Exploring the local conformational space of a membrane protein by site-directed spin labeling

Journal of Chemical Information and Modeling

Volumn 45, Issue 6, 2005, Pages 1621-1627

  Stopar, David ^a   Štrancar, Janez ^b   Spruijt, Ruud B ^c   Hemminga, Marcus A ^a,c,d  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b JO EF STEFAN INSTITUTE   (Slovenia)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d NONE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOLOGICAL MEMBRANES; CONDENSATION; CONFORMATIONS; MOLECULAR DYNAMICS; OPTIMIZATION; PARAMAGNETIC RESONANCE;

COAT PROTEIN; MEMBRANE PROTEIN; MEMBRANE SYSTEM; SPIN LABEL;

PROTEINS;

1,2 OLEOYLPHOSPHATIDYLCHOLINE; 1,2-OLEOYLPHOSPHATIDYLCHOLINE; AMINO ACID; MEMBRANE PROTEIN; OXYGEN; PHOSPHATIDYLCHOLINE;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTRON SPIN RESONANCE; LIPID BILAYER; PROTEIN CONFORMATION; SOLUTION AND SOLUBILITY; SPIN LABELING; STATISTICAL MODEL;

ALGORITHMS; AMINO ACIDS; ELECTRON SPIN RESONANCE SPECTROSCOPY; LIPID BILAYERS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; OXYGEN; PHOSPHATIDYLCHOLINES; PROTEIN CONFORMATION; SOLUTIONS; SPIN LABELS;

EID: 28944451650     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0501490     Document Type: Conference Paper

References (43)

