Abstract
Experimentalists interested in obtaining spectroscopic measurements of membrane protein secondary structure must keep in mind one general critical issue: the measurements must be reliable and specific enough to help distinguish between competing models of structure or function. An example of how this issue plays itself out can be seen in a series of papers beginning with that of Jap et al. (1983), in which it was proposed that some of the images in the in-plane electron diffraction map of bacteriorhodopsin may be due to transmembrane β-sheets instead of helices. This proposal was supported by circular dichroism (CD) and infrared (IR) measurements of secondary structures. The calculated helix content was only about 50%, and β-sheet content was about 20%. The investigators carefully corrected for differential light scattering in their CD measurements, but (according to subsequent studies) did not correct for absorption flattening effects. IR spectra were clearly not consistent with the hypothesis that the protein was 80% helix. The amide I maximum was at about 1,686 cm−1, while an 80% helical protein should have an amide I maximum at about 1,652 cm−1. Other CD results by Wallace and Mao (1984) that corrected for the absorption flattening effects did not support the β-sheet hypothesis. Their calculated helix content was about 80%. However, this calculation included a normalization of the results to correct for what was assumed to be an inaccurate determination of protein concentration. The data upon which it was based was actually similar to those obtained by Jap et al. (1983). Glaeser and Jap (1985) subsequently made a convincing argument that the normalization procedure was not valid. Nevertheless, in the face of recent evidence, Glaeser et al. (1991) subsequently acknowledged that all of the transmembrane segments are clearly helical and that their β-sheet hypothesis was wrong.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bazzi, M., and Woody, R. W. (1985) Oriented secondary structure in integral membrane proteins. Biophys. J. 48: 957–966.
Berjot, M., Marx, J., and Alix, A.J.P. (1987) The determination of the secondary structure of proteins from the Raman amide I band: the reference intensity profiles method. J. Raman Spec. 18: 289–300.
Bolotina, I. A., Chekhov, V. O., Lugauskas, V. Y., and Ptitsyn, O. B. (1980) Determination of the secondary structure of proteins from the circular dichroism spectra. II. Consideration of the contribution of 0-bends. Mol. Biol. (Mosc.) 14: 709–715.
Bolotina, I. A., Chekhov, V. O., Lugauskas, V. Y., and Ptitsyn, O. B. (1981) Determination of the secondary structure of proteins from the circular dichroism spectra. III. Protein-derived reference spectra for antiparallel and parallel 0-structures. Mol. Biol. (Mosc.) 15: 130–137.
Brahms, S., and Brahms, J. (1980) Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J. Mol. Biol. 138: 149–178.
Braiman, M. S., Mogi, T., Marti, T., Stern, L. J., Hackett, N. R., Chao, B. H,. Khorana, H. G., and Rothschild, K. J. (1988a) Vibrational spectroscopy of bacteriorhodopsin mutants: I. Tyrosine-185 protonates and deprotonates during the photocycle. Proteins Struct. Funct. Genet. 3: 219–229.
Braiman, M. S., Mogi, T., Marti, T., Stern, L. J., Khorana, H. G., and Rothschild, K. J. (1988b) Vibrational spectroscopy of bacteriorhodopsin mutants: light-driven protein transport involves protonation changes of aspartic acid residues 85, 96, and 212. Biochemistry 27: 8516–8520.
Braiman, M. S. and Rothschild, K. J. (1988) Fourier transform infrared techniques for probing membrane protein structure. Annu. Rev. Biophys. Biophys. Chem. 17: 541–570.
Bussian, B. M., and Sander, C. (1989) How to determine protein secondary structure in solution by Raman spectroscopy: practical guide and test case DNase I. Biochemistry 28: 4271–4277.
Byler, M., and Susi, H. (1986) Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25: 469–487.
Cascio, M., Gogol, E., and Wallace, B. A. (1990) The secondary structure of gap junctions. J. Biol. Chem. 265: 2358–2364.
Chang, C. T., Wu, C. S., and Yang, J. T. (1978) Circular dichroic analysis of protein conformation: inclusion of the ß-turns. Anal. Biochem. 92: 13–31.
Chirgadze, Y. N., Shestopalov, B. V., and Venyaminov, S. Y. (1973) Intensities and other spectral parameters of infrared amide bands of polypeptides in the ß-and random forms. Biopolymers 12: 1337 1351.
Chirgadze, Y. N., and Brazhnikov, E. V. (1974) Intensities and other spectral parameters of infrared amide bands of polypeptides in the a-helical form. Biopolymers 13: 1701–1712.
