Chubarov AS, Krumkacheva OA, Trukhin DV, Rogozhnikova OY, Spitsyna AS, Kuzhelev AA, Koval VV, Fedin MV, Godovikova TS, Bowman MK, Bagryanskaya EG. Methanethiosulfonate Derivative of OX063 Trityl: A Promising and Efficient Reagent for Side-Directed Spin Labeling of Proteins. Chemistry 2020; 26:2705-2712. [PMID: 31851392 DOI: 10.1002/chem.201904587] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/30/2019] [Indexed: 12/20/2022]
Abstract
Trityl radicals (TAMs) have recently appeared as an alternative source of spin labels for measuring long distances in biological systems. Finland trityl radical (FTAM) served as the basis for this new generation of spin labels, but FTAM is rather lipophilic and susceptible to self-aggregation, noncovalent binding with lipophilic sites of proteins, and noncovalent docking at the termini of duplex DNA. In this paper the very hydrophilic OX063 TAM with very low toxicity and little tendency for aggregation is used as the basis for a spin label. Human serum albumin (HSA) labeled with OX063 has an intense narrow line typical of TAM radicals in solution, whereas HSA labeled with FTAM shows broad lines and extensive aggregation. In pulse EPR measurements, the measured phase memory time TM for HSA labeled with OX063 is 6.3 μs at 50 K, the longest yet obtained with a TAM-based spin label. The lowered lipophilicity also decreases side products in the labeling reaction.
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Affiliation(s)
- Victor M Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Olesya A Krumkacheva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia.,International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk, 630090, Russia
| | - Dmitry V Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Olga Yu Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Anna S Spitsyna
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Andrey A Kuzhelev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Institutskaya Str. 3a, Novosibirsk, 630090, Russia
| | - Tatyana S Godovikova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | - Michael K Bowman
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama, 35487-0336, USA
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Pr. Lavrentjeva 9, Novosibirsk, 630090, Russia
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