Isotope-edited IR spectroscopy for the study of membrane proteins

Current Opinion in Chemical Biology

Volumn 10, Issue 5, 2006, Pages 394-401

  Arkin, Isaiah T ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

INFRARED SPECTROSCOPY; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW; VIBRATION;

CARBON ISOTOPES; MEMBRANE PROTEINS; NITROGEN ISOTOPES; OXYGEN ISOTOPES; SENSITIVITY AND SPECIFICITY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 33748715411     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.08.013     Document Type: Review

References (47)

1. Krimm S., and Bandekar J. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv Protein Chem 38 (1986) 181-364
2. Braiman M.S., and Rothschild K.J. Fourier transform infrared techniques for probing membrane protein structure. Annu Rev Biophys Biophys Chem 17 (1988) 541-570
3. Surewicz W.K., Mantsch H.H., and Chapman D. Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment. Biochemistry 32 (1993) 389-394
4. Tatulian S.A. Attenuated total reflection Fourier transform infrared spectroscopy: a method of choice for studying membrane proteins and lipids. Biochemistry 42 (2003) 11898-11907
5. Wallace B.A., and Teeters C.L. Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments. Biochemistry 26 (1987) 65-70
6. Tadesse L., Nazarbaghi R., and Walters L. Isotopically enhanced infrared spectroscopy: a novel method for examining the secondary structure at specific sites in conformationally heterogeneous peptides. J Am Chem Soc 113 (1991) 7036-7037
7. 18O, in the determination of a structural model of phospholamban in a lipid bilayer. Spatial restraints resolve the ambiguity arising from interpretations of mutagenesis data. J Mol Biol 300 (2000) 677-685
8. 18O group as a novel infrared probe. Biopolymers 59 (2001) 396-401
9. 13C-enhanced Fourier transform infrared spectroscopy. Protein Sci 13 (2004) 1012-1030. An example of determining the local secondary structure of a protein composed of different secondary structure elements.
10. Gordon L.M., Mobley P.W., Pilpa R., Sherman M.A., and Waring A.J. Conformational mapping of the N-terminal peptide of HIV-1 gp41 in membrane environments using (13)C-enhanced Fourier transform infrared spectroscopy. Biochim Biophys Acta 1559 (2002) 96-120
11. 13C FTIR study. J Mol Biol 350 (2005) 790-805. Analysis of local secondary structure and its change as a function of time in a heterogeneous system.
12. Paul C., Wang J., Wimley W.C., Hochstrasser R.M., and Axelsen P.H. Vibrational coupling, isotopic editing, and beta-sheet structure in a membrane-bound polypeptide. J Am Chem Soc 126 (2004) 5843-5850. Detailed analysis of coupling between individual vibrational modes in a model peptide.
13. Patzlaff J.S., Zhang J., Brooker R.J., and Barry B.A. An isotope-edited FT-IR study of a symporter, the lactose permease. Biochemistry 41 (2002) 7366-7372. An elegant demonstration of reaction induced difference FTIR analysis of a large membrane protein: the lactose permease.
14. Martin I., Goormaghtigh E., and Ruysschaert J.M. Attenuated total reflection IR spectroscopy as a tool to investigate the orientation and tertiary structure changes in fusion proteins. Biochim Biophys Acta 1614 (2003) 97-103
15. Vigano C., Manciu L., Buyse F., Goormaghtigh E., and Ruysschaert J.M. Attenuated total reflection IR spectroscopy as a tool to investigate the structure, orientation and tertiary structure changes in peptides and membrane proteins. Biopolymers 55 (2000) 373-380
16. Goormaghtigh E., Raussens V., and Ruysschaert J.M. Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. Biochim Biophys Acta 1422 (1999) 105-185
17. Fraser R.D.B. The interpretation of infrared dichroism in fibrous protein structures. J Chem Phys 70 (1953) 1511-1515
18. Fraser R.D.B. Interpretation of infrared dichroism in axially oriented polymers. J Chem Phys 28 (1958) 1113-1115
19. Kass I., Arbely E., and Arkin I.T. Modeling sample disorder in site-specific dichroism studies of uniaxial systems. Biophys J 86 (2004) 2502-2507
20. Manor J., Khattari Z., Salditt T., and Arkin I.T. Disorder influence on linear dichroism analyses of smectic phases. Biophys J 89 (2005) 563-571. The authors present a method to accurately deconvolve sample disorder from simple IR dichroism analyses using X-ray reflectivity.
21. Arkin I.T., MacKenzie K.R., and Brunger A.T. Site-directed dichroism as a method for obtaining rotational and orientational constraints for oriented polymers. J Am Chem Soc 119 (1997) 8973-8980
22. Marsh D. Infrared dichroism of isotope-edited alpha helices and beta-sheets. J Mol Biol 338 (2004) 353-367. A thorough theoretical analysis of site-specific dichroism in β-sheet and α-helical proteins.
23. + channel. J Mol Biol 286 (1999) 951-962
24. Kukol A., and Arkin I.T. vpu transmembrane peptide structure obtained by site-specific Fourier transform infrared dichroism and global molecular dynamics searching. Biophys J 77 (1999) 1594-1601