Compton, L. A., and Johnson, W. C. Jr. (1986) Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication. Anal. Biochem. 155: 155–167.
Dailey, H. A., and Strittmatter, P. (1978) Structural and functional properties of the membrane binding segment of cytochrome 6 5. J. Biol. Chem. 253: 8203–8209.
Dong, A., Huang, P., and Caughey, W. S. (1990) Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 29: 3303–3308.
Dousseau, F., and Pézolet, M. (1990) Determination of the secondary structure content of proteins in aqueous solutions from their amide I and amide II infrared bands. Comparison between classical and partial least-squares methods. Biochemistry 29: 8771–8779.
Draheim, J. E., Gibson, N. J., and Cassim, J. Y. (1991) Dramatic in situ conformational dynamics of the transmembrane protein bacteriorhodopsin. Biophys. J. 60: 89–100.
Dunker, A. K., Fodor, S., and Williams, R. W. (1982) Lipid dependent structural changes of an amphomorphic membrane protein. Biophys. J. 37: 201–203.
Eisele, J. L., and Rosenbusch, J. P. (1990) In vitro folding and oligomerization of a membrane protein. J. Biol. Chem. 265: 10217–10220.
Eckert, K., Grosse, R., Malur, J., and Repke, K.R.H. (1977) Calculation and use of protein-derived conformation related spectra for the estimate of the secondary structure of proteins from their infrared spectra. Biopolymers 16: 2549–2563.
Earnest, T. N., Herzfeld, J., and Rothschild, K. J. (1990) Polarized FTIR of bacteriorhodopsin: transmembrane a-helices are resistant to hydrogen-deuterium exchange. Biophys. J. 58: 1539–1546.
Fodor, S.P.A., Dunker, A. K., Ng, Y. C., Carsten, D., and Williams, R. W. (1981) Lipid-tail group dependent structure of the fd gene 8 protein. In: Bacteriophage Assembly. New York: Alan R. Liss, Inc., pp. 441–455.
Fogarasi, G., and Pulay, P. (1985) Ab initio calculation of force fields and vibrational spectra. In: Vibrational Spectra and Structure: a Series of Advances, edited by J. R. Durig. New York: Elsevier, vol. 14, pp. 125–219.
Fong, T. M., and McNamee, M. G. (1987) Stabilization of acetylcholine receptor secondary structure by cholesterol and negatively charged phospholipids in membranes. Biochemistry 26: 38713880.
Frisch, M. J., Head-Gordon, M., Schlegel, H. B. Raghavachari, K., Binkley, J. S., Gonzalez, C., Defrees, D. J., Fox, D. J., Whiteside, R. A., Seeger, R. C., Melius, F., Baker, J., Martin, R. L., Kahn, L. R., Stewart, J.J.P., Fluder, E. M., Topiol, S., and Pople, J. A. (1989) Gaussian 90. Pittsburgh: Gaussian, Inc.
Glaeser, R. M., Downing, K. H., and Jap, B. K. (1991) What spectroscopy can still tell us about the secondary structure of bacteriorhodopsin. Biophys. J. 59: 934–938.
Glaeser, R. M., and Jap, B. K. (1985) Absorption flattening in the circular dichroism spectra of small membrane fragments. Biochemistry 24: 6398–6401.
Goormaghtigh, E., Cabiaux, V., and Ruysschaert, J. M. (1990) Secondary structure and dosage of soluble and membrane proteins by attenuated total reflection Fourier-transform infrared spectroscopy on hydrated films. Eur. J. Biochem. 193: 409–420.
Grosse, R., Malur, J., and Repke, K.R.H. (1972) Determination of secondary structures in isolated or membrane proteins by computer curve-fitting analysis of infrared and circular dichroic spectra. FEBS Lett. 25: 313–315.
Han, S., Ching, Y., Hammes, S. L., and Rousseau, D. L. (1991) Vibrational structure of the formyl group on heme A. Biophys. J. 60: 45–52.
He, W.-Z., Newell, W. R., Haris, P. I., Chapman, D. and Barber, J. (1991) Protein secondary structure of the isolated photosystem II reaction center and conformational changes studied by Fourier transform infrared spectroscopy. Biochemistry 30: 4552–4559.
Hennessey, J. P., Jr., and Johnson, W. C., Jr. (1981) Information content in the circular dichroism of proteins. Biochemistry 20: 1085–1094.
Hennessey, J. P., Jr., and Johnson, W. C., Jr. (1982) Experimental errors and their effect on analyzing circular dichroism spectra of proteins. Anal. Biochem. 125: 177–188.
