251
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Ji M, Ruthstein S, Saxena S. Paramagnetic metal ions in pulsed ESR distance distribution measurements. Acc Chem Res 2014; 47:688-95. [PMID: 24289139 DOI: 10.1021/ar400245z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of pulsed electron spin resonance (ESR) to measure interspin distance distributions has advanced biophysical research. The three major techniques that use pulsed ESR are relaxation rate based distance measurements, double quantum coherence (DQC), and double electron electron resonance (DEER). Among these methods, the DEER technique has become particularly popular largely because it is easy to implement on commercial instruments and because programs are available to analyze experimental data. Researchers have widely used DEER to measure the structure and conformational dynamics of molecules labeled with the methanethiosulfonate spin label (MTSSL). Recently, researchers have exploited endogenously bound paramagnetic metal ions as spin probes as a way to determine structural constraints in metalloproteins. In this context Cu(2+) has served as a useful paramagnetic metal probe at X-band for DEER based distance measurements. Sample preparation is simple, and a coordinated-Cu(2+) ion offers limited spatial flexibility, making it an attractive probe for DEER experiments. On the other hand, Cu(2+) has a broad absorption ESR spectrum at low temperature, which leads to two potential complications. First, the Cu(2+)-based DEER time domain data has lower signal to noise ratio compared with MTSSL. Second, accurate distance distribution analysis often requires high-quality experimental data at different external magnetic fields or with different frequency offsets. In this Account, we summarize characteristics of Cu(2+)-based DEER distance distribution measurements and data analysis methods. We highlight a novel application of such measurements in a protein-DNA complex to identify the metal ion binding site and to elucidate its chemical mechanism of function. We also survey the progress of research on other metal ions in high frequency DEER experiments.
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Affiliation(s)
- Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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252
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Goldfarb D. Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy. Phys Chem Chem Phys 2014; 16:9685-99. [DOI: 10.1039/c3cp53822b] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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253
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Kattnig DR, Reichenwallner J, Hinderberger D. Modeling Excluded Volume Effects for the Faithful Description of the Background Signal in Double Electron–Electron Resonance. J Phys Chem B 2013; 117:16542-57. [DOI: 10.1021/jp408338q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Jörg Reichenwallner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
| | - Dariush Hinderberger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
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254
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Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ. Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Res 2013; 42:2789-97. [PMID: 24293651 PMCID: PMC3936745 DOI: 10.1093/nar/gkt1219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein-DNA interactions.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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255
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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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256
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Branigan E, Pliotas C, Hagelueken G, Naismith JH. Quantification of free cysteines in membrane and soluble proteins using a fluorescent dye and thermal unfolding. Nat Protoc 2013; 8:2090-7. [PMID: 24091556 PMCID: PMC3836627 DOI: 10.1038/nprot.2013.128] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cysteine is an extremely useful site for selective attachment of labels to proteins for many applications, including the study of protein structure in solution by electron paramagnetic resonance (EPR), fluorescence spectroscopy and medical imaging. The demand for quantitative data for these applications means that it is important to determine the extent of the cysteine labeling. The efficiency of labeling is sensitive to the 3D context of cysteine within the protein. Where the label or modification is not directly measurable by optical or magnetic spectroscopy, for example, in cysteine modification to dehydroalanine, assessing labeling efficiency is difficult. We describe a simple assay for determining the efficiency of modification of cysteine residues, which is based on an approach previously used to determine membrane protein stability. The assay involves a reaction between the thermally unfolded protein and a thiol-specific coumarin fluorophore that is only fluorescent upon conjugation with thiols. Monitoring fluorescence during thermal denaturation of the protein in the presence of the dye identifies the temperature at which the maximum fluorescence occurs; this temperature differs among proteins. Comparison of the fluorescence intensity at the identified temperature between modified, unmodified (positive control) and cysteine-less protein (negative control) allows for the quantification of free cysteine. We have quantified both site-directed spin labeling and dehydroalanine formation. The method relies on a commonly available fluorescence 96-well plate reader, which rapidly screens numerous samples within 1.5 h and uses <100 μg of material. The approach is robust for both soluble and detergent-solubilized membrane proteins.
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Affiliation(s)
- Emma Branigan
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - Christos Pliotas
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - Gregor Hagelueken
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
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257
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Roy A, Sarrou I, Vaughn MD, Astashkin AV, Ghirlanda G. De Novo Design of an Artificial Bis[4Fe-4S] Binding Protein. Biochemistry 2013; 52:7586-94. [DOI: 10.1021/bi401199s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Iosifina Sarrou
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei V. Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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258
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Kunjir NC, Reginsson GW, Schiemann O, Sigurdsson ST. Measurements of short distances between trityl spin labels with CW EPR, DQC and PELDOR. Phys Chem Chem Phys 2013; 15:19673-85. [PMID: 24135783 DOI: 10.1039/c3cp52789a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trityl based spin labels are emerging as a complement to nitroxides in nanometer distance measurements using EPR methods. The narrow spectral width of the trityl radicals prompts us to ask the question at which distance between these spin centers, the pseudo-secular part of the dipolar coupling and spin density delocalization have to be taken into account. For this, two trityl-trityl and one trityl-nitroxide model compounds were synthesized with well-defined interspin distances. Continuous wave (CW) EPR, double quantum coherence (DQC) and pulsed electron-electron double resonance (PELDOR) spectra were acquired from these compounds at commercial X-band frequencies. The data analysis shows that two of the compounds, with distances of up to 25 Å, fall into the strong coupling regime and that precise distances can only be obtained if both the spin density delocalization and the pseudo-secular part of the dipolar coupling are included in the analysis.
