351
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Krstić I, Endeward B, Margraf D, Marko A, Prisner TF. Structure and dynamics of nucleic acids. Top Curr Chem (Cham) 2011; 321:159-98. [PMID: 22160388 DOI: 10.1007/128_2011_300] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In this chapter we describe the application of CW and pulsed EPR methods for the investigation of structural and dynamical properties of RNA and DNA molecules and their interaction with small molecules and proteins. Special emphasis will be given to recent applications of dipolar spectroscopy on nucleic acids.
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Affiliation(s)
- Ivan Krstić
- Goethe University Frankfurt, Frankfurt am Main, Germany
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352
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Kuznetsov NA, Milov AD, Isaev NP, Vorobjev YN, Koval VV, Dzuba SA, Fedorova OS, Tsvetkov YD. PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes. MOLECULAR BIOSYSTEMS 2011; 7:2670-80. [DOI: 10.1039/c1mb05189j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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353
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354
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Kaminker I, Florent M, Epel B, Goldfarb D. Simultaneous acquisition of pulse EPR orientation selective spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 208:95-102. [PMID: 21075028 DOI: 10.1016/j.jmr.2010.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/14/2010] [Accepted: 10/14/2010] [Indexed: 05/30/2023]
Abstract
High resolution pulse EPR methods are usually applied to resolve weak magnetic electron-nuclear or electron-electron interactions that are otherwise unresolved in the EPR spectrum. Complete information regarding different magnetic interactions, namely, principal components and orientation of principal axis system with respect to the molecular frame, can be derived from orientation selective pulsed EPR measurements that are performed at different magnetic field positions within the inhomogeneously broadened EPR spectrum. These experiments are usually carried out consecutively, namely a particular field position is chosen, data are accumulated until the signal to noise ratio is satisfactory, and then the next field position is chosen and data are accumulated. Here we present a new approach for data acquisition of pulsed EPR experiments referred to as parallel acquisition. It is applicable when the spectral width is much broader than the excitation bandwidth of the applied pulse sequence and it is particularly useful for orientation selective pulse EPR experiments. In this approach several pulse EPR measurements are performed within the waiting (repetition) time between consecutive pulse sequences during which spin lattice relaxation takes place. This is achieved by rapidly changing the main magnetic field, B(0), to different values within the EPR spectrum, performing the same experiment on the otherwise idle spins. This scheme represents an efficient utilization of the spectrometer and provides the same spectral information in a shorter time. This approach is demonstrated on W-band orientation selective electron-nuclear double resonance (ENDOR), electron spin echo envelope modulation (ESEEM), electron-electron double resonance (ELDOR)--detected NMR and double electron-electron resonance (DEER) measurements on frozen solutions of nitroxides. We show that a factors of 3-6 reduction in total acquisition time can be obtained, depending on the experiment applied.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
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355
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Shelke SA, Sigurdsson ST. Site-Directed Nitroxide Spin Labeling of Biopolymers. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2011. [DOI: 10.1007/430_2011_62] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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356
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Gordon-Grossman M, Kaminker I, Gofman Y, Shai Y, Goldfarb D. W-Band pulse EPR distance measurements in peptides using Gd3+–dipicolinic acid derivatives as spin labels. Phys Chem Chem Phys 2011; 13:10771-80. [DOI: 10.1039/c1cp00011j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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357
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Probing structural transitions in the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by vibrational spectroscopy of cyanylated cysteines. Biophys J 2010; 99:1676-83. [PMID: 20816082 DOI: 10.1016/j.bpj.2010.06.060] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/23/2010] [Accepted: 06/28/2010] [Indexed: 11/23/2022] Open
Abstract
Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) were cyanylated at cysteine and their infrared spectra in the C triple bond N stretching region were recorded both in the absence and in the presence of one of the physiological partners of N(TAIL), namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within N(TAIL), the C triple bond N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level.
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358
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Astashkin AV, Elmore BO, Fan W, Guillemette JG, Feng C. Pulsed EPR determination of the distance between heme iron and FMN centers in a human inducible nitric oxide synthase. J Am Chem Soc 2010; 132:12059-67. [PMID: 20695464 DOI: 10.1021/ja104461p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian nitric oxide synthase (NOS) is a homodimeric flavo-hemoprotein that catalyzes the oxidation of L-arginine to nitric oxide (NO). Regulation of NO biosynthesis by NOS is primarily through control of interdomain electron transfer (IET) processes in NOS catalysis. The IET from the flavin mononucleotide (FMN) to heme domains is essential in the delivery of electrons required for O(2) activation in the heme domain and the subsequent NO synthesis by NOS. The NOS output state for NO production is an IET-competent complex of the FMN-binding domain and heme domain, and thereby it facilitates the IET from the FMN to the catalytic heme site. The structure of the functional output state has not yet been determined. In the absence of crystal structure data for NOS holoenzyme, it is important to experimentally determine the Fe...FMN distance to provide a key calibration for computational docking studies and for the IET kinetics studies. Here we used the relaxation-induced dipolar modulation enhancement (RIDME) technique to measure the electron spin echo envelope modulation caused by the dipole interactions between paramagnetic FMN and heme iron centers in the [Fe(III)][FMNH(*)] (FMNH(*): FMN semiquinone) form of a human inducible NOS (iNOS) bidomain oxygenase/FMN construct. The FMNH(*)...Fe distance has been directly determined from the RIDME spectrum. This distance (18.8 +/- 0.1 A) is in excellent agreement with the IET rate constant measured by laser flash photolysis [Feng, C. J.; Dupont, A.; Nahm, N.; Spratt, D.; Hazzard, J. T.; Weinberg, J.; Guillemette, J.; Tollin, G.; Ghosh, D. K. J. Biol. Inorg. Chem. 2009, 14, 133-142].
