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Hecker F, Fries L, Hiller M, Chiesa M, Bennati M. 17 O Hyperfine Spectroscopy Reveals Hydration Structure of Nitroxide Radicals in Aqueous Solutions. Angew Chem Int Ed Engl 2023; 62:e202213700. [PMID: 36399425 PMCID: PMC10107301 DOI: 10.1002/anie.202213700] [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: 09/18/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022]
Abstract
The hydration structure of nitroxide radicals in aqueous solutions is elucidated by advanced 17 O hyperfine (hf) spectroscopy with support of quantum chemical calculations and MD simulations. A piperidine and a pyrrolidine-based nitroxide radical are compared and show clear differences in the preferred directionality of H-bond formation. We demonstrate that these scenarios are best represented in 17 O hf spectra, where in-plane coordination over σ ${\sigma }$ -type H-bonding leads to little spin density transfer on the water oxygen and small hf couplings, whereas π ${{\rm \pi }}$ -type perpendicular coordination generates much larger hf couplings. Quantitative analysis of the spectra based on MD simulations and DFT predicted hf parameters is consistent with a distribution of close solvating water molecules, in which directionality is influenced by subtle steric effects of the ring and the methyl group substituents.
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Affiliation(s)
- Fabian Hecker
- Research Group EPR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Lisa Fries
- Research Group EPR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.,Current address: Center for Biostructural Imaging of Neurodegeneration, Medical Center Göttingen, Von-Siebold-Straße 3a, 37075, Göttingen, Germany.,NMR Signal Enhancement Group, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Hiller
- Research Group EPR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.,Current address: Isotope Technologies Dresden, Rossendorfer Ring 42, 01328, Dresden, Germany
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Marina Bennati
- Research Group EPR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.,Department of Chemistry, Georg August University Göttingen, Tammanstrasse 2, 37077, Göttingen, Germany
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2
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Drew DL, Ahammad T, Serafin RA, Sahu ID, Khan RH, Faul E, McCarrick RM, Lorigan GA. Probing the local secondary structure of bacteriophage S 21 pinholin membrane protein using electron spin echo envelope modulation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183836. [PMID: 34906602 DOI: 10.1016/j.bbamem.2021.183836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
There have recently been advances in methods for detecting local secondary structures of membrane protein using electron paramagnetic resonance (EPR). A three pulsed electron spin echo envelope modulation (ESEEM) approach was used to determine the local helical secondary structure of the small hole forming membrane protein, S21 pinholin. This ESEEM approach uses a combination of site-directed spin labeling and 2H-labeled side chains. Pinholin S21 is responsible for the permeabilization of the inner cytosolic membrane of double stranded DNA bacteriophage host cells. In this study, we report on the overall global helical structure using circular dichroism (CD) spectroscopy for the active form and the negative-dominant inactive mutant form of S21 pinholin. The local helical secondary structure was confirmed for both transmembrane domains (TMDs) for the active and inactive S21 pinholin using the ESEEM spectroscopic technique. Comparison of the ESEEM normalized frequency domain intensity for each transmembrane domain gives an insight into the α-helical folding nature of these domains as opposed to a π or 310-helix which have been observed in other channel forming proteins.