Herzyk, E., Owen, J. S., and Chapman, D. (1988) The secondary structure of apolipoproteins in human HDL3 particles after chemical modification of their tyrosine, lysine, cysteine or arginine residues. A Fourier transform infrared spectroscopy study. Biochim. Biophys. Acta 962: 131–142.
Heyn, M. P. (1989) Circular dichroism for determining secondary structure and state of aggregation of membrane proteins. Methods Enzymol. 172: 575–584.
Horwitz, J., and Bok, D. (1987) Conformational properties of the main intrinsic polypeptide (MIP26) isolated from lens plasma membranes. Biochemistry 26: 8092–8098.
Hunt, J. F., Earnest, T. N., Bousche, O., Engelman, D. M., and Rothschild, K. J. (1993) The origin of the anomalous amide I vibrational frequency of purple membrane. Biophys. J. 64: A293.
Jap, B. K., Maestre, M. F., Hayward, S. B., and Glaeser, R. M. (1983) Peptide-chain secondary structure of bacteriorhodopsin. Biophys. J. 43: 81–89.
Kahan, I., Epand, R. M., and Moscarello, M. A. (1988) The secondary structure of a membrane-embedded peptide from the carboxy terminus of lipophilin as revealed by circular dichroism. Biochim. Biophys. Acta 952: 230–237.
Kalnin, N. N., Baikalov, I. A., and Venyaminov, S. Y. (1990) Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. III. Estimation of the protein secondary structure. Bio-polymers 30: 1273–1280.
Khan, M. Y., Villanueva, G., and Newman, S. A. (1989) On the origin of the positive band in the farultraviolet circular dichroic spectrum of fibronectin. J. Biol. Chem. 264: 2139–2142.
Kleffel, B., Garavito, R. M., and Baumeister, W. (1985) Secondary structure of a channel-forming protein: porin from E. coli outer membranes. EMBO J. 4: 1589–1592.
Krimm, S., and Bandekar, J. (1986) Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. in Ada. Protein Chem. 38: 183–364.
Krimm, S., and Dwivedi, A. M. (1982) Infrared spectrum of the purple membrane: clue to a proton conduction mechanism? Science 216: 407–408.
Lawson, C. L., and Hanson, F. J. (1974) Solving Least Squares Problems. Englewood Cliffs, NJ: Prentice-Hall, Inc.
Lee, D. C., Haris, P. I., Chapman, D., and Mitchell, R. C. (1990) Determination of protein secondary structure using factor analysis of infrared spectra. Biochemistry 29: 9185–9193.
Levitt, M., and Greer, J. (1977) Automatic identification of secondary structure in globular proteins. J. Mol. Biol. 114: 181–293.
Lippert, J. L., Tyminski, D., and Desmeules, P. J. (1976) Determination of the secondary structure of proteins by laser Raman spectroscopy. J. Am. Chem. Soc. 98: 7075–7080.
Manavalan, P., and Johnson, W. C. Jr. (1987) Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal. Biochem. 167: 76–85.
Mao, D., and Wallace, B. A. (1984) Differential light scattering and absorption flattening optical effects are minimal in the circular dichroism spectra of small unilamellar vesicles. Biochemistry 23: 2667 2673.
Mao, D., Wachter, E., and Wallace, B. A. (1982) Folding of the mitochondrial proton adenosinetriphos-phatase proteolipid channel in phospholipid vesicles. Biochemistry 21: 4960–4968.
Mielke, D. L., and Wallace, B. A. (1988) Secondary structural analyses of the nicotinic acetylcholine receptor as a test of molecular models. J. Biol. Chem. 263: 3177–3182.
Mims, M. P., Soma, M. R., and Morrisett, J. D. (1990) Effect of particle size and temperature on the conformation and physiological behavior of apolipoprotein E bound to model lipoprotein particles. Biochemistry 29: 6639–6647.
Mitchell, R. C., Haris, P. I., Fallowfield, C., Keeling, D. J., and Chapman, D. (1988) Fourier transform infrared spectroscopic studies on gastric H+/K+-ATPase. Biochim. Biophys. Acta 941: 31–38.
Nabedryk, E., Garavito, R. M., and Breton, J. (1988) The orientation of 0-sheets in porin. A polarized Fourier transform infrared spectroscopic investigation. Biophys. J. 53: 671–676.
Palmö, K., Pietilä, L.-O, and Krimm, S. (1991) Construction of molecular mechanics energy functions by mathematical transformation of ab initio force fields and structures. J. Comp. Chem. 12: 385–390.