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Affiliation(s)
- Nitin C Kunjir
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavík, Iceland.
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259
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Lovett JE, Abbott RJM, Roversi P, Johnson S, Caesar JJE, Doria M, Jeschke G, Timmel CR, Lea SM. Investigating the structure of the factor B vWF-A domain/CD55 protein-protein complex using DEER spectroscopy: successes and pitfalls. Mol Phys 2013; 111:2865-2872. [PMID: 24954957 PMCID: PMC4056885 DOI: 10.1080/00268976.2013.827754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/05/2013] [Indexed: 01/03/2023]
Abstract
The electron paramagnetic resonance technique of double electron-electron resonance (DEER) was used to measure nanometre-scale distances between nitroxide spin labels attached to the complement regulatory protein CD55 (also known as decay accelerating factor) and the von Willebrand factor A (vWF-A) domain of factor B. Following a thorough assessment of the quality of the data, distances obtained from good-quality measurements are compared to predicted distances from a previously hypothesised model for the complex and are found to be incompatible. The success of using these distances as restraints in multi-body docking routines is presented critically.
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Affiliation(s)
- Janet E Lovett
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK ; EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Rachel J M Abbott
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pietro Roversi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK ; Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Marianna Doria
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK ; Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Gunnar Jeschke
- Laboratory for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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260
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Kaufmann T, Keller TJ, Franck JM, Barnes RP, Glaser SJ, Martinis JM, Han S. DAC-board based X-band EPR spectrometer with arbitrary waveform control. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 235:95-108. [PMID: 23999530 PMCID: PMC3863685 DOI: 10.1016/j.jmr.2013.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 05/07/2023]
Abstract
We present arbitrary control over a homogenous spin system, demonstrated on a simple, home-built, electron paramagnetic resonance (EPR) spectrometer operating at 8-10 GHz (X-band) and controlled by a 1 GHz arbitrary waveform generator (AWG) with 42 dB (i.e. 14-bit) of dynamic range. Such a spectrometer can be relatively easily built from a single DAC (digital to analog converter) board with a modest number of stock components and offers powerful capabilities for automated digital calibration and correction routines that allow it to generate shaped X-band pulses with precise amplitude and phase control. It can precisely tailor the excitation profiles "seen" by the spins in the microwave resonator, based on feedback calibration with experimental input. We demonstrate the capability to generate a variety of pulse shapes, including rectangular, triangular, Gaussian, sinc, and adiabatic rapid passage waveforms. We then show how one can precisely compensate for the distortion and broadening caused by transmission into the microwave cavity in order to optimize corrected waveforms that are distinctly different from the initial, uncorrected waveforms. Specifically, we exploit a narrow EPR signal whose width is finer than the features of any distortions in order to map out the response to a short pulse, which, in turn, yields the precise transfer function of the spectrometer system. This transfer function is found to be consistent for all pulse shapes in the linear response regime. In addition to allowing precise waveform shaping capabilities, the spectrometer presented here offers complete digital control and calibration of the spectrometer that allows one to phase cycle the pulse phase with 0.007° resolution and to specify the inter-pulse delays and pulse durations to ≤ 250 ps resolution. The implications and potential applications of these capabilities will be discussed.
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Affiliation(s)
- Thomas Kaufmann
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Timothy J. Keller
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - John M. Franck
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Ryan P. Barnes
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - John M. Martinis
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Corresponding author. Address: Department of Chemistry and Biochemistry, 9510, University of California Santa Barbara, CA, USA. (S. Han)
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261
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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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262
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Razzaghi S, Brooks EK, Bordignon E, Hubbell WL, Yulikov M, Jeschke G. EPR relaxation-enhancement-based distance measurements on orthogonally spin-labeled T4-lysozyme. Chembiochem 2013; 14:1883-90. [PMID: 23775845 PMCID: PMC3804414 DOI: 10.1002/cbic.201300165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 12/20/2022]
Abstract
Lanthanide-induced enhancement of the longitudinal relaxation of nitroxide radicals in combination with orthogonal site-directed spin labeling is presented as a systematic distance measurement method intended for studies of bio-macromolecules and bio-macromolecular complexes. The approach is tested on a water-soluble protein (T4-lysozyme) for two different commercially available lanthanide labels, and complemented by previously reported data on a membrane-inserted polypeptide. Single temperature measurements are shown to be sufficient for reliable distance determination, with an upper measurable distance limit of about 5-6 nm. The extracted averaged distances represent the closest approach in Ln(III) -nitroxide distance distributions. Studies of conformational changes and of bio-macromolecule association-dissociation are proposed as possible application area of the relaxation-enhancement-based distance measurements.