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Affiliation(s)
- Daniel L Drew
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Tanbir Ahammad
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Rachel A Serafin
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA; Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Rasal H Khan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Emily Faul
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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3
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Isaev N, Steinhoff HJ. Protein and solutes freeze-concentration in water/glycerol mixtures revealed by pulse EPR. Eur J Pharm Biopharm 2021; 169:44-51. [PMID: 34534655 DOI: 10.1016/j.ejpb.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Lyophilization can extend protein drugs stability and shelf life, but it also can lead to protein degradation in some cases. The development of safe freeze-drying approaches for sensitive proteins requires a better understanding of lyophilization on the molecular level. The evaluation of the freezing process and its impact on the protein environment in the nm scale is challenging because feasible experimental methods are scarce. In the present work we apply pulse EPR as a tool to study the local concentrations of the solute in the 20 nm range and of the solvent in the 1 nm range for a spin labeled 27 kDa monomeric green fluorescent protein, mEGFP, and the 172 Da TEMPOL spin probe, frozen in different water/glycerol-d5 mixtures. For average glycerol volume fractions, φgly-d5avg, ≥ 0.4 we observed transparent glassy media; the local concentration and the 1 nm solvent shell of TEMPOL and the protein correspond to those of a uniform vitrified glass. At φgly-d5avg ≤ 0.3 we observed partial ice crystallization, which led to ice exclusion of glycerol and TEMPOL with freeze-concentration up to the glycerol maximal-freeze local volume fraction, φgly-d5loc, of 0.64. The protein concentration and its shell behavior was similar except for the lowest φgly-d5avg (0.1), which showed a 4.7-fold freeze-concentration factor compared to sevenfold for TEMPOL, and also a smaller φgly-d5loc. We explain this behavior with an increased probability for proteins to get stuck in the ice phase during fast freezing at higher freeze-concentration and the related large-scale mass transfer.
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Affiliation(s)
- Nikolay Isaev
- Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, Novosibirsk, Russia.
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Geometry and water accessibility of the inhibitor binding site of Na +-pump: Pulse- and CW-EPR study. Biophys J 2021; 120:2679-2690. [PMID: 34087213 PMCID: PMC8390900 DOI: 10.1016/j.bpj.2021.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/22/2022] Open
Abstract
Spin labels based on cinobufagin, a specific inhibitor of the Na,K-ATPase, have proved valuable tools to characterize the binding site of cardiotonic steroids (CTSs), which also constitutes the extracellular cation pathway. Because existing literature suggests variations in the physiological responses caused by binding of different CTSs, we extended the original set of spin-labeled inhibitors to the more potent bufalin derivatives. Positioning of the spin labels within the Na,K-ATPase site was defined and visualized by molecular docking. Although the original cinobufagin labels exhibited lower affinity, continuous-wave electron paramagnetic resonance spectra of spin-labeled bufalins and cinobufagins revealed a high degree of pairwise similarity, implying that these two types of CTS bind in the same way. Further analysis of the spectral lineshapes of bound spin labels was performed with emphasis on their structure (PROXYL vs. TEMPO), as well as length and rigidity of the linkers. For comparable structures, the dynamic flexibility increased in parallel with linker length, with the longest linker placing the spin label at the entrance to the binding site. Temperature-related changes in spectral lineshapes indicate that six-membered nitroxide rings undergo boat-chair transitions, showing that the binding-site cross section can accommodate the accompanying changes in methyl-group orientation. D2O-electron spin echo envelope modulation in pulse-electron paramagnetic resonance measurements revealed high water accessibilities and similar polarity profiles for all bound spin labels, implying that the vestibule leading to steroid-binding site and cation-binding sites is relatively wide and water-filled.
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Aloi E, Bartucci R. Cryogenically frozen PEGylated liposomes and micelles: Water penetration and polarity profiles. Biophys Chem 2020; 266:106463. [PMID: 32911450 DOI: 10.1016/j.bpc.2020.106463] [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: 07/15/2020] [Revised: 08/23/2020] [Accepted: 08/23/2020] [Indexed: 11/24/2022]
Abstract
Poly(ethylene glycol) (PEG)-grafted lipid dispersions are widely investigated in fundamental and biotechnological research for their successful use in drug-delivery. Here, we consider mixtures of the bilayer-forming lipid dipalmitoylphosphatidylcholine (DPPC) with the micelle-forming lipid PEG:2000-phosphatidilethanolamine (PEG:2000-DPPE) fully hydrated in D2O and measured at 77 K. Electron Spin Echo Envelope Modulation and continuous wave Electron Paramagnetic Resonance of chain-labelled lipids are employed to detect the extent of solvent permeation and the environmental polarity, respectively, across the hydrocarbon regions of the lipid assemblies. Sigmoidal water penetration and polarity profiles are described in sterically stabilized liposomes (SSL) formed at submicellar content of PEG:2000-DPPE incorporated in DPPC. Compared to DPPC bilayers, SSL show increased hydrophobicity at both the polar/apolar interface and the chain termini, and a broader transition that is shifted toward the interface. Solvent exposure and polarity decrease on going down the chain in PEG:2000-DPPE micelles. However, compared to SSL, polymer-lipid micelles show higher solvent permeation at any chain segment and the chain termini are accessible to water. In any sample, heterogeneity is found in H-bond formation between the spin-label nitroxide groups and the solvent molecules. The results at cryogenic temperature add new insights into the biophysico-chemical characterization of PEGylated lipid dispersions.