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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359
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Sicoli G, Wachowius F, Bennati M, Höbartner C. Probing secondary structures of spin-labeled RNA by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 2010; 49:6443-7. [PMID: 20665607 DOI: 10.1002/anie.201000713] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Giuseppe Sicoli
- Research group Electron Paramagnetic Resonance, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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360
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Margraf D, Bode BE, Marko A, Schiemann O, Prisner TF. Conformational flexibility of nitroxide biradicals determined by X-band PELDOR experiments. Mol Phys 2010. [DOI: 10.1080/00268970701724982] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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361
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Polyhach Y, Bordignon E, Jeschke G. Rotamer libraries of spin labelled cysteines for protein studies. Phys Chem Chem Phys 2010; 13:2356-66. [PMID: 21116569 DOI: 10.1039/c0cp01865a] [Citation(s) in RCA: 348] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.
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Affiliation(s)
- Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
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362
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Jakobsen U, Shelke SA, Vogel S, Sigurdsson ST. Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc 2010; 132:10424-8. [PMID: 20617829 DOI: 10.1021/ja102797k] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This paper describes a spin label that can detect and identify local structural deformations in duplex DNA, in particular abasic sites. The spin label was incorporated into DNA by a new postsynthetic approach using click-chemistry on a solid support, which simplified both the synthesis and purification of the spin-labeled oligonucleotides. A nitroxide-functionalized azide, prepared by a short synthetic route, was reacted with an oligomer containing 5-ethynyl-2'-dU. The conjugation proceeded in quantitative yield and resulted in a fairly rigid linker between the modified nucleotide and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair with T was consistent with the spin label displacing the T from the duplex. Addition of mercury(II) to this mispair resulted in a substantial increase in the motion of the spin label, consistent with formation of a metallopair between the T and the spin-labeled base that results in movement of the spin label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids and other macromolecules.
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Affiliation(s)
- Ulla Jakobsen
- Department of Physics and Chemistry, University of Southern Denmark, Nucleic Acid Center Campusvej 55, 5230 Odense, Denmark
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363
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Lai AL, Huang H, Herrick DZ, Epp N, Cafiso DS. Synaptotagmin 1 and SNAREs form a complex that is structurally heterogeneous. J Mol Biol 2010; 405:696-706. [PMID: 21087613 DOI: 10.1016/j.jmb.2010.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 10/14/2010] [Accepted: 11/05/2010] [Indexed: 01/08/2023]
Abstract
Synaptotagmin 1 (syt1) functions as a Ca(2+)-sensor for neuronal exocytosis. Here, site-directed spin labeling was used to examine the complex formed between a soluble fragment of syt1, which contains its two C2 domains, and the neuronal core soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex. Changes in electron paramagnetic resonance lineshape and accessibility for spin-labeled syt1 mutants indicate that in solution, the assembled core SNARE complex contacts syt1 in several regions. For the C2B domain, contact occurs in the polybasic face and sites opposite the Ca(2+)-binding loops. For the C2A domain, contact is seen with the SNARE complex in a region near loop 2. Double electron-electron resonance was used to estimate distances between the two C2 domains of syt1. These distances have broad distributions in solution, which do not significantly change when syt1 is fully associated with the core SNARE complex. The broad distance distributions indicate that syt1 is structurally heterogeneous when bound to the SNAREs and does not assume a well-defined structure. Simulated annealing using electron paramagnetic resonance-derived distance restraints produces a family of syt1 structures where the Ca(2+)-binding regions of each domain face in roughly opposite directions. The results suggest that when associated with the SNAREs, syt1 is configured to bind opposing bilayers, but that the syt1/SNARE complex samples multiple conformational states.
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Affiliation(s)
- Alex L Lai
- Department of Chemistry, Biophysics Program and Center for Membrane Biology at the University of Virginia, Charlottesville, VA 22904-4319, USA
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364
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Lillington JED, Lovett JE, Johnson S, Roversi P, Timmel CR, Lea SM. Shigella flexneri Spa15 crystal structure verified in solution by double electron electron resonance. J Mol Biol 2010; 405:427-35. [PMID: 21075116 PMCID: PMC3021122 DOI: 10.1016/j.jmb.2010.10.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/25/2010] [Accepted: 10/27/2010] [Indexed: 12/20/2022]
Abstract
Shigella flexneri Spa15 is a chaperone of the type 3 secretion system, which binds a number of effectors to ensure their stabilization prior to secretion. One of these effectors is IpgB1, a mimic of the human Ras-like Rho guanosine triphosphatase RhoG. In this study, Spa15 alone and in complex with IpgB1 has been studied by double electron electron resonance, an experiment that gives distance information showing the spacial separation of attached spin labels. This distance is explained by determining the crystal structure of the spin-labeled Spa15 where labels are seen to be buried in hydrophobic pockets. The double electron electron resonance experiment on the Spa15 complex with IpgB1 shows that IpgB1 does not bind Spa15 in the same way as is seen in the homologous Salmonella sp. chaperone:effector complex InvB:SipA.
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365
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Dastvan R, Bode BE, Karuppiah MPR, Marko A, Lyubenova S, Schwalbe H, Prisner TF. Optimization of Transversal Relaxation of Nitroxides for Pulsed Electron−Electron Double Resonance Spectroscopy in Phospholipid Membranes. J Phys Chem B 2010; 114:13507-16. [DOI: 10.1021/jp1060039] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Reza Dastvan
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Bela E. Bode
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Muruga Poopathi Raja Karuppiah
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Andriy Marko
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Sevdalina Lyubenova
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry, Institute of Organic Chemistry and Chemical Biology, and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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366
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Rao JN, Jao CC, Hegde BG, Langen R, Ulmer TS. A combinatorial NMR and EPR approach for evaluating the structural ensemble of partially folded proteins. J Am Chem Soc 2010; 132:8657-68. [PMID: 20524659 DOI: 10.1021/ja100646t] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partially folded proteins, characterized as exhibiting secondary structure elements with loose or absent tertiary contacts, represent important intermediates in both physiological protein folding and pathological protein misfolding. To aid in the characterization of the structural state(s) of such proteins, a novel structure calculation scheme is presented that combines structural restraints derived from pulsed EPR and NMR spectroscopy. The methodology is established for the protein alpha-synuclein (alphaS), which exhibits characteristics of a partially folded protein when bound to a micelle of the detergent sodium lauroyl sarcosinate (SLAS). By combining 18 EPR-derived interelectron spin label distance distributions with NMR-based secondary structure definitions and bond vector restraints, interelectron distances were correlated and a set of theoretical ensemble basis populations was calculated. A minimal set of basis structures, representing the partially folded state of SLAS-bound alphaS, was subsequently derived by back-calculating correlated distance distributions. A surprising variety of well-defined protein-micelle interactions was thus revealed in which the micelle is engulfed by two differently arranged antiparallel alphaS helices. The methodology further provided the population ratios between dominant ensemble structural states, whereas limitation in obtainable structural resolution arose from spin label flexibility and residual uncertainties in secondary structure definitions. To advance the understanding of protein-micelle interactions, the present study concludes by showing that, in marked contrast to secondary structure stability, helix dynamics of SLAS-bound alphaS correlate with the degree of protein-induced departures from free micelle dimensions.