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Affiliation(s)
| | - Evan K. Brooks
- Jules Stein Eye Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | | | - Wayne L. Hubbell
- Jules Stein Eye Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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263
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Sahu ID, McCarrick RM, Lorigan GA. Use of electron paramagnetic resonance to solve biochemical problems. Biochemistry 2013; 52:5967-84. [PMID: 23961941 PMCID: PMC3839053 DOI: 10.1021/bi400834a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a very powerful biophysical tool that can provide valuable structural and dynamic information about a wide variety of biological systems. The intent of this review is to provide a general overview for biochemists and biological researchers of the most commonly used EPR methods and how these techniques can be used to answer important biological questions. The topics discussed could easily fill one or more textbooks; thus, we present a brief background on several important biological EPR techniques and an overview of several interesting studies that have successfully used EPR to solve pertinent biological problems. The review consists of the following sections: an introduction to EPR techniques, spin-labeling methods, and studies of naturally occurring organic radicals and EPR active transition metal systems that are presented as a series of case studies in which EPR spectroscopy has been used to greatly further our understanding of several important biological systems.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
| | | | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH
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264
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Wilson ME, Maksaev G, Haswell ES. MscS-like mechanosensitive channels in plants and microbes. Biochemistry 2013; 52:5708-22. [PMID: 23947546 DOI: 10.1021/bi400804z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. The latter of these two families, the MscS family, consists of members from bacteria, archaea, fungi, and plants. Genetic and electrophysiological analysis of these family members has provided insight into how organisms use mechanosensitive channels for osmotic regulation in response to changing environmental and developmental circumstances. Furthermore, determining the crystal structure of E. coli MscS and several homologues in several conformational states has contributed to our understanding of the gating mechanisms of these channels. Here we summarize our current knowledge of MscS homologues from all three domains of life and address their structure, proposed physiological functions, electrophysiological behaviors, and topological diversity.
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Affiliation(s)
- Margaret E Wilson
- Department of Biology, Washington University in St. Louis, Missouri 63130, United States
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265
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Pornsuwan S, Giller K, Riedel D, Becker S, Griesinger C, Bennati M. Long-Range Distances in Amyloid Fibrils of α-Synuclein from PELDOR Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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266
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Pornsuwan S, Giller K, Riedel D, Becker S, Griesinger C, Bennati M. Long-range distances in amyloid fibrils of α-synuclein from PELDOR spectroscopy. Angew Chem Int Ed Engl 2013; 52:10290-4. [PMID: 23934970 PMCID: PMC4138985 DOI: 10.1002/anie.201304747] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Indexed: 11/05/2022]
Affiliation(s)
- S Pornsuwan
- Research Group EPR Spectroscopy, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany) http://www.mpibpc.mpg.de/english/research/ags/bennati/; Current address: Department of Chemistry, Faculty of Science, Mahidol University, 10400 Bangkok (Thailand)
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267
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Matalon E, Faingold O, Eisenstein M, Shai Y, Goldfarb D. The topology, in model membranes, of the core peptide derived from the T-cell receptor transmembrane domain. Chembiochem 2013; 14:1867-75. [PMID: 23881822 DOI: 10.1002/cbic.201300191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 01/16/2023]
Abstract
The T-cell receptor-CD3 complex (TCR-CD3) serves a critical role in protecting organisms from infectious agents. The TCR is a heterodimer composed of α- and β-chains, which are responsible for antigen recognition. Within the transmembrane domain of the α-subunit, a region has been identified to be crucial for the assembly and function of the TCR. This region, termed core peptide (CP), consists of nine amino acids (GLRILLLKV), two of which are charged (lysine and arginine) and are crucial for the interaction with CD3. Earlier studies have shown that a synthetic peptide corresponding to the CP sequence can suppress the immune response in animal models of T-cell-mediated inflammation, by disrupting proper assembly of the TCR. As a step towards the understanding of the source of the CP activity, we focused on CP in egg phosphatidylcholine/cholesterol (9:1, mol/mol) model membranes and determined its secondary structure, oligomerization state, and orientation with respect to the membrane. To achieve this goal, 15-residue segments of TCRα, containing the CP, were synthesized and spin-labeled at different locations with a nitroxide derivative. Electron spin-echo envelope modulation spectroscopy was used to probe the position and orientation of the peptides within the membrane, and double electron-electron resonance measurements were used to probe its conformation and oligomerization state. We found that the peptide is predominantly helical in a membrane environment and tends to form oligomers (mostly dimers) that are parallel to the membrane plane.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, 234 Hertzl St, Rehovot, 7632700 (Israel)
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268
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Edwards DT, Ma Z, Meade TJ, Goldfarb D, Han S, Sherwin MS. Extending the distance range accessed with continuous wave EPR with Gd3+ spin probes at high magnetic fields. Phys Chem Chem Phys 2013; 15:11313-26. [PMID: 23732863 PMCID: PMC4142211 DOI: 10.1039/c3cp43787f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Interspin distances between 0.8 nm and 2.0 nm can be measured through the dipolar broadening of the continuous wave (cw) EPR spectrum of nitroxide spin labels at X-band (9.4 GHz, 0.35 T). We introduce Gd(3+) as a promising alternative spin label for distance measurements by cw EPR above 7 Tesla, where the |-1/2〉 to |1/2〉 transition narrows below 1 mT and becomes extremely sensitive to dipolar broadening. To estimate the distance limits of cw EPR with Gd(3+), we have measured spectra of frozen solutions of GdCl3 at 8.6 T (240 GHz) and 10 K at concentrations ranging from 50 mM to 0.1 mM, covering a range of average interspin distances. These experiments show substantial dipolar broadening at distances where line broadening cannot be observed with nitroxides at X-band. This data, and its agreement with calculated dipolar-broadened lineshapes, show Gd(3+) to be sensitive to distances as long as ∼3.8 nm. Further, the linewidth of a bis-Gd(3+) complex with a flexible ∼1.6 nm bridge is strongly broadened as compared to the mono-Gd(3+) complex, demonstrating the potential for application to pairwise distances. Gd-DOTA-based chelates that can be functionalized to protein surfaces display linewidths narrower than aqueous GdCl3, implying they should be even more sensitive to dipolar broadening. Therefore, we suggest that the combination of tailored Gd(3+) labels and high magnetic fields can extend the longest interspin distances measurable by cw EPR from 2.0 nm to 3.8 nm. cw EPR data at 260 K demonstrate that the line broadening remains clear out to similar average interspin distances, offering Gd(3+) probes as promising distance rulers at temperatures higher than possible with conventional pulsed EPR distance measurements.