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Affiliation(s)
- Erika Aloi
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Rosa Bartucci
- Molecular Biophysics Laboratory, Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy.
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Aloi E, Bartucci R. Solvent accessibility in interdigitated and micellar phases formed by DPPC/Lyso-PPC mixtures: D2O-ESEEM of chain labeled lipids. Chem Phys Lipids 2019; 221:39-45. [DOI: 10.1016/j.chemphyslip.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/27/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022]
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Bottorf L, Sahu ID, McCarrick RM, Lorigan GA. Utilization of 13C-labeled amino acids to probe the α-helical local secondary structure of a membrane peptide using electron spin echo envelope modulation (ESEEM) spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1447-1451. [PMID: 29694834 PMCID: PMC5957090 DOI: 10.1016/j.bbamem.2018.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/27/2018] [Accepted: 04/09/2018] [Indexed: 11/22/2022]
Abstract
Electron spin echo envelope modulation (ESEEM) spectroscopy in combination with site-directed spin labeling (SDSL) has been established as a valuable biophysical technique to provide site-specific local secondary structure of membrane proteins. This pulsed electron paramagnetic resonance (EPR) method can successfully distinguish between α-helices, β-sheets, and 310-helices by strategically using 2H-labeled amino acids and SDSL. In this study, we have explored the use of 13C-labeled residues as the NMR active nuclei for this approach for the first time. 13C-labeled d5-valine (Val) or 13C-labeled d6-leucine (Leu) were substituted at a specific Val or Leu residue (i), and a nitroxide spin label was positioned 2 or 3 residues away (denoted i-2 and i-3) on the acetylcholine receptor M2δ (AChR M2δ) in a lipid bilayer. The 13C ESEEM peaks in the FT frequency domain data were observed for the i-3 samples, and no 13C peaks were observed in the i-2 samples. The resulting spectra were indicative of the α-helical local secondary structure of AChR M2δ in bicelles. This study provides more versatility and alternative options when using this ESEEM approach to study the more challenging recombinant membrane protein secondary structures.
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Affiliation(s)
- Lauren Bottorf
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States.
