Determination of Soluble and Membrane Protein Structure by Fourier Transform Infrared Spectroscopy (original) (raw)

References

• Alvarez, J., Lee, D. C., Baldwin, S. A., and Chapman, D., 1987a, Fourier-transform infrared spectroscopy study of the structure and conformational changes of the human erythrocyte glucose transporter, J. Biol. Chem. 262:3502–3509.
  PubMed CAS Google Scholar
• Ameloot, M., 1992, Laplace deconvolution of fluorescence decay surfaces, Methods Enzymol. 210:279–304.
  CAS Google Scholar
• Arrondo, J. L. R., Muga, A., Castresana, J. and Goñi, F. M., 1993, Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy, Prog. Biophys. Molec. Biol. 59:23–56.
  CAS Google Scholar
• Baenziger, J. E., Miller, K. W., and Rothschild, K. J., 1992a, Incorporation of the nicotinic acetylcholine receptor into planar multilamellar films: Characterization by fluorescence and Fourier transform infrared difference spectroscopy, Biophys. J. 61:983–992.
  PubMed CAS Google Scholar
• Baenziger, J. E., Miller, K. W., McCarthy, M. P., and Rothschild, K. J., 1992b, Probing conformational changes in the nicotinic acetylcholine receptor by Fourier-transform infrared difference spectroscopy, Biophys. J. 62:64–66.
  PubMed CAS Google Scholar
• Baenzinger, J. E., Miller, K. W., and Rothschild, K. J., 1993, Fourier-transform infrared difference spectroscopy of the nicotinic acetylcholine receptor: Evidence for specific protein structural changes upon desensitization, Biochemistry 32:5448–5454.
  Google Scholar
• Barth, A., Kreutz, W., and Mäntele, W., 1990, Molecular changes in the sarcoplasmic reticulum calcium ATPase during catalytic activity. A Fourier transform infrared (FTIR) study using photolysis of caged ATP to trigger the reaction cycle, FEBS Lett. 277:147–150.
  PubMed CAS Google Scholar
• Barth, A., Mäntele, W., and Kreutz, W., 1991, Infrared spectroscopy signals arising from ligand binding and conformational changes in the catalytic cycle of sarcoplasmic reticulum calcium ATPase, Biochim. Biophys. Acta 1057:115–123.
  PubMed CAS Google Scholar
• Benson, E. S., Hallaway, B. E., and Lumry, R. W., 1964, Deuterium-hydrogen exchange analaysis of pH-dependent transitions in bovine plasma albumin, J. Biol. Chem. 239:122–129.
  PubMed CAS Google Scholar
• Bentley, G. A., Delepierre, M., Dobson, C. M., Wedin, R. E., Mason, S. A. and Poulsen, F. M., 1983, Exchange of individual hydrogens for a protein in a crystal and in solution, J. Mol. Biol. 170:243–247.
  PubMed CAS Google Scholar
• Braiman, M. S., and Rothschild, K. J., 1988, Fourier transform infrared techniques for probing membrane protein structure, Ann. Rev. Biophys. Chem. 17:541–570.
  CAS Google Scholar
• Brandi, C. J., and Deber, C. M., 1986, Hypothesis about the membrane-buried proline residues in transport proteins, Proc. Natl. Acad. Sci. U.S.A. 83:917–921.
  Google Scholar
• Breton, J., and Nabedryk, E., 1984, Transmembrane orientation for alpha-helices and the organization of chlorophylls in photosynthetic pigment-protein complexes, FEBS Lett. 176:355–359.
  CAS Google Scholar
• Buchet, R., Varga, S., Seilder, N. W., Molnar, E., and Martonosi, A., 1991, Polarized infrared attenuated total reflectance spectroscopy of the Ca2+-ATPase of the sarcoplasmic reticulum, Biochim. Biophys. Acta 1068:201–216.
  PubMed CAS Google Scholar
• Burget, U., and Zundel, G., 1987, Glutamic acid-dihydrogen phosphate hydrogen-bonded networks: Their proton polarizability as a function of cations present, Biophys. J. 52:1065–1070.
  PubMed CAS Google Scholar
• Cabiaux, V., Brasseur, R., Wattiez, R., Falmagne, P., Ruysschaert, J. M., and Goormaghtigh, E., 1989a, Secondary structure of diphtheria toxin and its fragments interacting with acidic liposomes studied by polarized infrared spectroscopy, J. Biol. Chem., 264: 4928–4938.
  PubMed CAS Google Scholar
• Cabiaux, V., Goormaghtigh, E., Wattiez, R., Falmagne, P., and Ruysschaert, J. M., 1989b, Secondary structure of diphtheria toxin interacting with asolectin liposomes: An infrared spectroscopy study, Biochimie 71:153–158.