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Affiliation(s)
- Devin T. Edwards
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Zhidong Ma
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Thomas J. Meade
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
- Department of Molecular Biosciences, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
- Department of Neurobiology & Physiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
- Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
- Institute for Terahertz Science and Technology, Santa Barbara, California 93106, USA
| | - Mark S. Sherwin
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
- Institute for Terahertz Science and Technology, Santa Barbara, California 93106, USA
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269
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Warshaviak DT, Khramtzov VV, Cascio D, Altenbach C, Hubbell WL. Structure and dynamics of an imidazoline nitroxide side chain with strongly hindered internal motion in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 232:53-61. [PMID: 23694751 PMCID: PMC3758229 DOI: 10.1016/j.jmr.2013.04.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/19/2013] [Accepted: 04/21/2013] [Indexed: 05/03/2023]
Abstract
A disulfide-linked imidazoline nitroxide side chain (V1) has a similar and highly constrained internal motion at diverse topological sites in a protein, unlike that for the disulfide-linked pyrroline nitroxide side chain (R1) widely used in site directed spin labeling EPR. Crystal structures of V1 at two positions in a helix of T4 Lysozyme and quantum mechanical calculations suggest the source of the constraints as intra-side chain interactions of the disulfide sulfur atoms with both the protein backbone and the 3-nitrogen in the imidazoline ring. These interactions apparently limit the conformation of the side chain to one of only three possible rotamers, two of which are observed in the crystal structure. An inter-spin distance measurement in frozen solution using double electron-electron resonance (DEER) gives a value essentially identical to that determined from the crystal structure of the protein containing two copies of V1, indicating that lattice forces do not dictate the rotamers observed. Collectively, the results suggest the possibility of predetermining a unique rotamer of V1 in helical structures. In general, the reduced rotameric space of V1 compared to R1 should simplify interpretation of inter-spin distance information in terms of protein structure, while the highly constrained internal motion is expected to extend the dynamic range for characterizing large amplitude nanosecond backbone fluctuations.
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Affiliation(s)
- Dora Toledo Warshaviak
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Valery V. Khramtzov
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, The Department of Internal Medicine, The Ohio State University, 473 West 12th Ave., room 201, Columbus, Ohio 43210
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Christian Altenbach
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Corresponding author , Jules Stein Eye Institute, UCLA, 100 Stein Plaza, Los Angeles, CA 90095, 310-206-8830
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270
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Hagelueken G, Abdullin D, Ward R, Schiemann O. mtsslSuite: In silico spin labelling, trilateration and distance-constrained rigid body docking in PyMOL. Mol Phys 2013; 111:2757-2766. [PMID: 24954955 PMCID: PMC4056886 DOI: 10.1080/00268976.2013.809804] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/18/2013] [Indexed: 01/07/2023]
Abstract
Nanometer distance measurements based on electron paramagnetic resonance methods in combination with site-directed spin labelling are powerful tools for the structural analysis of macromolecules. The software package mtsslSuite provides scientists with a set of tools for the translation of experimental distance distributions into structural information. The package is based on the previously published mtsslWizard software for in silico spin labelling. The mtsslSuite includes a new version of MtsslWizard that has improved performance and now includes additional types of spin labels. Moreover, it contains applications for the trilateration of paramagnetic centres in biomolecules and for rigid-body docking of subdomains of macromolecular complexes. The mtsslSuite is tested on a number of challenging test cases and its strengths and weaknesses are evaluated.
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Affiliation(s)
- Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Richard Ward
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, UK
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany ; Biomedical Sciences Research Complex, The University of St. Andrews, Fife, UK
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271
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272
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Lueders P, Razzaghi S, Jäger H, Tschaggelar R, Hemminga MA, Yulikov M, Jeschke G. Distance determination from dysprosium induced relaxation enhancement: a case study on membrane-inserted WALP23 polypeptides. Mol Phys 2013. [DOI: 10.1080/00268976.2013.806683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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273
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Frecus B, Rinkevicius Z, Ågren H. π-Stacking effects on the EPR parameters of a prototypical DNA spin label. Phys Chem Chem Phys 2013; 15:10466-71. [PMID: 23685812 DOI: 10.1039/c3cp51129d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The character and value of spin labels for probing environments like double-stranded DNA depend on the degree of change in the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoretical investigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusing on the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporating the spin label into the selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label are only negligibly affected by its incorporation into DNA, when compared to its free form. This result gives a theoretical ground for the common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurements of the distance between spin labels incorporated into DNA.
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Affiliation(s)
- Bogdan Frecus
- KTH Royal Institute of Technology, School of Biotechnology, Division of Theoretical Chemistry & Biology, SE-106 91 Stockholm, Sweden.
