EPR Relaxation‐Enhancement‐Based Distance Measurements on Orthogonally Spin‐Labeled T4‐Lysozyme

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 LnIII–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.

[1]  G. Jeschke,et al.  Adiabatic and fast passage ultra-wideband inversion in pulsed EPR. , 2013, Journal of magnetic resonance.

[2]  W. Hubbell,et al.  Orthogonal spin labeling and Gd(III)-nitroxide distance measurements on bacteriophage T4-lysozyme. , 2013, The journal of physical chemistry. B.

[3]  G. Jeschke,et al.  Distance measurements on orthogonally spin-labeled membrane spanning WALP23 polypeptides. , 2013, The journal of physical chemistry. B.

[4]  H. Steinhoff,et al.  Conformational heterogeneity of the aspartate transporter GltPh , 2013, Nature Structural &Molecular Biology.

[5]  Jack H. Freed,et al.  Conformational ensemble of the sodium coupled aspartate transporter , 2012, Nature Structural &Molecular Biology.

[6]  S. Sigurdsson,et al.  Trityl radicals: spin labels for nanometer-distance measurements. , 2012, Chemistry.

[7]  O. Fedorov,et al.  Structural plasticity of histones H3-H4 facilitates their allosteric exchange between RbAp48 and ASF1 , 2012, Nature Structural &Molecular Biology.

[8]  G. Jeschke,et al.  Distance measurements in Au nanoparticles functionalized with nitroxide radicals and Gd(3+)-DTPA chelate complexes. , 2012, Physical chemistry chemical physics : PCCP.

[9]  G. Jeschke,et al.  Multiple Pathway Relaxation Enhancement in the System Composed of Three Paramagnetic Species: Nitroxide Radical-Ln(3+)-O2. , 2012, The journal of physical chemistry letters.

[10]  Gunnar Jeschke,et al.  DEER distance measurements on proteins. , 2012, Annual review of physical chemistry.

[11]  G. Otting,et al.  Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels. , 2012, Physical chemistry chemical physics : PCCP.

[12]  C. Copéret,et al.  A slowly relaxing rigid biradical for efficient dynamic nuclear polarization surface-enhanced NMR spectroscopy: expeditious characterization of functional group manipulation in hybrid materials. , 2012, Journal of the American Chemical Society.

[13]  Gabriel Waksman,et al.  Crystal structure of the FimD usher bound to its cognate FimC:FimH substrate , 2011, Nature.

[14]  G. Jeschke,et al.  Double Electron-Electron Resonance Measured Between Gd3+ Ions and Nitroxide Radicals , 2011 .

[15]  P. Keizers,et al.  Paramagnetic tagging for protein structure and dynamics analysis. , 2011, Progress in nuclear magnetic resonance spectroscopy.

[16]  T. Owen-Hughes,et al.  EPR distance measurements in deuterated proteins. , 2010, Journal of magnetic resonance.

[17]  Francis B. Peters,et al.  Site-directed spin labeling of a genetically encoded unnatural amino acid , 2009, Proceedings of the National Academy of Sciences.

[18]  Johann P. Klare,et al.  Spin labeling EPR , 2009, Photosynthesis Research.

[19]  B. Bowler,et al.  Electron-electron distances in spin-labeled low-spin metmyoglobin variants by relaxation enhancement. , 2008, Biophysical journal.

[20]  G. Jeschke,et al.  Relaxation-based distance measurements between a nitroxide and a lanthanide spin label. , 2008, Journal of magnetic resonance.

[21]  A. Milov,et al.  Pulsed electron–electron double resonance (PELDOR) as EPR spectroscopy in nanometre range , 2008 .

[22]  T. Prisner,et al.  PELDOR measurements on a nitroxide-labeled Cu(II) porphyrin: orientation selection, spin-density distribution, and conformational flexibility. , 2008, The journal of physical chemistry. A.

[23]  S. Eaton,et al.  Impact of electron-electron spin interaction on electron spin relaxation of nitroxide diradicals and tetraradical in glassy solvents between 10 and 300 k. , 2008, The journal of physical chemistry. B.

[24]  S. Eaton,et al.  Electron spin relaxation enhancement measurements of interspin distances in human, porcine, and Rhodobacter electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO). , 2008, Journal of magnetic resonance.

[25]  G. Jeschke,et al.  Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. , 2007, Physical chemistry chemical physics : PCCP.

[26]  R. V. Van Duyne,et al.  Localized surface plasmon resonance spectroscopy and sensing. , 2007, Annual review of physical chemistry.

[27]  M. P. D. Vries,et al.  Protein-protein interactions studied by EPR relaxation measurements: cytochrome c and cytochrome c oxidase. , 2007, The journal of physical chemistry. B.

[28]  T. Prisner,et al.  Long-range distance determinations in biomacromolecules by EPR spectroscopy , 2007, Quarterly Reviews of Biophysics.

[29]  G. Cravotto,et al.  How to determine free Gd and free ligand in solution of Gd chelates. A technical note. , 2006, Contrast media & molecular imaging.