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Affiliation(s)
- Jampani Nageswara Rao
- Department of Biochemistry & Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, California 90033, USA
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367
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Kim NK, Bowman MK, DeRose VJ. Precise mapping of RNA tertiary structure via nanometer distance measurements with double electron-electron resonance spectroscopy. J Am Chem Soc 2010; 132:8882-4. [PMID: 20557039 DOI: 10.1021/ja101317g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Divalent metal (Mg(2+)) ion-dependent folding of the hammerhead ribozyme from Schistosoma mansoni was monitored with double electron-electron resonance (DEER) pulsed electron paramagnetic resonance spectroscopy by measuring nanometer-scale distances between paramagnetic spin-labels attached to the RNA. DEER measurements detect global folding of the ribozyme with excellent agreement between predictions from experimental, modeled, and crystallographic measurements. These measurements demonstrate the use of DEER spectroscopy as a tool for structural analysis of complex RNAs.
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Affiliation(s)
- Nak-Kyoon Kim
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
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368
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Junk MJN, Spiess HW, Hinderberger D. The Distribution of Fatty Acids Reveals the Functional Structure of Human Serum Albumin. Angew Chem Int Ed Engl 2010; 49:8755-9. [DOI: 10.1002/anie.201003495] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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369
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Junk MJN, Spiess HW, Hinderberger D. Die Verteilung gebundener Fettsäuren enthüllt die funktionelle Struktur von menschlichem Serumalbumin. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003495] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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370
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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371
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Shelke SA, Sigurdsson ST. Noncovalent and Site-Directed Spin Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2010; 49:7984-6. [DOI: 10.1002/anie.201002637] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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372
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Köhler SD, Weber A, Howard SP, Welte W, Drescher M. The proline-rich domain of TonB possesses an extended polyproline II-like conformation of sufficient length to span the periplasm of Gram-negative bacteria. Protein Sci 2010; 19:625-30. [PMID: 20095050 DOI: 10.1002/pro.345] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
TonB from Escherichia coli and its homologues are critical for the uptake of siderophores through the outer membrane of Gram-negative bacteria using chemiosmotic energy. When different models for the mechanism of TonB mediated energy transfer from the inner to the outer membrane are discussed, one of the key questions is whether TonB spans the periplasm. In this article, we use long range distance measurements by spin-label pulsed EPR (Double Electron-Electron Resonance, DEER) and CD spectroscopy to show that the proline-rich segment of TonB exists in a PPII-like conformation. The result implies that the proline-rich segment of TonB possesses a length of more than 15 nm, sufficient to span the periplasm of Gram-negative bacteria.
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373
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Sicoli G, Wachowius F, Bennati M, Höbartner C. Sekundärstrukturanalyse von spinmarkierter RNA mit Puls-EPR-Spektroskopie. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000713] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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374
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Drescher M, van Rooijen BD, Veldhuis G, Subramaniam V, Huber M. A stable lipid-induced aggregate of alpha-synuclein. J Am Chem Soc 2010; 132:4080-2. [PMID: 20199073 DOI: 10.1021/ja909247j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Parkinson's disease-related protein alpha-Synuclein (alphaS) is a 140 residue intrinsically disordered protein. Its membrane-binding properties are thought to be relevant for its physiological or pathologic activity. Here, the interaction of alphaS with POPG [1-Palmitoyl-2-Oleoyl-sn-Glycero-3-(Phosphorac-(1-glycerol))] small unilamellar vesicles (SUVs) is investigated by spin-label EPR using double electron-electron resonance (DEER). Intermolecular distances between four single mutants reveal that well-defined aggregates are formed. The data suggest a coexistence of two dimer structures with main interactions in the helix 2, encompassing residues 50-100. Previously, the horseshoe conformation was detected by intramolecular restraints obtained by DEER on alphaS double mutants (Drescher et al. J. Am. Chem. Soc. 2008, 130, 7796). The present study suggests that interdigitation of two monomers in the aggregate fills the void between the two helices of each of the monomers thus providing a rationale for the horseshoe structure. This aggregate is lipid induced and affects the structure of the POPG SUVs, which become leaky and diminish in size upon contact with alphaS suggesting a possible origin of conflicting results in the recent literature (Jao et al. Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (50), 19666; Georgieva et al. J. Am. Chem. Soc. 2008, 130 (39), 12856; Bortolus et al. J. Am. Chem. Soc. 2008, 130, 6690).