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274
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Kattnig DR, Hinderberger D. Analytical distance distributions in systems of spherical symmetry with applications to double electron-electron resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:50-63. [PMID: 23454574 DOI: 10.1016/j.jmr.2013.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 05/24/2023]
Abstract
Based on a simple geometrical approach, we derive analytical expression of the probability density functions (pdfs) of distance of probe molecules distributed homogeneously in spherical aggregates with shell structure. These distance distributions can be utilized in the investigation of double electron-electron resonance (DEER) data of disordered nanometer-sized spin clusters. Structural insights and geometrical parameters of the aggregates can be extracted by modeling the DEER time traces based on the analytical pdfs. This approach is efficient and avoids difficulties of the model-free solution of the inverse problem that are related to multi-spin effects, limited excitation bandwidth, bias introduced by the regularization scheme, or ambiguity resulting from broad distance distributions. The derived pdfs can serve as building blocks, from which the distance distributions in arbitrary spherically symmetric objects can be assembled. The scenario of the pumped species being chemically distinct from the observed species is covered as well as that of a single type of probe molecules. We demonstrate the merits of analytical distance distributions by studying the distribution of three different spin probes in SDS micelles. By simultaneously analyzing DEER data corresponding to different spin probe concentrations, the distribution of the spin probes over the micelle can be determined. Employing Bayesian inference it is found that for all probes studied, a spherical shell model is most appropriate among the studied models and by orders of magnitude more likely than a homogeneous distribution in a ball. This statement also applies to probes that are deemed nonpolar. We envisage that the spin probe distributions in disordered soft and hard matter systems can now be quantified using DEER spectroscopy with greater precision and reduced ambiguity.
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Affiliation(s)
- Daniel R Kattnig
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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275
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The architecture of EssB, an integral membrane component of the type VII secretion system. Structure 2013; 21:595-603. [PMID: 23499020 PMCID: PMC3694306 DOI: 10.1016/j.str.2013.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/03/2013] [Accepted: 02/05/2013] [Indexed: 11/22/2022]
Abstract
The membrane-bound EssB is an integral and essential component of the bacterial type VII secretion system that can contribute to pathogenicity. The architecture of Geobacillus thermodenitrificans EssB has been investigated by combining crystallographic and EPR spectroscopic methods. The protein forms a dimer that straddles the cytoplasmic membrane. A helical fold is observed for the C-terminal segment, which is positioned on the exterior of the membrane. This segment contributes most to dimer formation. The N-terminal segment displays a structure related to the pseudokinase fold and may contribute to function by recognizing substrates or secretion system partners. The remaining part of EssB may serve as an anchor point for the secretion apparatus, which is embedded in the cytoplasmic membrane with the C-terminal domain protruding out to interact with partner proteins or components of peptidoglycan.
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276
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Garbuio L, Bordignon E, Brooks EK, Hubbell WL, Jeschke G, Yulikov M. Orthogonal spin labeling and Gd(III)-nitroxide distance measurements on bacteriophage T4-lysozyme. J Phys Chem B 2013; 117:3145-53. [PMID: 23442004 DOI: 10.1021/jp401806g] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the first example of chemoselective site-specific spin labeling of a monomeric protein with two spectroscopically orthogonal spin labels: a gadolinium(III) chelate complex and a nitroxide radical. A detailed analysis of the performance of two commercially available Gd(III) ligands in the Gd(III)-nitroxide pulse double electron-electron resonance (DEER or PELDOR) experiment is reported. A modification of the flip angle of the pump pulse in the Gd(III)-nitroxide DEER experiment is proposed to optimize sensitivity.
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Affiliation(s)
- Luca Garbuio
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
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277
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Spindler PE, Glaser SJ, Skinner TE, Prisner TF. Broadband Inversion PELDOR Spectroscopy with Partially Adiabatic Shaped Pulses. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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278
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Spindler PE, Glaser SJ, Skinner TE, Prisner TF. Broadband inversion PELDOR spectroscopy with partially adiabatic shaped pulses. Angew Chem Int Ed Engl 2013; 52:3425-9. [PMID: 23424088 DOI: 10.1002/anie.201207777] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Indexed: 12/14/2022]
Affiliation(s)
- Philipp E Spindler
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum, Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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279
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Matalon E, Kaminker I, Zimmermann H, Eisenstein M, Shai Y, Goldfarb D. Topology of the trans-membrane peptide WALP23 in model membranes under negative mismatch conditions. J Phys Chem B 2013; 117:2280-93. [PMID: 23311473 DOI: 10.1021/jp310056h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The organization and orientation of membrane-inserted helices is important for better understanding the mode of action of membrane-active peptides and of protein-membrane interactions. Here we report on the application of ESEEM (electron spin-echo envelope modulation) and DEER (double electron-electron resonance) techniques to probe the orientation and oligomeric state of an α-helical trans-membrane model peptide, WALP23, under conditions of negative mismatch between the hydrophobic cores of the model membrane and the peptide. Using ESEEM, we measured weak dipolar interactions between spin-labeled WALP23 and (2)H nuclei of either the solvent (D2O) or of lipids specifically deuterated at the choline group. The ESEEM data obtained from the deuterated lipids were fitted using a model that provided the spin label average distance from a layer of (2)H nuclei in the hydrophilic region of the membrane and the density of the (2)H nuclei in the layer. DEER was used to probe oligomerization through the dipolar interaction between two spin-labels on different peptides. We observed that the center of WALP23 does not coincide with the bilayer midplane and its N-terminus is more buried than the C-terminus. In addition, the ESEEM data fitting yielded a (2)H layer density that was much lower than expected. The DEER experiments revealed the presence of oligomers, the presence of which was attributable to the negative mismatch and the electrostatic dipole of the peptide. A discussion of a possible arrangement of the individual helices in the oligomers that is consistent with the ESEEM and DEER data is presented.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel 76100
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280
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Lueders P, Jäger H, Hemminga MA, Jeschke G, Yulikov M. Distance Measurements on Orthogonally Spin-Labeled Membrane Spanning WALP23 Polypeptides. J Phys Chem B 2013; 117:2061-8. [DOI: 10.1021/jp311287t] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Petra Lueders
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Heidrun Jäger
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Marcus A. Hemminga
- Laboratory
of Biophysics, Wageningen University, Wageningen,
The Netherlands
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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281
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Tkach I, Pornsuwan S, Höbartner C, Wachowius F, Sigurdsson ST, Baranova TY, Diederichsen U, Sicoli G, Bennati M. Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation. Phys Chem Chem Phys 2013; 15:3433-7. [PMID: 23381580 DOI: 10.1039/c3cp44415e] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pulsed electron-electron double resonance (PELDOR, also known as DEER) has become a method of choice to measure distances in biomolecules. In this work we show how the performance of the method can be improved at high EPR frequencies (94 GHz) using variable dual frequency irradiation in a dual mode cavity in order to obtain enhanced resolution toward orientation selection. Dipolar evolution traces of a representative RNA duplex and an α-helical peptide were analysed in terms of possible bi-radical structures by considering the inherent ambiguity of symmetry-related solutions.