Pemberton, J. E., Sobocinski, R. L., Bryant, M. A., and Carter, D. A. (1990) Raman spectroscopy using charge-coupled device detection. Spectroscopy 5: 26–36.
Peterson, G. L. (1977) A simplification of the protein assay method of Lowry et al which is more generally applicable. Anal. Biochem. 83: 346–356.
Pézolet, M., Pigeon-Gosselin, M., and Coulombe, L. (1976) Laser Raman investigation of the conformation of human immunoglobulin G. Biochim. Biophys. Acta 453: 502–512.
Provencher, S. W., and Glöckner, J. (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20: 33–37.
Rath, P., Bousché, O., Merril, A. R., Cramer, W. A., and Rothschild, K. J. (1991) Fourier transform infrared evidence for a predominantly alpha-helical structure of the membrane bound channel forming COOH-terminal peptide of colicin EI. Biophys. J. 59: 516–522.
Reich, C., Maestre, M. F., Edmondson, S., and Gray, D. M. (1980) Circular dichroism and fluorescence-detected circular dichroism of deoxyribonucleic acid and poly[d(A — C) d(G — T)] in ethanolic solutions: a new method for estimating circular intensity differential scattering. Biochemistry 19: 5208–5213.
Rial, E., Muga, A., Valpuesta, J. M., Arrondo, J.L.R., and Goni, F. M. (1990) Infrared spectroscopic studies of detergent-solubilized uncoupling protein from brown-adipose-tissue mitochondria. Eur. J. Biochem. 188: 83–89.
Rodriguez-Vico, R., Martinez-Cayuela, M., Garcia-Peregrin, E., and Ramirez, H. (1989) A procedure for eliminating interferences in the Lowry method of protein determination. Anal. Biochem. 183: 275–278.
Rolka, K., Erne, D., and Schwyzer, R. (1986) Membrane structure of substance P II. Secondary structure of substance P, [9-leucine]substance P, and shorter segments in 2,2,2-trifluoroethanol, methanol, and on liposomes studied by circular dichroism. Hela. Chim. Acta 69: 1798–1806.
Sarver Jr., R. W., and Krueger, W. C. (1991) Protein secondary structure from Fourier transform infrared spectroscopy: a data base analysis. Anal. Biochem. 194: 89–100.
Surewicz, W. K., and Mantsch, H. H. (1988) New insight into protein secondary structure from resolution-enhanced infrared spectra. Biochim. Biophys. Acta 952: 115–130.
Surewicz, W. K., Moscarello, M. A., and Mantsch, H. H. (1987) Fourier transform infrared spectroscopic investigation of the interaction between myelin basic protein and dimyristoylphosphatidylglycerol bilayers. Biochemistry 26: 3881–3886.
Susi, H., and Byler, M. (1983) Protein structure by Fourier transform infrared spectroscopy: second derivative spectra. Biochem. Biophys. Res. Commun. 115: 391–397.
Susi, H., and Byler, M. (1986) Resolution-enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol. 130: 290–311.
Susi, H., and Byler, M. (1987) Fourier transform infrared study of proteins with parallel ß-chains. Arch. Biochem. Biophys. 258: 465–469.
Susi, H., and Byler, M. (1988) Fourier deconvolution of the amide I Raman band of proteins as related to conformation. Appl. Spec. 42: 819–826.
Thomas, G. J., Jr., and Agard, D. A. (1984) Quantitative analysis of nucleic acids, proteins, and viruses by Raman band deconvolution. Biophys. J. 46: 763–768.
Tinoco, I., Jr., Maestre, M. F., and Bustamante, C. (1983) Circular dichroism in samples which scatter light. Trends Biochem. Sci. 8: 41–44.
Torii, H., and Tasumi, M. (1992) Model calculations on the amide-I infrared bands of globular proteins. J. Chem. Phys. 96: 3379–3387.
van Stokkum, I.H.M., Spoelder, H.J.W., Bloemendal, M., van Grondelle, R., and Groen, F.C.A. (1990) Estimation of protein secondary structure and error analysis from circular dichroism spectra. Anal. Biochem. 191: 110–118.
Venyaminov, S. Y., Baikalov, I. A., Wu, C.-S.C., and Yang, J. T. (1991) Some problems of CD analyses of protein conformation. Anal. Biochem. 198: 250–255.
Venyaminov, S. Y., and Kalnin, N. N. (1990a) Quantitative IR spectrophotometry of peptide compounds in water (H20) solutions. I. Spectral parameters of amino acid residue absorption bands. Bio-polymers 30: 1243–1257.