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Affiliation(s)
- Malte Drescher
- Department of Molecular Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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375
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Potapov A, Song Y, Meade TJ, Goldfarb D, Astashkin A, Raitsimring A. Distance measurements in model bis-Gd(III) complexes with flexible "bridge". Emulation of biological molecules having flexible structure with Gd(III) labels attached. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:38-49. [PMID: 20418132 PMCID: PMC2885582 DOI: 10.1016/j.jmr.2010.03.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 03/30/2010] [Accepted: 03/30/2010] [Indexed: 05/18/2023]
Abstract
In this work, we continue to explore Gd(III) as a possible spin label for high-field Double Electron-Electron Resonance (DEER) based distance measurements in biological molecules with flexible geometry. For this purpose, a bis-Gd(III) complex with a flexible "bridge" was used as a model. The distances in the model were expected to be distributed in the range of 5-26 A, allowing us to probe the shortest limits of accessible distances which were found to be as small as 13 A. The upper distance limit for these labels was also evaluated and was found to be about 60 A. Various pulse duration setups can result in apparent differences in the distribution function derived from DEER kinetics due to short distance limit variations. The advantages, such as the ability to perform measurements at cryogenic temperatures and high repetition rates simultaneously, the use of very short pumping and observation pulses without mutual interference, the lack of orientational selectivity, as well as the shortcomings, such as the limited mw operational frequency range and intrinsically smaller amplitude of oscillation related to dipolar interaction as compared with nitroxide spin labels are discussed. Most probably the use of nitroxide and Gd-based labels for distance measurements will be complementary depending on the particulars of the problem and the availability of instrumentation.
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Affiliation(s)
- A. Potapov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Y. Song
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - T. J. Meade
- Department of Chemistry; Department of Biochemistry, Cell Biology, and Molecular Biology; Neurobiology & Physiology; Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - D. Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - A.V. Astashkin
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
- Corresponding author: Dr. A. Raitsimring, University of Arizona, Department of Chemistry, 1306 E. University Blvd, Tucson, AZ 85721. ; tel (520)621-9968; fax (520)621-8407
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376
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Potapov A, Yagi H, Huber T, Jergic S, Dixon NE, Otting G, Goldfarb D. Nanometer-Scale Distance Measurements in Proteins Using Gd3+ Spin Labeling. J Am Chem Soc 2010; 132:9040-8. [DOI: 10.1021/ja1015662] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexey Potapov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Hiromasa Yagi
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Thomas Huber
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Slobodan Jergic
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Nicholas E. Dixon
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Gottfried Otting
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
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377
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Wachowius F, Höbartner C. Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 2010; 11:469-80. [PMID: 20135663 DOI: 10.1002/cbic.200900697] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Falk Wachowius
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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378
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Bhatnagar J, Borbat PP, Pollard AM, Bilwes AM, Freed JH, Crane BR. Structure of the ternary complex formed by a chemotaxis receptor signaling domain, the CheA histidine kinase, and the coupling protein CheW as determined by pulsed dipolar ESR spectroscopy. Biochemistry 2010; 49:3824-41. [PMID: 20355710 DOI: 10.1021/bi100055m] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The signaling apparatus that controls bacterial chemotaxis is composed of a core complex containing chemoreceptors, the histidine autokinase CheA, and the coupling protein CheW. Site-specific spin labeling and pulsed dipolar ESR spectroscopy (PDS) have been applied to investigate the structure of a soluble ternary complex formed by Thermotoga maritima CheA (TmCheA), CheW, and receptor signaling domains. Thirty-five symmetric spin-label sites (SLSs) were engineered into the five domains of the CheA dimer and CheW to provide distance restraints within the CheA:CheW complex in the absence and presence of a soluble receptor that inhibits kinase activity (Tm14). Additional PDS restraints among spin-labeled CheA, CheW, and an engineered single-chain receptor labeled at six different sites allow docking of the receptor structure relative to the CheA:CheW complex. Disulfide cross-linking between selectively incorporated Cys residues finds two pairs of positions that provide further constraints within the ternary complex: one involving Tm14 and CheW and another involving Tm14 and CheA. The derived structure of the ternary complex indicates a primary site of interaction between CheW and Tm14 that agrees well with previous biochemical and genetic data for transmembrane chemoreceptors. The PDS distance distributions are most consistent with only one CheW directly engaging one dimeric Tm14. The CheA dimerization domain (P3) aligns roughly antiparallel to the receptor-conserved signaling tip but does not interact strongly with it. The angle of the receptor axis with respect to P3 and the CheW-binding P5 domains is bound by two limits differing by approximately 20 degrees . In one limit, Tm14 aligns roughly along P3 and may interact to some extent with the hinge region near the P3 hairpin loop. In the other limit, Tm14 tilts to interact with the P5 domain of the opposite subunit in an interface that mimics that observed with the P5 homologue CheW. The time domain ESR data can be simulated from the model only if orientational variability is introduced for the P5 and, especially, P3 domains. The Tm14 tip also binds beside one of the CheA kinase domains (P4); however, in both bound and unbound states, P4 samples a broad range of distributions that are only minimally affected by Tm14 binding. The CheA P1 domains that contain the substrate histidine are also broadly distributed in space under all conditions. In the context of the hexagonal lattice formed by trimeric transmembrane chemoreceptors, the PDS structure is best accommodated with the P3 domain in the center of a honeycomb edge.
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Affiliation(s)
- Jaya Bhatnagar
- Center for Advanced ESR Studies, Cornell University, Ithaca, New York 14853, USA
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379
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Böhme S, Meyer S, Krüger A, Steinhoff HJ, Wittinghofer A, Klare JP. Stabilization of G domain conformations in the tRNA-modifying MnmE-GidA complex observed with double electron electron resonance spectroscopy. J Biol Chem 2010; 285:16991-7000. [PMID: 20353943 DOI: 10.1074/jbc.m109.096131] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MnmE is a GTP-binding protein conserved between bacteria and eukarya. It is a dimeric three-domain protein where the two G domains have to approach each other for activation of the potassium-stimulated GTPase reaction. Together with GidA, in a heterotetrameric alpha(2)beta(2) complex, it is involved in the modification of the wobble uridine base U34 of the first anticodon position of particular tRNAs. Here we show, using various spin-labeled MnmE mutants and EPR spectroscopy, that GidA binding induces large conformational and dynamic changes in MnmE. It stimulates the GTPase reaction by stabilizing the GTP-bound conformation in a potassium-independent manner. Surprisingly, GidA binding influences not only the GTP- but also the GDP-bound conformation. Thus GidA is a new type of regulator for a G protein activated by dimerization.