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Affiliation(s)
- Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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282
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Kaminker I, Tkach I, Manukovsky N, Huber T, Yagi H, Otting G, Bennati M, Goldfarb D. W-band orientation selective DEER measurements on a Gd3+/nitroxide mixed-labeled protein dimer with a dual mode cavity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 227:66-71. [PMID: 23314001 DOI: 10.1016/j.jmr.2012.11.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 06/01/2023]
Abstract
Double electron-electron resonance (DEER) at W-band (95 GHz) was applied to measure the distance between a pair of nitroxide and Gd(3+) chelate spin labels, about 6 nm apart, in a homodimer of the protein ERp29. While high-field DEER measurements on systems with such mixed labels can be highly attractive in terms of sensitivity and the potential to access long distances, a major difficulty arises from the large frequency spacing (about 700 MHz) between the narrow, intense signal of the Gd(3+) central transition and the nitroxide signal. This is particularly problematic when using standard single-mode cavities. Here we show that a novel dual-mode cavity that matches this large frequency separation dramatically increases the sensitivity of DEER measurements, allowing evolution times as long as 12 μs in a protein. This opens the possibility of accessing distances of 8 nm and longer. In addition, orientation selection can be resolved and analyzed, thus providing additional structural information. In the case of W-band DEER on a Gd(3+)-nitroxide pair, only two angles and their distributions have to be determined, which is a much simpler problem to solve than the five angles and their distributions associated with two nitroxide spin labels.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
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283
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van Wonderen JH, Kostrz DN, Dennison C, MacMillan F. Refined distances between paramagnetic centers of a multi-copper nitrite reductase determined by pulsed EPR (iDEER) spectroscopy. Angew Chem Int Ed Engl 2013; 52:1990-3. [PMID: 23296685 PMCID: PMC3596801 DOI: 10.1002/anie.201208166] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Jessica H van Wonderen
- Henry Wellcome Unit of Biological EPR, School of Chemistry, University of East Anglia, Norwich, UK
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284
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van Wonderen JH, Kostrz DN, Dennison C, MacMillan F. Refined Distances Between Paramagnetic Centers of a Multi-Copper Nitrite Reductase Determined by Pulsed EPR (iDEER) Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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285
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Borbat PP, Georgieva ER, Freed JH. Improved Sensitivity for Long-Distance Measurements in Biomolecules: Five-Pulse Double Electron-Electron Resonance. J Phys Chem Lett 2013; 4:170-175. [PMID: 23301118 PMCID: PMC3538160 DOI: 10.1021/jz301788n] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 12/19/2012] [Indexed: 05/15/2023]
Abstract
We describe significantly improved long-distance measurements in biomolecules by use of the new multipulse double electron-electron spin resonance (DEER) illustrated with the example of a five-pulse DEER sequence. In this sequence, an extra pulse at the pump frequency is used compared with standard four-pulse DEER. The position of the extra pulse is fixed relative to the three pulses of the detection sequence. This significantly reduces the effect of nuclear spin-diffusion on the electron-spin phase relaxation, thereby enabling longer dipolar evolution times that are required to measure longer distances. Using spin-labeled T4 lysozyme at a concentration less than 50 μM, as an example, we show that the evolution time increases by a factor of 1.8 in protonated solution and 1.4 in deuterated solution to 8 and 12 μs, respectively, with the potential to increase them further. This enables a significant increase in the measurable distances, improved distance resolution, or both.
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Affiliation(s)
- Peter P. Borbat
- E-mail: ; Tel: (607) 255-6132;
Fax: (607) 255-6969 (P.P.B.). E-mail: ; Tel: (607)
255-3647; Fax: (607) 255-6969 (J.H.F.)
| | | | - Jack H. Freed
- E-mail: ; Tel: (607) 255-6132;
Fax: (607) 255-6969 (P.P.B.). E-mail: ; Tel: (607)
255-3647; Fax: (607) 255-6969 (J.H.F.)