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8
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Liu L, Sahu ID, Bottorf L, McCarrick RM, Lorigan GA. Investigating the Secondary Structure of Membrane Peptides Utilizing Multiple 2H-Labeled Hydrophobic Amino Acids via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. J Phys Chem B 2018; 122:4388-4396. [PMID: 29614227 DOI: 10.1021/acs.jpcb.7b11890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An electron spin echo envelope modulation (ESEEM) approach was used to probe local secondary structures of membrane proteins and peptides. This ESEEM method detects dipolar couplings between 2H-labeled nuclei on the side chains of an amino acid (Leu or Val) and a strategically placed nitroxide spin-label in the proximity up to 8 Å. ESEEM spectra patterns for different samples correlate directly to the periodic structural feature of different secondary structures. Since this pattern can be affected by the side chain length and flexibility of the 2H-labeled amino acid used in the experiment, it is important to examine several different hydrophobic amino acids (d3 Ala, d8 Val, d8 Phe) utilizing this ESEEM approach. In this work, a series of ESEEM data were collected on the AChR M2δ membrane peptide to build a reference for the future application of this approach for various biological systems. The results indicate that, despite the relative intensity and signal-to-noise level, all amino acids share a similar ESEEM modulation pattern for α-helical structures. Thus, all commercially available 2H-labeled hydrophobic amino acids can be utilized as probes for the further application of this ESEEM approach. Also, the ESEEM signal intensities increase as the side chain length gets longer or less rigid. In addition, longer side chain amino acids had a larger 2H ESEEM FT peak centered at the 2H Larmor frequency for the i ± 4 sample when compared to the corresponding i ± 3 sample. For shorter side chain amino acids, the 2H ESEEM FT peak intensity ratio between i ± 4 and i ± 3 was not well-defined.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
| | - Lauren Bottorf
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry , Miami University , Oxford , Ohio 45056 , United States
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9
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Syryamina VN, De Zotti M, Toniolo C, Formaggio F, Dzuba SA. Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels. Phys Chem Chem Phys 2018; 20:3592-3601. [DOI: 10.1039/c7cp07298h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation.
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Affiliation(s)
- Victoria N. Syryamina
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Fernando Formaggio
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
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10
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Liu L, Hess J, Sahu ID, FitzGerald PG, McCarrick RM, Lorigan GA. Probing the Local Secondary Structure of Human Vimentin with Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. J Phys Chem B 2016; 120:12321-12326. [PMID: 27934222 DOI: 10.1021/acs.jpcb.6b10054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, an electron spin echo envelope modulation (ESEEM) spectroscopic approach was established to probe the local secondary structure of membrane proteins and peptides utilizing site-directed spin-labeling (SDSL). In this method, the side chain of one amino acid residue is selectively 2H-labeled and a nitroxide spin label is strategically placed 1, 2, 3, or 4 amino acids away from the 2H-labeled amino acid (denoted as i ± 1 to i ± 4, i represents the 2H-labeled amino acid). ESEEM can detect the dipolar coupling between the nitroxide spin label and 2H atoms on the amino acid side chain. Due to the periodicity of different secondary structures, different ESEEM patterns can be revealed to probe the structure. For an α-helical structural component, a 2H ESEEM signal can be detected for i ± 3 and i ± 4 samples, but not for i ± 1 or i ± 2 samples. Several 2H-labeled hydrophobic amino acids have been demonstrated in model system that can be utilized to identify local secondary structures via this ESEEM approach in an extremely efficient fashion. In this study, the ESEEM approach was used to investigate the rod 2B region of the full-length intermediate filament protein human vimentin. Consistent with previous EPR and X-ray crystallography results, our ESEEM results indicated helical structural components within this region. Thus, this ESEEM approach is able to identify α-helical structural components despite the coiled-coil nature of the vimentin structure. The data show that the human vimentin rod 2B adapted a typical α-helical structure around residue Leu309. This result is consistent with the X-ray data from fragmented protein segments and continuous wave EPR data on the full-length vimentin. Finally, the ESEEM data suggested that a local secondary structure slightly different from a typical α-helix was adopted around residue 340.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - John Hess
- Dept of Cell Biology and Human Anatomy, School of Medicine, University of California , Davis, California 95616, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Paul G FitzGerald
- Dept of Cell Biology and Human Anatomy, School of Medicine, University of California , Davis, California 95616, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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Abdullin D, Hagelueken G, Schiemann O. Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography. Phys Chem Chem Phys 2016; 18:10428-37. [DOI: 10.1039/c6cp01307d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PELDOR is used to unravel the position and orientation of MTSSL in six singly-labelled azurin mutants. A comparison with X-ray structures of the mutants shows good agreement with respect to the position and orientation of the nitroxide group.