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Affiliation(s)
- Sabine Böhme
- Department of Physics, University of Osnabrück, Barbarastrasse 7, D-49076 Osnabrück, Germany
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380
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Truflandier LA, Boucher F, Payen C, Hajjar R, Millot Y, Bonhomme C, Steunou N. DFT-NMR Investigation and 51V 3QMAS Experiments for Probing Surface OH Ligands and the Hydrogen-Bond Network in a Polyoxovanadate Cluster: The Case of Cs4[H2V10O28]·4H2O. J Am Chem Soc 2010; 132:4653-68. [DOI: 10.1021/ja908973y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lionel A. Truflandier
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Florent Boucher
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Christophe Payen
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Redouane Hajjar
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Yannick Millot
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Christian Bonhomme
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Nathalie Steunou
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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381
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Krstić I, Frolow O, Sezer D, Endeward B, Weigand JE, Suess B, Engels JW, Prisner TF. PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure. J Am Chem Soc 2010; 132:1454-5. [PMID: 20078041 DOI: 10.1021/ja9077914] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pulsed electron double resonance (PELDOR) spectroscopy reveals a prearranged tertiary structure of the 27 nucleotides long engineered neomycin-responsive riboswitch. Measured distances between spin labels at positions U4-U14, U4-U15, U14-U26, and U15-U26 were unchanged upon neomycin binding which implies that the global stem-loop architecture is preserved in the absence and presence of the ligand. On the basis of our results, we infer that low-temperature PELDOR data unambiguously demonstrate the existence of an enthalpically favorable set of RNA conformations ready to bind the ligand without major global rearrangement.
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Affiliation(s)
- Ivan Krstić
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
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382
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Hilger D, Polyhach Y, Jung H, Jeschke G. Backbone structure of transmembrane domain IX of the Na+/proline transporter PutP of Escherichia coli. Biophys J 2010; 96:217-25. [PMID: 19134477 DOI: 10.1016/j.bpj.2008.09.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022] Open
Abstract
The backbone structure is determined by site-directed spin labeling, double electron electron resonance measurements of distances, and modeling in terms of a helix-loop-helix construct for a transmembrane domain that is supposed to line the translocation pathway in the 54.3 kDa Na(+)/proline symporter PutP of Escherichia coli. The conformational distribution of the spin labels is accounted for by a rotamer library. An ensemble of backbone models with a root mean-square deviation of less than 2 A is obtained. These models exhibit a pronounced kink near residue T341, which is involved in substrate binding. The kink may be associated with a hinge that allows the protein to open and close an inwardly oriented cavity.
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Affiliation(s)
- Daniel Hilger
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität Munich, Munich, Germany
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383
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Endeward B, Butterwick JA, MacKinnon R, Prisner TF. Pulsed electron-electron double-resonance determination of spin-label distances and orientations on the tetrameric potassium ion channel KcsA. J Am Chem Soc 2010; 131:15246-50. [PMID: 19919160 DOI: 10.1021/ja904808n] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pulsed electron-electron double-resonance (PELDOR) measurements are presented from the potassium ion channel KcsA both solubilized in detergent and reconstituted in lipids. Site-directed spin-labeling using (1-oxyl-2,2,5,5-tetramethyl-3-pyrrolin-3-yl)methyl methanethiosulfonate was performed with a R64C mutant of the protein. The orientations of the spin-labels in the tetramer were determined by PELDOR experiments performed at two magnetic field strengths (0.3 T/X-band and 1.2 T/Q-band) and variable probe frequency. Quantitative simulation of the PELDOR data supports a strongly restricted nitroxide, oriented at an angle of 65 degrees relative to the central channel axis. In general, poorer quality PELDOR data were obtained from membrane-reconstituted preparations compared to soluble proteins or detergent-solubilized samples. One reason for this is the reduced transverse spin relaxation time T(2) of nitroxides due to crowding of tetramers within the membrane that occurs even at low protein to lipid ratios. This reduced T(2) can be overcome by reconstituting mixtures of unlabeled and labeled proteins, yielding high-quality PELDOR data. Identical PELDOR oscillation frequencies and their dependencies on the probe frequency were observed in the detergent and membrane-reconstituted preparations, indicating that the position and orientation of the spin-labels are the same in both environments.
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Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
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384
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Lyubenova S, Maly T, Zwicker K, Brandt U, Ludwig B, Prisner T. Multifrequency pulsed electron paramagnetic resonance on metalloproteins. Acc Chem Res 2010; 43:181-9. [PMID: 19842617 DOI: 10.1021/ar900050d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.
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Affiliation(s)
- Sevdalina Lyubenova
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thorsten Maly
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Ulrich Brandt
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Bernd Ludwig
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thomas Prisner
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
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385
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Marko A, Margraf D, Cekan P, Sigurdsson ST, Schiemann O, Prisner TF. Analytical method to determine the orientation of rigid spin labels in DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021911. [PMID: 20365599 DOI: 10.1103/physreve.81.021911] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Indexed: 05/29/2023]
Abstract
We demonstrate the ability of pulsed electron double resonance (PELDOR) experiments to determine the orientation of spin labels in biological macromolecules. Thus, the distance information usually obtained from PELDOR data can be complemented by the mutual orientation of macromolecular domains. A method to determine the angle beta between the spin label normal and the interspin axis is proposed and analyzed mathematically. The obtained analytical expression allows extraction of angles beta without a fitting procedure if these angles are equal for both nitroxide of biradical. The method was applied to the experimental data gathered on ten spin-labeled DNA samples. The angles estimated from the PELDOR data are in excellent agreement with literature values.
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Affiliation(s)
- Andriy Marko
- Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.