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286
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von Hagens T, Polyhach Y, Sajid M, Godt A, Jeschke G. Suppression of ghost distances in multiple-spin double electron–electron resonance. Phys Chem Chem Phys 2013; 15:5854-66. [DOI: 10.1039/c3cp44462g] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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287
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Klare JP, Steinhoff HJ. Structural Information from Spin-Labelled Membrane-Bound Proteins. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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288
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Marko A, Prisner TF. An algorithm to analyze PELDOR data of rigid spin label pairs. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp42942j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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289
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Gophane DB, Sigurdsson ST. Hydrogen-bonding controlled rigidity of an isoindoline-derived nitroxide spin label for nucleic acids. Chem Commun (Camb) 2013; 49:999-1001. [DOI: 10.1039/c2cc36389e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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290
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Bhatnagar J, Sircar R, Borbat PP, Freed JH, Crane BR. Self-association of the histidine kinase CheA as studied by pulsed dipolar ESR spectroscopy. Biophys J 2012; 102:2192-201. [PMID: 22824284 DOI: 10.1016/j.bpj.2012.03.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/29/2012] [Accepted: 03/12/2012] [Indexed: 11/26/2022] Open
Abstract
Biologically important protein complexes often involve molecular interactions that are low affinity or transient. We apply pulsed dipolar electron spin resonance spectroscopy and site-directed spin labeling in what to our knowledge is a new approach to study aggregation and to identify regions on protein surfaces that participate in weak, but specific molecular interactions. As a test case, we have probed the self-association of the chemotaxis kinase CheA, which forms signaling clusters with chemoreceptors and the coupling protein CheW at the poles of bacterial cells. By measuring the intermolecular dipolar interactions sensed by spin-labels distributed over the protein surface, we show that the soluble CheA kinase aggregates to a small extent through interactions mediated by its regulatory (P5) domain. Direct dipolar distance measurements confirm that a hydrophobic surface at the periphery of P5 subdomain 2 associates CheA dimers in solution. This result is further supported by differential disulfide cross-linking from engineered cysteine reporter sites. We suggest that the periphery of P5 is an interaction site on CheA for other similar hydrophobic surfaces and plays an important role in structuring the signaling particle.
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Affiliation(s)
- Jaya Bhatnagar
- Advanced Center for ESR Studies (ACERT), Cornell University, Ithaca, NY, USA
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291
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Gaffney BJ, Bradshaw MD, Frausto SD, Wu F, Freed JH, Borbat P. Locating a lipid at the portal to the lipoxygenase active site. Biophys J 2012; 103:2134-44. [PMID: 23200047 PMCID: PMC3512035 DOI: 10.1016/j.bpj.2012.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/28/2022] Open
Abstract
Lipoxygenase enzymes initiate diverse signaling pathways by specifically directing oxygen to different carbons of arachidonate and other polyunsaturated acyl chains, but structural origins of this specificity have remained unclear. We therefore determined the nature of the lipoxygenase interaction with the polar-end of a paramagnetic lipid by electron paramagnetic resonance spectroscopy. Distances between selected grid points on soybean seed lipoxygenase-1 (SBL1) and a lysolecithin spin-labeled on choline were measured by pulsed (electron) dipolar spectroscopy. The protein grid was designed by structure-based modeling so that five natural side chains were replaced with spin labels. Pairwise distances in 10 doubly spin-labeled mutants were examined by pulsed dipolar spectroscopy, and a fit to the model was optimized. Finally, experimental distances between the lysolecithin spin and each single spin site on SBL1 were also obtained. With these 15 distances, distance geometry localized the polar-end and the spin of the lysolecithin to the region between the two domains in the SBL1 structure, nearest to E236, K260, Q264, and Q544. Mutation of a nearby residue, E256A, relieved the high pH requirement for enzyme activity of SBL1 and allowed lipid binding at pH 7.2. This general approach could be used to locate other flexible molecules in macromolecular complexes.
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Affiliation(s)
- Betty J Gaffney
- Department of Biological Science Department, Florida State University, Tallahassee, FL, USA.
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292
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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293
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Abstract
Arrestin-1 (visual arrestin) binds to light-activated phosphorylated rhodopsin (P-Rh*) to terminate G-protein signaling. To map conformational changes upon binding to the receptor, pairs of spin labels were introduced in arrestin-1 and double electron-electron resonance was used to monitor interspin distance changes upon P-Rh* binding. The results indicate that the relative position of the N and C domains remains largely unchanged, contrary to expectations of a "clam-shell" model. A loop implicated in P-Rh* binding that connects β-strands V and VI (the "finger loop," residues 67-79) moves toward the expected location of P-Rh* in the complex, but does not assume a fully extended conformation. A striking and unexpected movement of a loop containing residue 139 away from the adjacent finger loop is observed, which appears to facilitate P-Rh* binding. This change is accompanied by smaller movements of distal loops containing residues 157 and 344 at the tips of the N and C domains, which correspond to "plastic" regions of arrestin-1 that have distinct conformations in monomers of the crystal tetramer. Remarkably, the loops containing residues 139, 157, and 344 appear to have high flexibility in both free arrestin-1 and the P-Rh*complex.
