EPR techniques to probe insertion and conformation of spin-labeled proteins in lipid bilayers

Methods in Molecular Biology

Volumn 974, Issue , 2013, Pages 329-355

  Bordignon, Enrica ^a   Polyhach, Yevhen ^a  

^a NONE

Author keywords

Accessibility; Bilayer; Distances; Double electron electron resonance (DEER); EPR; High field; Membrane proteins; Mobility; Nitroxide; Site directed spin labeling

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; AMINO ACID; DEUTERIUM; LIPID; LIPOSOME; MEMBRANE PROTEIN; NITROXIDE; PROTEIN BAX; WATER;

ARTICLE; DOUBLE ELECTRON ELECTRON SPIN RESONANCE; ELECTRON; ELECTRON SPIN RESONANCE; ELECTRON SPIN RESONANCE SPECTROMETER; HUMAN; INTERMETHOD COMPARISON; LIPID BILAYER; LOW TEMPERATURE; METHODOLOGY; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN LIPID INTERACTION; PROTEIN STRUCTURE; SPECTROMETER; SPIN LABELING; X RAY CRYSTALLOGRAPHY; CHEMISTRY; CONFORMATION; METABOLISM; PROTEIN SECONDARY STRUCTURE; TEMPERATURE;

BCL-2-ASSOCIATED X PROTEIN; ELECTRON SPIN RESONANCE SPECTROSCOPY; ELECTRONS; HUMANS; LIPID BILAYERS; MEMBRANE PROTEINS; MOLECULAR CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SPIN LABELS; TEMPERATURE; WATER;

MLCS; MLOWN;

EID: 84881049277     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-275-9_15     Document Type: Article

References (38)