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386
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Bowman A, Ward R, El-Mkami H, Owen-Hughes T, Norman DG. Probing the (H3-H4)2 histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling. Nucleic Acids Res 2010; 38:695-707. [PMID: 19914933 PMCID: PMC2810997 DOI: 10.1093/nar/gkp1003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 10/06/2009] [Accepted: 10/12/2009] [Indexed: 12/30/2022] Open
Abstract
The (H3-H4)(2) histone tetramer forms the central core of nucleosomes and, as such, plays a prominent role in assembly, disassembly and positioning of nucleosomes. Despite its fundamental role in chromatin, the tetramer has received little structural investigation. Here, through the use of pulsed electron-electron double resonance spectroscopy coupled with site-directed spin labelling, we survey the structure of the tetramer in solution. We find that tetramer is structurally more heterogeneous on its own than when sequestered in the octamer or nucleosome. In particular, while the central region including the H3-H3' interface retains a structure similar to that observed in nucleosomes, other regions such as the H3 alphaN helix display increased structural heterogeneity. Flexibility of the H3 alphaN helix in the free tetramer also illustrates the potential for post-translational modifications to alter the structure of this region and mediate interactions with histone chaperones. The approach described here promises to prove a powerful system for investigating the structure of additional assemblies of histones with other important factors in chromatin assembly/fluidity.
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Affiliation(s)
- Andrew Bowman
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - Richard Ward
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - Hassane El-Mkami
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
| | - David G. Norman
- Wellcome Trust Centre for Gene Regulation and Expression, Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH and School of Physics and Astronomy, University of St Andrews, St Andrews FE2 4KM, UK
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387
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Site-directed spin labeling of a genetically encoded unnatural amino acid. Proc Natl Acad Sci U S A 2009; 106:21637-42. [PMID: 19995976 DOI: 10.1073/pnas.0912009106] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The traditional site-directed spin labeling (SDSL) method, which utilizes cysteine residues and sulfhydryl-reactive nitroxide reagents, can be challenging for proteins that contain functionally important native cysteine residues or disulfide bonds. To make SDSL amenable to any protein, we introduce an orthogonal labeling strategy, i.e., one that does not rely on any of the functional groups found in the common 20 amino acids. In this method, the genetically encoded unnatural amino acid p-acetyl-L-phenylalanine (p-AcPhe) is reacted with a hydroxylamine reagent to generate a nitroxide side chain (K1). The utility of this scheme was demonstrated with seven mutants of T4 lysozyme, each containing a single p-AcPhe at a solvent-exposed helix site; the mutants were expressed in amounts qualitatively similar to the wild-type protein. In general, the EPR spectra of the resulting K1 mutants reflect higher nitroxide mobilities than the spectra of analogous mutants containing the more constrained disulfide-linked side chain (R1) commonly used in SDSL. Despite this increased flexibility, site dependence of the EPR spectra suggests that K1 will be a useful sensor of local structure and of conformational changes in solution. Distance measurements between pairs of K1 residues using double electron electron resonance (DEER) spectroscopy indicate that K1 will also be useful for distance mapping.
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388
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Sajid M, Jeschke G, Wiebcke M, Godt A. Conformationally Unambiguous Spin Labeling for Distance Measurements. Chemistry 2009; 15:12960-2. [DOI: 10.1002/chem.200902162] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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389
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Abstract
The understanding of structure-dynamics-function relationships in oligonucleotides or oligonucleotide/protein complexes calls for biophysical methods that can resolve the structure and dynamics of such systems on the critical nanometer length scale. A modern electron paramagnetic resonance (EPR) method called pulsed electron-electron double resonance (PELDOR or DEER) has been shown to reliably and precisely provide distances and distance distributions in the range of 1.5-8nm. In addition, recent experiments proved that a PELDOR experiment also contains information on the orientation of labels, enables easy separation of coupling mechanisms and allows for counting the number of monomers in complexes. This chapter briefly summarizes the theory, describes how to perform and analyze such experiments and discusses the limitations.
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390
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Milikisyants S, Scarpelli F, Finiguerra MG, Ubbink M, Huber M. A pulsed EPR method to determine distances between paramagnetic centers with strong spectral anisotropy and radicals: the dead-time free RIDME sequence. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 201:48-56. [PMID: 19758831 DOI: 10.1016/j.jmr.2009.08.008] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/15/2009] [Accepted: 08/07/2009] [Indexed: 05/09/2023]
Abstract
Methods to determine distances between paramagnetic metal centers and radicals are scarce. This is unfortunate because paramagnetic metal centers are frequent in biological systems and so far have not been employed much as distance markers. Successful pulse sequences that directly target the dipolar interactions cannot be applied to paramagnetic metal centers with fast relaxation rates and large g-anisotropy, if no echos can be detected and the excitation bandwidth is not sufficient to cover a sufficiently large part of the spectrum. The RIDME method Kulik et al. (2002) [20] circumvents this problem by making use of the T(1)-induced spin-flip of the transition-metal ion. Designed to measure distance between such a fast relaxing metal center and a radical, it suffers from a dead time problem. We show that this is severe because the anisotropy of the metal center broadens the dipolar curves, which therefore, only can be analyzed if the full curve is known. Here, we introduce five-pulse RIDME (5p-RIDME) that is intrinsically dead-time free. Proper functioning of the sequence is demonstrated on a nitroxide biradical. The distance between a low-spin Fe(III) center and a spin label in spin-labeled cytochrome f shows the complete dipolar trace of a transition-metal ion center and a spin label, yielding the distance expected from the structure.