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294
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Lovett JE, Lovett BW, Harmer J. DEER-Stitch: combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:98-106. [PMID: 22975240 DOI: 10.1016/j.jmr.2012.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/20/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
Over approximately the last 15 years the electron paramagnetic resonance (EPR) technique of double electron electron resonance (DEER) has attracted considerable attention since it allows for the precise measurement of the dipole-dipole coupling between radicals and thus can lead to distance information between pairs of radicals separated by up to ca. 8 nm. The "deadtime free" 4-pulse DEER sequence is widely used but can suffer from poor sensitivity if the electron spin-echo decays too quickly to allow collection of a sufficiently long time trace. In this paper we present a method which takes advantage of the much greater sensitivity that the 3-pulse sequence offers over the 4-pulse sequence since the measured electron spin-echo intensity (for equal sequence lengths) is greater. By combining 3- and 4-pulse DEER time traces using a method coined DEER-Stitch (DEERS) accurate dipole-dipole coupling measurements can be made which combine the sensitivity of the 3-pulse DEER sequence with the deadtime free advantage of the 4-pulse DEER sequence. To develop the DEER-Stitch method three systems were measured: a semi-rigid bis-nitroxide labeled nanowire, the bis-nitroxide labeled protein CD55 with a distance between labels of almost 8 nm and a dimeric copper amine oxidase from Arthrobacter globiformis (AGAO).
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Affiliation(s)
- J E Lovett
- EaStCHEM School of Chemistry, Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, UK.
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295
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Edwards DT, Takahashi S, Sherwin MS, Han S. Distance measurements across randomly distributed nitroxide probes from the temperature dependence of the electron spin phase memory time at 240 GHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:198-206. [PMID: 22975249 DOI: 10.1016/j.jmr.2012.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/27/2012] [Accepted: 07/05/2012] [Indexed: 06/01/2023]
Abstract
At 8.5 T, the polarization of an ensemble of electron spins is essentially 100% at 2 K, and decreases to 30% at 20 K. The strong temperature dependence of the electron spin polarization between 2 and 20 K leads to the phenomenon of spin bath quenching: temporal fluctuations of the dipolar magnetic fields associated with the energy-conserving spin "flip-flop" process are quenched as the temperature of the spin bath is lowered to the point of nearly complete spin polarization. This work uses pulsed electron paramagnetic resonance (EPR) at 240 GHz to investigate the effects of spin bath quenching on the phase memory times (T(M)) of randomly-distributed ensembles of nitroxide molecules below 20 K at 8.5 T. For a given electron spin concentration, a characteristic, dipolar flip-flop rate (W) is extracted by fitting the temperature dependence of T(M) to a simple model of decoherence driven by the spin flip-flop process. In frozen solutions of 4-Amino-TEMPO, a stable nitroxide radical in a deuterated water-glass, a calibration is used to quantify average spin-spin distances as large as r=6.6 nm from the dipolar flip-flop rate. For longer distances, nuclear spin fluctuations, which are not frozen out, begin to dominate over the electron spin flip-flop processes, placing an effective ceiling on this method for nitroxide molecules. For a bulk solution with a three-dimensional distribution of nitroxide molecules at concentration n, we find W∝n∝1/r(3), which is consistent with magnetic dipolar spin interactions. Alternatively, we observe W∝n(32) for nitroxides tethered to a quasi two-dimensional surface of large (Ø∼200 nm), unilamellar, lipid vesicles, demonstrating that the quantification of spin bath quenching can also be used to discern the geometry of molecular assembly or organization.
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Affiliation(s)
- Devin T Edwards
- Department of Physics, University of California, Santa Barbara, CA 93106, United States
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296
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Reginsson GW, Kunjir NC, Sigurdsson ST, Schiemann O. Trityl radicals: spin labels for nanometer-distance measurements. Chemistry 2012; 18:13580-4. [PMID: 22996284 DOI: 10.1002/chem.201203014] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Indexed: 12/11/2022]
Abstract
Spin labelling with trityls: to gather information about the structure and dynamics of trityl radicals, spin-labelled polymers were measured with pulsed electron-electron double resonance (PELDOR) and double-quantum coherence (DQC). This study demonstrates that trityl radicals have great potential as spin labels that eliminate some limitations of nitroxide spin labels.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, St. Andrews, UK
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297
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Conformational state of the MscS mechanosensitive channel in solution revealed by pulsed electron-electron double resonance (PELDOR) spectroscopy. Proc Natl Acad Sci U S A 2012; 109:E2675-82. [PMID: 23012406 DOI: 10.1073/pnas.1202286109] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The heptameric mechanosensitive channel of small conductance (MscS) provides a critical function in Escherichia coli where it opens in response to increased bilayer tension. Three approaches have defined different closed and open structures of the channel, resulting in mutually incompatible models of gating. We have attached spin labels to cysteine mutants on key secondary structural elements specifically chosen to discriminate between the competing models. The resulting pulsed electron-electron double resonance (PELDOR) spectra matched predicted distance distributions for the open crystal structure of MscS. The fit for the predictions by structural models of MscS derived by other techniques was not convincing. The assignment of MscS as open in detergent by PELDOR was unexpected but is supported by two crystal structures of spin-labeled MscS. PELDOR is therefore shown to be a powerful experimental tool to interrogate the conformation of transmembrane regions of integral membrane proteins.
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298
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Reginsson GW, Shelke SA, Rouillon C, White MF, Sigurdsson ST, Schiemann O. Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR. Nucleic Acids Res 2012; 41:e11. [PMID: 22941643 PMCID: PMC3592447 DOI: 10.1093/nar/gks817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Site-directed spin labeling and pulsed electron-electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
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299
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Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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300
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Griesinger C, Bennati M, Vieth HM, Luchinat C, Parigi G, Höfer P, Engelke F, Glaser SJ, Denysenkov V, Prisner TF. Dynamic nuclear polarization at high magnetic fields in liquids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 64:4-28. [PMID: 22578315 DOI: 10.1016/j.pnmrs.2011.10.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 10/11/2011] [Indexed: 05/03/2023]
Affiliation(s)
- C Griesinger
- MPI for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
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