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Affiliation(s)
- D. Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - G. Hagelueken
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - O. Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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12
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Rhodes CJ. The Role of ESR Spectroscopy in Advancing Catalytic Science: Some Recent Developments. PROGRESS IN REACTION KINETICS AND MECHANISM 2015. [DOI: 10.3184/146867815x14297237081532] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent progress is surveyed in regard to the importance of molecular species containing unpaired electrons in catalytic systems, as revealed using ESR spectroscopy. The review begins with studies of enzymes and their role directly in biological systems, and then discusses investigations of various artificially created catalysts with potential human and environmental significance, including zeolites. Among the specific types of catalytic media considered are those for photocatalysis, water splitting, the degradation of environmental pollutants, hydrocarbon conversions, fuel cells, ionic liquids and sensor devices employing graphene. Studies of muonium-labelled radicals in zeolites are also reviewed, as a means for determining the dynamics of transient radicals in these nanoporous materials.
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Klare JP, Steinhoff HJ. Spin Labeling Studies of Transmembrane Signaling and Transport. Methods Enzymol 2015; 564:315-47. [DOI: 10.1016/bs.mie.2015.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Florin N, Schiemann O, Hagelueken G. High-resolution crystal structure of spin labelled (T21R1) azurin from Pseudomonas aeruginosa: a challenging structural benchmark for in silico spin labelling algorithms. BMC STRUCTURAL BIOLOGY 2014; 14:16. [PMID: 24884565 PMCID: PMC4055355 DOI: 10.1186/1472-6807-14-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/08/2014] [Indexed: 01/23/2023]
Abstract
Background EPR-based distance measurements between spin labels in proteins have become a valuable tool in structural biology. The direct translation of the experimental distances into structural information is however often impaired by the intrinsic flexibility of the spin labelled side chains. Different algorithms exist that predict the approximate conformation of the spin label either by using pre-computed rotamer libraries of the labelled side chain (rotamer approach) or by simply determining its accessible volume (accessible volume approach). Surprisingly, comparisons with many experimental distances have shown that both approaches deliver the same distance prediction accuracy of about 3 Å. Results Here, instead of comparing predicted and experimental distances, we test the ability of both approaches to predict the actual conformations of spin labels found in a new high-resolution crystal structure of spin labelled azurin (T21R1). Inside the crystal, the label is found in two very different environments which serve as a challenging test for the in silico approaches. Conclusions Our results illustrate why simple and more sophisticated programs lead to the same prediciton error. Thus, a more precise treatment of the complete environment of the label and also its interactions with the environment will be needed to increase the accuracy of in silico spin labelling algorithms.
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Affiliation(s)
| | | | - Gregor Hagelueken
- Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr, 12, Bonn, NRW 53115, Germany.
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15
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Nalepa A, Möbius K, Lubitz W, Savitsky A. High-field ELDOR-detected NMR study of a nitroxide radical in disordered solids: towards characterization of heterogeneity of microenvironments in spin-labeled systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:203-213. [PMID: 24685717 DOI: 10.1016/j.jmr.2014.02.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/27/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
The combination of high-field EPR with site-directed spin-labeling (SDSL) techniques employing nitroxide radicals has turned out to be particularly powerful in probing the polarity and proticity characteristics of protein/matrix systems. This information is concluded from the principal components of the nitroxide Zeeman (g), nitrogen hyperfine (A) and quadrupole (P) tensors of the spin labels attached to specific sites. Recent multi-frequency high-field EPR studies underlined the complexity of the problem to treat the nitroxide microenvironment in proteins adequately due to inherent heterogeneities which result in several principal x-components of the nitroxide g-tensor. Concomitant, but distinctly different nitrogen hyperfine components could, however, not be determined from high-field cw EPR experiments owing to the large intrinsic EPR linewidth in fully protonated guest/host systems. It is shown in this work that, using the W-band (95GHz) ELDOR- (electron-electron double resonance) detected NMR (EDNMR) method, different principal nitrogen hyperfine, Azz, and quadrupole, Pzz, tensor values of a nitroxide radical in glassy 2-propanol matrix can be measured with high accuracy. They belong to nitroxides with different hydrogen-bond situations. The satisfactory resolution and superior sensitivity of EDNMR as compared to the standard ENDOR (electron-nuclear double resonance) method are demonstrated.