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Affiliation(s)
- Sergey Milikisyants
- Department of Molecular Physics, Huygens Laboratory, Leiden University, 2300 RA Leiden, The Netherlands
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391
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Savitsky A, Möbius K. High-field EPR. PHOTOSYNTHESIS RESEARCH 2009; 102:311-333. [PMID: 19468856 DOI: 10.1007/s11120-009-9432-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 04/29/2009] [Indexed: 05/27/2023]
Abstract
Among the numerous spectroscopic techniques utilized in photosynthesis research, high-field/high-frequency EPR and its pulse extensions ESE, ENDOR, ESEEM, and PELDOR play an important role in the endeavor to understand, on the basis of structure and dynamics data, dominant factors that control specificity and efficiency of light-induced electron- and proton-transfer processes in primary photosynthesis. Short-lived transient intermediates of the photocycle can be characterized by high-field EPR techniques, and detailed structural information can be obtained even from disordered sample preparations. The chapter describes how multifrequency high-field EPR methodology, in conjunction with mutation strategies for site-specific isotope or spin labeling and with the support of modern quantum-chemical computation methods for data interpretation, is capable of providing new insights into the photosynthetic transfer processes. The information obtained is complementary to that of protein crystallography, solid-state NMR and laser spectroscopy.
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Affiliation(s)
- Anton Savitsky
- Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
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392
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Klare JP, Steinhoff HJ. Spin labeling EPR. PHOTOSYNTHESIS RESEARCH 2009; 102:377-390. [PMID: 19728138 DOI: 10.1007/s11120-009-9490-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 08/14/2009] [Indexed: 05/28/2023]
Abstract
Site-directed spin labeling in combination with electron paramagnetic resonance spectroscopy has emerged as an efficient tool to elucidate the structure and conformational dynamics of biomolecules under native-like conditions. This article summarizes the basics as well as recent progress of site-directed spin labeling. Continuous wave EPR spectra analyses and pulse EPR techniques are reviewed with special emphasis on applications to the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis and the photosynthetic reaction center from Rhodobacter sphaeroides R26.
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Affiliation(s)
- Johann P Klare
- Physics Department, University of Osnabrück, Barbarastr. 7, 49076, Osnabrück, Germany
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393
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Determination of interspin distance distributions by cw-ESR is a single linear inverse problem. Biophys J 2009; 97:930-6. [PMID: 19651052 DOI: 10.1016/j.bpj.2009.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/22/2009] [Accepted: 05/28/2009] [Indexed: 11/21/2022] Open
Abstract
Cw-ESR distance measurement method is extremely valuable for studying the dynamics-function relationship of biomolecules. However, extracting distance distributions from experiments has been a highly technique-demanding procedure. It has never been conclusively identified, to our knowledge, that the problems involved in the analysis are ill posed and are best solved using Tikhonov regularization. We treat the problems from a novel point of view. First of all, we identify the equations involved and uncover that they are actually two linear first-kind Fredholm integral equations. They can be combined into one single linear inverse problem and solved in a Tikhonov regularization procedure. The improvement with our new treatment is significant. Our approach is a direct and reliable mathematical method capable of providing an unambiguous solution to the ill-posed problem. It need not perform nonlinear least-squares fitting to infer a solution from noise-contaminated data and, accordingly, substantially reduces the computation time and the difficulty of analysis. Numerical tests and experimental data of polyproline II peptides with variant spin-labeled sites are provided to demonstrate our approach. The high resolution of the distance distributions obtainable with our new approach enables a detailed insight into the flexibility of dynamic structure and the identification of conformational species in solution state.
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394
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Meyer S, Böhme S, Krüger A, Steinhoff HJ, Klare JP, Wittinghofer A. Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. PLoS Biol 2009; 7:e1000212. [PMID: 19806182 PMCID: PMC2749940 DOI: 10.1371/journal.pbio.1000212] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 08/21/2009] [Indexed: 11/19/2022] Open
Abstract
The authors of this research article demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle, and show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein. These movements are of crucial importance for understanding the mechanistic principles of this GAD. MnmE, which is involved in the modification of the wobble position of certain tRNAs, belongs to the expanding class of G proteins activated by nucleotide-dependent dimerization (GADs). Previous models suggested the protein to be a multidomain protein whose G domains contact each other in a nucleotide dependent manner. Here we employ a combined approach of X-ray crystallography and pulse electron paramagnetic resonance (EPR) spectroscopy to show that large domain movements are coupled to the G protein cycle of MnmE. The X-ray structures show MnmE to be a constitutive homodimer where the highly mobile G domains face each other in various orientations but are not in close contact as suggested by the GDP-AlFx structure of the isolated domains. Distance measurements by pulse double electron-electron resonance (DEER) spectroscopy show that the G domains adopt an open conformation in the nucleotide free/GDP-bound and an open/closed two-state equilibrium in the GTP-bound state, with maximal distance variations of 18 Å. With GDP and AlFx, which mimic the transition state of the phosphoryl transfer reaction, only the closed conformation is observed. Dimerization of the active sites with GDP-AlFx requires the presence of specific monovalent cations, thus reflecting the requirements for the GTPase reaction of MnmE. Our results directly demonstrate the nature of the conformational changes MnmE was previously suggested to undergo during its GTPase cycle. They show the nucleotide-dependent dynamic movements of the G domains around two swivel positions relative to the rest of the protein, and they are of crucial importance for understanding the mechanistic principles of this GAD. MnmE is an evolutionary conserved G protein that is involved in modification of the wobble U position of certain tRNAs to suppress translational wobbling. Despite high homology between its G domain and the small G protein Ras, MnmE displays entirely different regulatory properties to that of many molecular switch-type G proteins of the Ras superfamily, as its GTPase is activated by nucleotide-dependent homodimerization across the nucleotide-binding site. Here we explore the unusual G domain cycle of the MnmE protein by combining X-ray crystallography with pulse electron paramagnetic resonance (EPR) spectroscopy, which enables distance determinations between spin markers introduced at specific sites within the G domain. We determined the structures of the full-length MnmE dimer in the diphosphate and triphosphate states, which represent distinct steps of the G domain cycle, and demonstrate that the G domain cycle of MnmE comprises large conformational changes and domain movements of up to 18 Å, in which the G domains of the dimeric protein traverse from a GDP-bound open state through an open/closed equilibrium in the triphosphate state to a closed conformation in the transition state, so as to assemble the catalytic machinery.