Venyaminov, S. Y., and Kalnin, N. N. (1990b) Quantitative IR spectrophotometry of peptide compounds in water (H20) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in alpha-, beta-, and random coil conformations. Biopolymers 30: 1259–1271.
Vogel, H., and Jähnig, F. (1986a) Models for the structure of outer-membrane proteins of Esche chia coli derived from Raman spectroscopy and prediction methods. J. Mol. Biol. 190: 191–199.
Vogel, H., and Jähnig, F. (1986b) The structure of mellitin in membranes. Biophys. J. 50: 573–582.
Vogel, H., Wright, J. K., and Jähnig, F. (1985) The structure of the lactose permease derived from Raman spectroscopy and prediction methods. EMBO J. 4: 3625–3631.
Wallace, B. A., and Mao, D. (1984) Circular dichroism analyses of membrane proteins: an examination of differential light scattering and absorption flattening effects in large membrane vesicles and membrane sheets. Anal. Biochem. 142: 317–328.
Weaver, J., and Williams, R. W. (1990) Amide III frequencies for Ala-X peptides depend on the X amino acid size. Biopolymers 30: 593–598.
Werner, P. K., and Reithmeier, R.A.F. (1985) Molecular characterization of the human erythrocyte anion transport protein in octyl glucoside. Biochemistry 24: 6375–6381.
Williams, R. W., Cutrera, T., Dunker, A. K., and Peticolas, W. L. (1980a) The estimation of protein secondary structure by laser Raman spectroscopy from the amide III intensity distribution. FEBS Lett. 115: 306–308.
Williams, R. W., Dunker, A. K., and Peticolas, W. L. (19806) A new method for determining protein secondary structure by laser Raman spectroscopy applied to fd phage. Biophys. J. 32: 232–234.
Williams, R. W., and Dunker, A. K. (1981) Determination of the secondary structure of proteins from the amide I band of the laser Raman spectrum. J. Mol. Biol. 152: 783–813.
Williams, R. W. (1983) Estimation of protein secondary structure from the laser Raman amide I spectrum. J. Mol. Biol. 166: 581–603.
Williams, R. W. (1986) Protein secondary structure analysis using Raman amide I and amide III spectra. Methods Enzymol. 130: 311–331.
Williams, R. W., Lowrey, A. H., and Weaver, J. (1990) Relation between calculated amide frequencies and solution structure in Ala-X peptides. Biopolymers 30: 599–608.
Williams, R. W., McIntyre, J. O., Gaber, B. P., and Fleischer, S. (1986) The secondary structure of calcium pump protein in light sarcoplasmic reticulum and reconstituted in a single lipid component as determined by Raman spectroscopy. J. Biol. Chem. 261: 14520–14524.
Williams, R. W., and Weaver, J. (1990) Secondary structure of substance P bound to liposomes, in organic solvents, and in solution from Raman and CD spectroscopy. J. Biol. Chem. 265: 2505–2513.
Williams, R. W., Starman, R., Taylor, K.M.P., Gable, K., Beeler, T. Zasloff, M., and Covell, D. (1990) Raman spectroscopy of synthetic antimicrobial frog peptides magainin 2a and PGLa. Biochemistry 29: 4490–4496.
Wu, C.-S.C., and Chen, G. C. (1989) Adsorption of proteins onto glass surfaces and its effect on the intensity of circular dichroism spectra. Anal. Biochem. 177: 178–182.
Wu, J. R., and Lentz, B. R. (1991) Fourier transform infrared spectroscopic study of Cat+ and membrane-induced secondary structural changes in bovine prothrombin fragment 1. Biophys. J. 60: 70–80.
Yager, P., Chang, E. L., Williams, R. W., and Dalziel, A. W. (1984) The secondary structure of acetylcholine receptor reconstituted in a single lipid component as determined by Raman spectroscopy. Biophys. J. 45: 26–28.
Yang, J. T., Wu, C.S.C., and Martinez, H. M. (1986) Calculation of protein conformation from circulation dichroism. Methods Enzymol. 130: 208–269.
Yu, N.-T. (1977) Raman spectroscopy: a conformational probe in biochemistry. CRC Crit. Rev. Biochem. 4: 229–280.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 American Physiological Society
About this chapter
Cite this chapter
Williams, R.W. (1994). Experimental Determination of Membrane Protein Secondary Structure Using Vibrational and CD Spectroscopies. In: White, S.H. (eds) Membrane Protein Structure. Methods in Physiology Series. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7515-6_8
Download citation
DOI: https://doi.org/10.1007/978-1-4614-7515-6_8
Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-7515-6
eBook Packages: Springer Book Archive