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Affiliation(s)
- Anna Nalepa
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany.
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16
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Gast P, Herbonnet RTL, Klare J, Nalepa A, Rickert C, Stellinga D, Urban L, Möbius K, Savitsky A, Steinhoff HJ, Groenen EJJ. Hydrogen bonding of nitroxide spin labels in membrane proteins. Phys Chem Chem Phys 2014; 16:15910-6. [DOI: 10.1039/c4cp01741b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On the basis of experiments at 275 GHz, we reconsider the dependence of the continuous-wave EPR spectra of nitroxide spin-labeled protein sites in sensory- and bacteriorhodopsin on the micro-environment.
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Affiliation(s)
- P. Gast
- Huygens-Kamerlingh Onnes Laboratory
- Department of Physics
- Leiden University
- NL-2300 RA Leiden, The Netherlands
| | - R. T. L. Herbonnet
- Huygens-Kamerlingh Onnes Laboratory
- Department of Physics
- Leiden University
- NL-2300 RA Leiden, The Netherlands
| | - J. Klare
- Department of Physics
- University of Osnabrück
- D-49076 Osnabrück, Germany
| | - A. Nalepa
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr, Germany
| | - C. Rickert
- Department of Physics
- University of Osnabrück
- D-49076 Osnabrück, Germany
| | - D. Stellinga
- Huygens-Kamerlingh Onnes Laboratory
- Department of Physics
- Leiden University
- NL-2300 RA Leiden, The Netherlands
| | - L. Urban
- Department of Physics
- University of Osnabrück
- D-49076 Osnabrück, Germany
| | - K. Möbius
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr, Germany
- Department of Physics
- Free University Berlin
- D-14195 Berlin, Germany
| | - A. Savitsky
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr, Germany
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- D-49076 Osnabrück, Germany
| | - E. J. J. Groenen
- Huygens-Kamerlingh Onnes Laboratory
- Department of Physics
- Leiden University
- NL-2300 RA Leiden, The Netherlands
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Abstract
An overview is provided of the importance of molecular species containing unpaired electrons in catalytic systems, as revealed using ESR spectroscopy. The review aims to demonstrate the considerable extent of scientific progress that has been made in this broad topic during the past few decades. Studies of catalytically active surfaces, including zeolites, are surveyed, and the detection of radical species, formed as intermediates in their reactions, using matrix isolation and spin-trapping techniques. Radical cation formation in zeolites is discussed, and the employment of muon spin rotation and relaxation techniques to study the mobility of labelled radicals in various porous and catalytic media. Among the specific types of catalytic media considered are those for photocatalysis, water splitting, degradation of environmental pollutants, hydrocarbon conversions, fuel cells and sensor devices employing graphene. The review concludes with recent developments in the study of enzymes and their reactions, using ESR-based methods.
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18
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Site-directed spin labeling EPR spectroscopy in protein research. Biol Chem 2013; 394:1281-300. [DOI: 10.1515/hsz-2013-0155] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/31/2013] [Indexed: 11/15/2022]
Abstract
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy has emerged as an efficient tool to elucidate the structure and the conformational dynamics of proteins under conditions close to the native state. This review article summarizes the basics as well as the recent progress in SDSL and EPR methods, especially for investigations on protein structure, protein function, and interaction of proteins with other proteins or nucleic acids. Labeling techniques as well as EPR methods are introduced and exemplified with applications to systems that have been studied in the author’s laboratory in the past 15 years, headmost the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis. Further examples underline the application of SDSL EPR spectroscopy to answer specific questions about the system under investigation, such as the nature and influence of interactions of proteins with other proteins or nucleic acids. Finally, it is discussed how SDSL EPR can be combined with other biophysical techniques to combine the strengths of the different methodologies.
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