25. Kukol A., and Arkin I.T. Structure of the influenza C virus CM2 protein transmembrane domain obtained by site-specific infrared dichroism and global molecular dynamics searching. J Biol Chem 275 (2000) 4225-4229
26. Kukol A., Torres J., and Arkin I.T. A structure for the trimeric MHC class II-associated invariant chain transmembrane domain. J Mol Biol 320 (2002) 1109-1117
27. 18O labels to derive a model for the protein in lipid bilayers.
28. Torres J., Briggs J.A., and Arkin I.T. Convergence of experimental, computational and evolutionary approaches predicts the presence of a tetrameric form for CD3-zeta. J Mol Biol 316 (2002) 375-384
29. Mukherjee P., Kass I., Arkin I.T., and Zanni M.T. Picosecond dynamics of a membrane protein revealed by 2D IR. Proc Natl Acad Sci USA 103 (2006) 3528-3533. A detailed 2D FTIR study of a membrane protein in lipid bilayers. In this study, the authors report for the first time the dynamics of the system at picosecond resolution that was previously unapproachable.
30. Arbely E., and Arkin I.T. Experimental measurement of the strength of a C α -H ⋯ O bond in a lipid bilayer. J Am Chem Soc 126 (2004) 5362-5363. This study presents an experimental measurement of the strength of the C α -H ⋯ O bond using isotope-edited FTIR.
31. Senes A., Ubarretxena-Belandia I., and Engelman D.M. The C α - H ⋯ O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci USA 98 (2001) 9056-9061
32. Lemmon M.A., Treutlein H.R., Adams P.D., Brunger A.T., and Engelman D.M. A dimerization motif for transmembrane alpha-helices. Nat Struct Biol 1 (1994) 157-163
33. Rozenberg M., Loewenschuss A., and Marcus Y. An empirical correlation between stretching vibration redshift and hydrogen length. Phys Chem Chem Phys 2 (2000) 2699-2702
34. Lanyi J.K. X-ray diffraction of bacteriorhodopsin photocycle intermediates. Mol Membr Biol 21 (2004) 143-150
35. 15N-labeled arginine. Biochemistry 43 (2004) 12809-12818. Analysis of dynamic behavior of a large protein using isotope-edited FTIR.
36. Tanimoto T., Shibata M., Belenky M., Herzfeld J., and Kandori H. Altered hydrogen bonding of Arg82 during the proton pump cycle of bacteriorhodopsin: a low temperature polarized FTIR spectroscopic study. Biochemistry 43 (2004) 9439-9447. Demonstration of site-specific labeling of a large membrane protein and the analysis that such a labeling strategy facilitates.
37. Bergo V., Mamaev S., Olejnik J., and Rothschild K.J. Methionine changes in bacteriorhodopsin detected by FTIR and cell-free selenomethionine substitution. Biophys J 84 (2003) 960-966. An elegant demonstration of the power of isotope-edited FTIR to clarify spectral assignments in a large membrane system.
38. Zanni M.T., and Hochstrasser R.M. Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures. Curr Opin Struct Biol 11 (2001) 516-522
39. Mukherjee P., Krummel A.T., Fulmer E.C., Kass I., Arkin I.T., and Zanni M.T. Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy. J Chem Phys 120 (2004) 10215-10224. The first 2D IR study of a membrane protein.
40. + exchange and it utility as probe of solvent exposure in proteins.
41. + exchange in a large membrane system.
42. Rigler P., Ulrich W.P., Hovius R., Ilegems E., Pick H., and Vogel H. Downscaling Fourier transform infrared spectroscopy to the micrometer and nanogram scale: secondary structure of serotonin and acetylcholine receptors. Biochemistry 42 (2003) 14017-14022. A powerful demonstration of the sensitivity of FTIR spectroscopy whereby the authors present spectra that are collected on nanogram amounts of large membrane proteins.
43. Kochendoerfer G.G., Clayton D., and Becker C. Chemical synthesis approaches to the engineering of ion channels. Protein Pept Lett 12 (2005) 737-741
44. Clayton D., Shapovalov G., Maurer J.A., Dougherty D.A., Lester H.A., and Kochendoerfer G.G. Total chemical synthesis and electrophysiological characterization of mechanosensitive channels from Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci USA 101 (2004) 4764-4769. The authors present the total synthesis and functional characterization of two complete membrane proteins, thereby pushing the envelope of chemical synthesis to systems that were considered beyond the synthetic range. This expands the applicable range of isotope-edited FTIR considerably.
45. Mamaev S., Olejnik J., Olejnik E.K., and Rothschild K.J. Cell-free N-terminal protein labeling using initiator suppressor tRNA. Anal Biochem 326 (2004) 25-32
46. Cremeens M.E., Fujisaki H., Zhang Y., Zimmermann J., Sagle L.B., Matsuda S., Dawson P.E., Straub J.E., and Romesberg F.E. Efforts toward developing direct probes of protein dynamics. J Am Chem Soc 128 (2006) 6028-6029
47. Arbely E., Khattari Z., Brotons G., Akkawi M., Salditt T., and Arkin I.T. A highly unusual palindromic transmembrane helical hairpin formed by SARS coronavirus E protein. J Mol Biol 341 (2004) 769-779