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Affiliation(s)
- Simon Meyer
- Department of Structural Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Sabine Böhme
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - André Krüger
- Department of Structural Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | | | - Johann P. Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
- * E-mail: (JPK); (AW)
| | - Alfred Wittinghofer
- Department of Structural Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
- * E-mail: (JPK); (AW)
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395
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Cruickshank PAS, Bolton DR, Robertson DA, Hunter RI, Wylde RJ, Smith GM. A kilowatt pulsed 94 GHz electron paramagnetic resonance spectrometer with high concentration sensitivity, high instantaneous bandwidth, and low dead time. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:103102. [PMID: 19895049 DOI: 10.1063/1.3239402] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We describe a quasioptical 94 GHz kW pulsed electron paramagnetic resonance spectrometer featuring pi/2 pulses as short as 5 ns and an instantaneous bandwidth of 1 GHz in nonresonant sample holders operating in induction mode and at low temperatures. Low power pulses can be as short as 200 ps and kilowatt pulses as short as 1.5 ns with timing resolution of a few hundred picoseconds. Phase and frequency can be changed on nanosecond time scales and complex high power pulse sequences can be run at repetition rates up to 80 kHz with low dead time. We demonstrate that the combination of high power pulses at high frequencies and nonresonant cavities can offer excellent concentration sensitivity for orientation selective pulsed electron double resonance (double electron-electron resonance), where we demonstrate measurements at 1 microM concentration levels.
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Affiliation(s)
- Paul A S Cruickshank
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
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396
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Lovett JE, Hoffmann M, Cnossen A, Shutter ATJ, Hogben HJ, Kay CWM, Timmel CR, Anderson HL. Probing Flexibility in Porphyrin-Based Molecular Wires Using Double Electron Electron Resonance. J Am Chem Soc 2009; 131:13852-9. [DOI: 10.1021/ja905796z] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janet E. Lovett
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Markus Hoffmann
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Arjen Cnossen
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Alexander T. J. Shutter
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Hannah J. Hogben
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Christopher W. M. Kay
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
| | - Harry L. Anderson
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom, Deptartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom, Synchrotron Radiation Source, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom, Department of Chemistry,
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397
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Gordon-Grossman M, Gofman Y, Zimmermann H, Frydman V, Shai Y, Ben-Tal N, Goldfarb D. A Combined Pulse EPR and Monte Carlo Simulation Study Provides Molecular Insight on Peptide−Membrane Interactions. J Phys Chem B 2009; 113:12687-95. [DOI: 10.1021/jp905129b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michal Gordon-Grossman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Yana Gofman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Herbert Zimmermann
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Veronica Frydman
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Yechiel Shai
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Nir Ben-Tal
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
| | - Daniella Goldfarb
- Departments of Chemical Physics, Chemical Infrastructure
Unit, Biological Chemistry, The Weizmann Institute of Science, Rehovot,
Israel 76100, GKSS Research Center, Geesthacht, Germany 21502, Max-Planck
Institute for Medical Research, Heidelberg, Germany, and Department
of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel-Aviv
University, Tel-Aviv, Israel 69978
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398
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Ward R, Zoltner M, Beer L, El Mkami H, Henderson I, Palmer T, Norman D. The Orientation of a Tandem POTRA Domain Pair, of the Beta-Barrel Assembly Protein BamA, Determined by PELDOR Spectroscopy. Structure 2009; 17:1187-94. [DOI: 10.1016/j.str.2009.07.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/23/2009] [Accepted: 07/24/2009] [Indexed: 11/29/2022]
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399
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Abstract
AbstractIn order to fulfill their function, membrane transport proteins have to cycle through a number of conformational and/or energetic states. Thus, understanding the role of conformational dynamics seems to be the key for elucidation of the functional mechanism of these proteins. However, membrane proteins in general are often difficult to express heterologously and in sufficient amounts for structural studies. It is especially challenging to trap a stable energy minimum, e.g., for crystallographic analysis. Furthermore, crystallization is often only possible by subjecting the protein to conditions that do not resemble its native environment and crystals can only be snapshots of selected conformational states. Nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy are complementary methods that offer unique possibilities for studying membrane proteins in their natural membrane environment and for investigating functional conformational changes, lipid interactions, substrate-lipid and substrate-protein interactions, oligomerization states and overall dynamics of membrane transporters. Here, we review recent progress in the field including studies from primary and secondary active transporters.
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400
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Herrick DZ, Kuo W, Huang H, Schwieters CD, Ellena JF, Cafiso DS. Solution and membrane-bound conformations of the tandem C2A and C2B domains of synaptotagmin 1: Evidence for bilayer bridging. J Mol Biol 2009; 390:913-23. [PMID: 19501597 DOI: 10.1016/j.jmb.2009.06.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 05/29/2009] [Accepted: 06/02/2009] [Indexed: 11/29/2022]
Abstract
Synaptotagmin 1 (syt1) is a synaptic vesicle membrane protein that functions as the Ca(2)(+) sensor in neuronal exocytosis. Here, site-directed spin labeling was used to generate models for the solution and membrane-bound structures of a soluble fragment of syt1 containing its two C2 domains, C2A and C2B. In solution, distance restraints between the two C2 domains of syt1 were measured using double electron-electron resonance and used in a simulated annealing routine to generate models for the structure of the tandem C2A-C2B fragment. The data indicate that the two C2 domains are flexibly linked and do not interact with each other in solution, with or without Ca(2+). However, the favored orientation is one where the Ca(2+)-binding loops are oriented in opposite directions. A similar approach was taken for membrane-associated C2A-C2B, combining both distances and bilayer depth restraints with simulated annealing. The restraints can only be satisfied if the Ca(2+) and membrane-binding surfaces of the domains are oriented in opposite directions so that C2A and C2B are docked to opposing bilayers. The result suggests that syt1 functions to bridge across the vesicle and plasma membrane surfaces in a Ca(2+)-dependent manner.
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Affiliation(s)
- Dawn Z Herrick
- Department of Chemistry and Biophysics, University of Virginia, Charlottesville, 22904-4319, USA
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