1. Berliner LJ, Reuben J (eds) (1989) Spin labeling theory and applications. Plenum Press, New York
2. Azarkh M, Okle O, Eyring P et al (2011) Evaluation of spin labels for in-cell EPR by analysis of nitroxide reduction in cell extract of Xenopus laevis oocytes. J Magn Reson 212: 450-454
3. Krstic I, Hansel R, Romainczyk O et al (2011) Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 50: 5070-5074
4. Fleissner MR, Bridges MD, Brooks EK et al (2011) Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy. Proc Natl Acad Sci USA 108: 16241-16246
5. Cooke JA, Brown L.J. (2011) Distance measurements by continuous wave EPR spectros-copy to monitor protein folding. Methods Mol Biol 752: 73-96
6. Hubbell WL, Mchaourab HS, Altenbach C et al (1996) Watching proteins move using site-directed spin labeling. Structure 4: 779-783
7. Bleicken S, Classen M, Padmavathi PV et al (2010) Molecular details of Bax activation, oligomerization, and membrane insertion. J Biol Chem 285: 6636-6647
8. Altenbach C, Greenhalgh DA, Khorana HG et al (1994) A collision gradient-method to determine the immersion depth of nitroxides in lipid bilayers - application to spin-labeled mutants of bacteriorhodopsin. Proc Natl Acad Sci USA 91: 1667-1671
9. Altenbach C, Froncisz W, Hemker R et al (2005) Accessibility of nitroxide side chains: absolute Heisenberg exchange rates from power saturation EPR. Biophys J 89: 2103-2112
10. Oh KJ, Altenbach C, Collier RJ et al (2000) Site-directed spin labeling of proteins. Applications to diphtheria toxin. Methods Mol Biol 145: 147-169
11. Subczynski WK, Widomska J, Wisniewska A et al (2007) Saturation-recovery electron paramagnetic resonance discrimination by oxygen transport (DOT) method for characterizing membrane domains. Methods Mol Biol 398: 143-157
12. Pyka J, Ilnicki J, Altenbach C et al (2005) Accessibility and dynamics of nitroxide side chains in T4 lysozyme measured by saturation recovery EPR. Biophys J 89: 2059-2068
13. Kurad D, Jeschke G, Marsh D. (2003) Lipid membrane polarity profiles by high-field EPR. Biophys J 85: 1025-1033
14. Plato M, Steinhoff HJ, Wegener C et al (2002) Molecular orbital study of polarity and hydrogen bonding effects on the g and hyperfine tensors of site directed NO spin labelled bacteriorhodopsin. Mol Phys 100: 3711-3721
15. Steinhoff HJ, Savitsky A, Wegener C et al (2000) High-field EPR studies of the structure and conformational changes of site-directed spin labeled bacteriorhodopsin. Biochim Biophys Acta Bioenerg 1457: 253-262
16. Stoll S, Schweiger A. (2006) EasySpin, a comprehensive software package for spectral simulation and analysis in EPR. J Magn Reson 178: 42-55
17. Bordignon E, Brutlach H, Urban L et al (2010) Heterogeneity in the nitroxide microenvironment: polarity and proticity effects in spin-labeled proteins studied by multi-frequency EPR. Appl Magn Reson 37: 391-403
18. Volkov A, Dockter C, Bund T et al (2009) Pulsed EPR determination of water accessibility to spin-labeled amino acid residues in LHCIIb. Biophys J 96: 1124-1141
19. Berliner LJ, Eaton SS, Eaton GR (eds) (2000) Distance measurements in biological systems by EPR. Kluwer Academic/Plenum, New York
20. Steinhoff HJ, Radzwill N, Thevis W et al (1997) Determination of interspin distances between spin labels attached to insulin: comparison of electron paramagnetic resonance data with the x-ray structure. Biophys J 73: 3287-3298
21. Altenbach C, Oh KJ, Trabanino RJ et al (2001) Estimation of inter-residue distances in spin labeled proteins at physiological temperatures: experimental strategies and practical limitations. Biochemistry 40: 15471-15482
22. Banham JE, Baker CM, Ceola S et al (2008) Distance measurements in the borderline region of applicability of CW EPR and DEER: a model study on a homologous series of spin-labelled peptides. J Magn Reson 191: 202-218
23. Grote M, Bordignon E, Polyhach Y et al (2008) A comparative electron paramagnetic resonance study of the nucleotide-binding domains' catalytic cycle in the assembled maltose ATP-binding cassette importer. Biophys J 95: 2924-2938
24. Pannier M, Veit S, Godt A et al (2000) Deadtime free measurement of dipole-dipole interactions between electron spins. J Magn Reson 142: 331-340
25. Polyhach Y, Bordignon E, Tschaggelar R et al (2012) High sensitivity and versatility of the DEER experiment on nitroxide radical pairs at Q-band frequencies. Phys Chem Chem Phys 14: 10762-10773
26. Jeschke G, Polyhach Y. (2007) Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. Phys Chem Chem Phys 9: 1895-1910
27. Jeschke G, Chechik V, Ionita P et al (2006) DeerAnalysis2006 - a comprehensive software package for analyzing pulsed ELDOR data. Appl Magn Reson 30: 473-498
28. Polyhach Y, Bordignon E, Jeschke G. (2011) Rotamer libraries of spin labelled cysteines for protein studies. Phys Chem Chem Phys 13: 2356-2366
29. Hvorup RN, Goetz BA, Niederer M et al (2007) Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF. Science 317: 1387-1390
30. Locher KP, Lee AT, Rees D.C. (2002) The E. Coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 296: 1091-1098
31. Pinkett HW, Lee AT, Lum P et al (2007) An inward-facing conformation of a putative metal-chelate-type ABC transporter. Science 315: 373-377
32. Joseph B, Jeschke G, Goetz BA et al (2011) Transmembrane gate movements in the type II ATP-binding cassette (ABC) importer BtuCDF during nucleotide cycle. J Biol Chem 286: 41008-41017
33. Korkhov VM, Mireku SA, Locher K.P. (2012) Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F. Nature 490: 367-372
34. Hilger D, Polyhach Y, Jung H et al (2009) Backbone structure of transmembrane domain IX of the Na+/proline transporter PutP of Escherichia coli. Biophys J 96: 217-225
35. Raba M, Baumgartner T, Hilger D et al (2008) Function of transmembrane domain IX in the Na+/proline transporter PutP. J Mol Biol 382: 884-893
36. Fleissner MR, Brustad EM, Kálai T et al (2009) Site-directed spin labeling of a genetically encoded unnatural amino acid. Proc Natl Acad Sci 106: 21637-21642
37. Toniolo C, Valente E, Formaggio F et al (1995) Synthesis and conformational studies of peptides containing TOAC, a spin-labelled Ca, a-disubstituted glycine. J Pept Sci 1: 45-57
38. Jeschke G, Sajid M, Schulte M et al (2009) Three-spin correlations in double electron-electron resonance. Phys Chem Chem Phys 11: 6580-6591