1. Fajer, P. G. Electron spin resonance spectroscopy labeling in peptide and protein analysis. In Encyclopedia of Analytical Chemistry; Mayers, R. A., Ed.; John Wiley & Sons Ltd.: Chichester, 2000.
2. Hubbell, W. L.; Altenbach, C. Investigation of structure and dynamics in membrane proteins using site-directed spin labeling. Curr. Opin. Struct. Biol. 1994, 4, 566-573.
3. Hubbell, W. L.; Mchaourab, H. S.; Altenbach, C.; Lietzow, M. A. Watching proteins move using site-directed spin labeling. Structure 1996, 4, 779-783.
4. Hustedt, E. J.; Beth, A. H. Nitroxide spin-spin interactions: applications to protein structure and dynamics. Annu. Rev. Biophys, Biomol. Struct. 1999, 28, 129-153.
5. Stopar, D.; Spruijt, R. B.; Wolfs, C. J. A. M.; Hemminga, M. A. Local dynamics of the M13 major coat protein in different membranemimicking systems. Biochemistry 1996, 35, 15467-15473.
6. Berengian, A. R.; Parfenova, M.; Mchaourab, H. S. Site-directed spin labeling study of subunit Interactions in the α-Crystallin domain of small heat-shock proteins. J. Biol. Chem. 1999, 274, 6305-6314.
7. Columbus, L.; Kalai, T.; Jeko, J.; Hideg, K.; Hubbell, W. L. Molecular motion of spin labeled side chains in α-helices: analysis by variation of side chain structure. Biochemistry 2001, 40, 3828-3846.
8. Klug, C. S.; Su, W.; Feix, J. B. Mapping of the residues involved in a proposed β-strand located in the Ferric Enterobactin Receptor FepA using site-directed spin labeling. Biochemistry 1997, 36, 13027-13033.
9. Liu, Y.-S.; Sompornpisut, P.; Perozo, E. Structure of the KcsA channel intracellular gate in the open state. Nature Struct. Biol. 2001, 8, 883-887.
10. Mchaourab, H. S.; Oh, K. J.; Fang, C. J.; Hubbell, W. L. Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling. Biochemistry 1997, 36, 307-16.
11. Meijer, A. B.; Spruijt, R. B.; Wolfs, C. J. A. M.; Hemminga, M. A. Configurations of the N-terminal amphipathic domain of the membrane-bound M13 major coat protein. Biochemistry 2001, 40, 5081-5086.
12. Perozo, E.; Cortes, M. D.; Sompornpisut, P.; Kloda, A.; Martinac, B. Open channel structure of MsdL and the gating mechanism of mechanosensitive channels. Nature 2002, 418, 942-948.
13. Stopar, D.; Jansen, K. A. J.; Páli, T.; Marsh, D.; Hemminga, M. A. Membrane location of spin-labeled M13 major coat protein mutants determined by paramagnetic relaxation agents. Biochemistry 1997, 36, 8261-8268.
14. Wegener, A. A.; Klare, J. P.; Engelhard, M.; Steinhoff, H.-J. Structural insights into early steps of receptor-transducer signal transfer in archaeal phototaxis. EMBO J. 2001, 20, 5312-5319.
15. Strancar, J.; Koklic, T.; Arsov, Z.; Filipic, B.; Stopar, D.; Hemminga, M. A. Spin label EPR-based characterization of biosystem complexity. J. Chem. Inf. Model. 2005, 45, 394-406.
16. Stopar, D.; Spruijt, R. B.; Wolfs, C. J.; Hemminga, M. A. Protein-lipid interactions of bacteriophage M13 major coat protein. Biochim. Biophys. Acta 2003, 1611, 5-15.
17. Meijer, A. B.; Spruijt, R. B.; Wolfs, C. J. A. M.; Hemminga, M. A. Membrane-anchoring interactions of M13 major coat protein. Biochemistry 2001, 40, 8815-8820.
18. Spruijt, R. B.; Meijer, A. B.; Wolfs, C. J. A. M.; Hemminga, M. A., Localization and rearrangement modulation of the N-terminal arm of the membrane-bound major coat protein of bacteriophage M13. Biochim. Biophys. Acta 2000, 1509, 311-323.
19. Spruijt, R. B.; Wolfs, C. J. A. M.; Hemminga, M. A. Aggregation-related conformational change of membrane-associated coat protein of bacteriophage M13. Biochemistry 1989, 28, 9158-9165.
20. Budil, D. E.; Lee, S.; Saxena, S.; Freed, J. H. Nonlinear-least-squares analysis of slow-motion EPR spectra in one and two dimensions using a modified Levenberg-Marquardt algorithm. J. Magn. Reson. 1996, 720, 155-189.
21. Robinson, B. T., H.; Beth, A.; Payer, P.; Dalton, L. R. The phenomenon of magnetic resonance: Theoretical considerations. In Advanced EPR Studies of Biological Systems; Dalton, L., Ed.; CRC Press: Boca Raton, FL, 1985; pp 11-110.
22. Schneider, D. J.; Freed, J. H. Calculating slow motional magnetic resonance spectra: a user's guide. In Biological Magnetic Resonance: Spin Labeling, Theory and Applications; Berliner, L. J., Reuben, J., Eds.; Plenum Press: New York, 1989; pp 1-76.
23. Filipic, B.; Strancar, J. Tuning EPR spectral parameters with a genetic algorithm. Appl. Soft Comput. 2001, 1, 83-90.
24. Steinhoff, H. J.; Savitsky, A.; Wegener, C.; Pfeiffer, M.; Plato, M.; Möbius, K. High-field EPR studies of the structure and conformational changes of site directed spin labeled bacteriorhodopsin. Biochim. Biophys. Acta 2000, 1457, 253-262.
25. Strancar, J.; Sentjurc, M.; Schara, M. Fast and accurate characterization of biological membranes by EPR spectral simulations of nitroxides. J. Magn. Reson. 2000, 142, 254-265.
26. Wickner, W. Asymmetric orientation of a phage coat protein in cytoplasmic membrane of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 4749-4753.
27. Ohkawa, I.; Webster, R. E. The orientation of the major coat protein of bacteriophage f1 in the cytoplasmic membrane of Escherichia coli. J. Biol. Chem. 1981, 256, 9951-9958.
28. Fernandes, F.; Loura, L. M.; Prieto, M.; Koehorst, R.; Spruijt, R. B.; Hemminga, M. A. Dependence of M13 major coat protein oligomerization and lateral segregation on bilayer composition. Biophys. J. 2003, 85, 2430-41.
29. Subczynski, W. K.; Hyde, J. S. The diffusion-concentration product of oxygen in lipid bilayers using the spin-label T1 method. Biochim. Biophys. Acta 1981, 643, 283-291.
30. Subczynski, W. K.; Hyde, J. S. Concentration of oxygen in lipid bilayers using a spin-label method. Biophys. J. 1983, 41, 283-286.
31. Subczynski, W. K. Spin-label oximetry in biological and model systems. Curr. Top. Biophys. 1999, 23, 69-77.
32. Bogusky, M. J.; Leo, G. C.; Opella, S. J. Comparison of the dynamics of the membrane-bound form of fd coat protein in micelles and in bilayers by solution and solid-state nitrogen-15 nuclear magnetic resonance spectroscopy. Proteins: Struct., Fund., Genet. 1988, 4, 123-130.
33. Hemminga, M. A.; Sanders, J. C.; Spruijt, R. B. Spectroscopy of lipid-protein interactions. Structural aspects of two different forms of the coat protein of bacteriophage M13 incorporated in model membranes. In Progress in Lipid Research; Sprecher, H., Ed.; Pergamon Press: Oxford, 1992; Vol. 31, pp 301-333.
34. Leo, G. C.; Colnago, L. A.; Valentine, K. G.; Opella, S. J. Dynamics of fd coat protein in lipid bilayers. Biochemistry 1987, 26, 854-862.
35. Marvin, D. A. Filamentous phage structure, infection and assembly. Curr. Opin. Struct. Biol. 1998, 5, 150-158.
36. McDonnell, P. A.; Shon, K.; Kim, Y.; Opella, S. J. Fd coat protein structure in membrane environments. J. Mol. Biol. 1993, 233, 447-463.
37. 13 major coat protein in detergent micelles; a basis for a model of phage assembly involving specific residues. J. Mol. Biol. 1998, 282, 401-419.
38. Spruijt, R. B.; Wolfs, C. J. M.; Hemminga, M. A. Membrane assembly of M13 major coat protein: evidence for a structural adaptation in the hinge region and a tilted transmembrane domain. Biochemistry 2004, 43, 13972-13980.
39. Marassi, F. M.; Opella, S. J. Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints. Protein Sci. 2003, 12, 403-411.
40. Papavoine, C. H. M.; Konings, R. N. H.; Hilbers, C. W.; Van de Ven, F. J. M. Location of M13 coat protein in sodium dodecyl sulfate micelles as determined by NMR. Biochemistry 1994, 33, 12990-12997.
41. Williams, K. A.; Glibowicka, M.; Li, Z.; Li, H.; Khan, A. R.; Chen, Y. M. Y.; Wang, J.; Marvin, D. A.; Deber, C. M. Packing of coat protein amphipathic and transmembrane helixes in filamentous bacteriophage M13: role of small residues in protein oligomerization. J. Mol. Biol. 1995, 252, 6-14.
42. 13C-MAS NMR spectroscopy. Biochim. Biophys. Acta 2000, 1463, 151-161.
43. 13 Major coat protein and bilayer polarity profile by site-directed fluorescence spectroscopy. Biophys. J. 2004, 87, 1445-1455.