[30]  S. Cotton Lanthanide and Actinide Chemistry: Cotton/Lanthanide and Actinide Chemistry , 2006 .

[31]  H. Zimmermann,et al.  Isotope selection in distance measurements between nitroxides. , 2006, Journal of magnetic resonance.

[32]  R. Tsien,et al.  The Fluorescent Toolbox for Assessing Protein Location and Function , 2006, Science.

[33]  P. Fajer Site directed spin labelling and pulsed dipolar electron paramagnetic resonance (double electron–electron resonance) of force activation in muscle , 2005 .

[34]  R. Corn,et al.  Surface plasmon resonance imaging measurements of ultrathin organic films. , 2003, Annual review of physical chemistry.

[35]  Gunnar Jeschke,et al.  Distance measurements in the nanometer range by pulse EPR. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.

[36]  G. Jeschke,et al.  Selective measurements of a nitroxide-nitroxide separation of 5 nm and a nitroxide-copper separation of 2.5 nm in a terpyridine-based copper(II) complex by pulse EPR spectroscopy. , 2002, Angewandte Chemie.

[37]  A. Rosato,et al.  Paramagnetically induced residual dipolar couplings for solution structure determination of lanthanide binding proteins. , 2002, Journal of the American Chemical Society.

[38]  I. Bertini,et al.  Paramagnetism-based versus classical constraints: An analysis of the solution structure of Ca Ln calbindin D9k , 2001, Journal of biomolecular NMR.

[39]  I. Bertini,et al.  Locating the Metal Ion in Calcium‐Binding Proteins by Using Cerium(III) as a Probe , 2001, Chembiochem : a European journal of chemical biology.

[40]  A. Rosato,et al.  Magnetic susceptibility tensor anisotropies for a lanthanide ion series in a fixed protein matrix. , 2001, Journal of the American Chemical Society.

[41]  W. Hubbell,et al.  Helix packing in the lactose permease of Escherichia coli: distances between site-directed nitroxides and a lanthanide. , 2001, Biochemistry.

[42]  David S. Cafiso,et al.  Identifying conformational changes with site-directed spin labeling , 2000, Nature Structural Biology.

[43]  Paul R. Selvin,et al.  The renaissance of fluorescence resonance energy transfer , 2000, Nature Structural Biology.

[44]  B. Bowler,et al.  Interspin distances in spin-labeled metmyoglobin variants determined by saturation recovery EPR. , 2000, Biophysical journal.

[45]  I. Bertini,et al.  Lanthanide-Induced Pseudocontact Shifts for Solution Structure Refinements of Macromolecules in Shells up to 40 Å from the Metal Ion , 2000 .

[46]  G. Jeschke,et al.  Dead-time free measurement of dipole-dipole interactions between electron spins. , 2000, Journal of magnetic resonance.

[47]  S. Weiss Fluorescence spectroscopy of single biomolecules. , 1999, Science.

[48]  Rainer E. Martin,et al.  Determination of End-to-End Distances in a Series of TEMPO Diradicals of up to 2.8 nm Length with a New Four-Pulse Double Electron Electron Resonance Experiment. , 1998, Angewandte Chemie.

[49]  H. Spiess,et al.  Bestimmung der Länge von bis zu 2.8 nm langen TEMPO‐Diradikalen mit einem neuen Vier‐Puls‐Doppel‐Elektron‐Elektron‐ Resonanz‐Experiment , 1998 .

[50]  W. Hubbell,et al.  Recent advances in site-directed spin labeling of proteins. , 1998, Current opinion in structural biology.

[51]  A. Milov,et al.  Electron-electron double resonance in electron spin echo: Model biradical systems and the sensitized photolysis of decalin , 1984 .

[52]  M. Cusanovich,et al.  Magnetic interactions between dysprosium complexes and two soluble iron-sulfur proteins. , 1981, The Journal of biological chemistry.

[53]  A. Kulikov,et al.  The use of spin relaxation phenomena in the investigation of the structure of model and biological systems by the method of spin labels , 1977 .

[54]  E. Bordignon Site-directed spin labeling of membrane proteins. , 2012, Topics in current chemistry.

[55]  Ivan Krstić,et al.  Structure and dynamics of nucleic acids. , 2012, Topics in current chemistry.

[56]  G. Otting,et al.  Paramagnetic labelling of proteins and oligonucleotides for NMR , 2010, Journal of biomolecular NMR.

[57]  Jack H Freed,et al.  Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases. , 2007, Methods in enzymology.

[58]  Jack H Freed,et al.  Rigid body refinement of protein complexes with long-range distance restraints from pulsed dipolar ESR. , 2007, Methods in enzymology.

[59]  S. Eaton,et al.  Determination of Distances Based on T 1 and T m Effects , 2002 .

[60]  C. Levinthal,et al.  Site‐directed mutagenesis of colicin E1 provides specific attachment sites for spin labels whose spectra are sensitive to local conformation , 1989, Proteins.

[61]  L. Stryer Fluorescence energy transfer as a spectroscopic ruler. , 1978, Annual review of biochemistry.