  PubMed CAS Google Scholar
• Careri, G., Gratton, E., Yang, P. H., and Rupley, J. A., 1980, Correlation of IR spectroscopic, heat capacity, diamagnetic susceptibility and enzymatic measurements on lysozyme powder, Nature 284:572–573.
  PubMed CAS Google Scholar
• Carpenter, J. F., and Crowe, J. H., 1989, An infrared spectroscopic study of the interactions of carbohydrates with dried proteins, Biochemistry 28:3916–3922.
  PubMed CAS Google Scholar
• Challou, N., Goormaghtigh, E., Cabiaux, V., Conrath, K., and Ruysschaert, J. M., 1994, Sequence and structure of the membrane-associated peptide of glycophorin A. Biochemistry 33:6902–6910.
  PubMed CAS Google Scholar
• Chang, C-W., Sekiya, N., and Yoshihara, K., 1991, O-H stretching vibration in Fourier-transform difference infrared spectra of bacteriorhodopsin, F.E.B.S. Lett. 287:157–159.
  CAS Google Scholar
• Chapman, D., Gomez-Fernandez, J. C., Goñi, F. M., and Barnard, M., 1980, Difference infrared spectroscopy of aqueous model and biological membranes using an infrared data station, J. Biochem. Biophys. Methods 2:315–323.
  PubMed CAS Google Scholar
• Chetverin, A. B., and Brazhikov, E. V., 1985, Do sodium and potassium forms of Na, K-ATPase differ in their secondary structure, J. Biol. Chem. 260:7817–7819.
  PubMed CAS Google Scholar
• Chiacchiera, S. M., and Kosower, E. M., 1992, Deuterium exchange on micrograms of proteins by attenuated total reflection Fourier-transform infrared spectroscopy on silver halide fiber, Anal. Biochem. 201:43–47.
  PubMed CAS Google Scholar
• Combelas, P., Garrigou-Lagrange, C., and Lascombe, J., 1974, Etude par spectroscopie infrarouge de la transformation hélice-chaîne statistique des polypetides. II. Etude de l’interaction de quelques polypetides à chaînes latérales polaires avec l’acide trifluoroacétique, Biopolymers 13:577–589.
  CAS Google Scholar
• Cortijo, M., Alonso, A., Gomez-Fernandez, J. C., and Chapman, D., 1982, Instrinsic protein-lipid interactions: Infrared spectroscopic studies of Gramicidin A, bacteriorhodopsin and Ca++AT-Pase in Biomembranes and reconstituted systems, J. Mol. Biol. 157:597–618.
  PubMed CAS Google Scholar
• Crowe, J. H., and Crowe, L. M., 1986, Water and carbohydrate interactions with membranes: studies with infrared spectroscopy and differential scanning calorimetry methods, Methods. Enzymol. 127:693–703.
  Google Scholar
• Crowe, J. H., Crowe, L. M., and Chapman, D., 1984, Infrared spectroscopy studies on the interactions of water and carbohydrates with a biological membrane, Arch. Biochem. Biophys. 232:400–407.
  PubMed CAS Google Scholar
• Crowe, J. H., Crowe, L. M., and Chapman, D., 1985, Interaction of carbohydrates with dry dipalmitoylphosphatidylcholine, Arch. Biochem. Biophys. 236:289–296.
  PubMed CAS Google Scholar
• Crowe, J. H., Spargo, B. J., and Crowe, L. M., 1987, Preservation of dry liposomes does not require retention of residual water, Proc. Natl. Acas. Sci. U.S.A. 84:1537–1540.
  CAS Google Scholar
• De Jongh, H. H. J., Killian, A., and de Kruijff, B., 1992, A water-lipid interface induces a highly dynamic folded state in apocytochrome c and cytochrome c which may represent a common folding intermediate, Biochemistry 31:1636–1643.
  PubMed Google Scholar
• Demel, R., Goormaghtigh, E., and de Kruijff, B., 1990, Lipid and peptide specificities in signal peptide-lipid interactions in model membranes, Biochim. Biophys. Acta, 1027: 155–162.
  PubMed CAS Google Scholar
• Dempsey, C. E., and Butler, G. S., 1992, Helical structure and orientation of melittin in dispersed phospholipid membranes from amide exchange analysis in situ, Biochemistry 31:11973–11977.
  PubMed CAS Google Scholar
• Dollinger, G., Eisenstein, L., Lin, S-L., Nakanishi, K., and Termini, J., 1986, Fourier transform infrared difference spectroscopy of bacteriorhodopsin and its photoproducts regenerated with deuterated tyrosine, Biochemistry 25:6524–6533.
  PubMed CAS Google Scholar
• Dollinger, G., Eisenstein, L., Lin, S-L., Nakanishi, K., Odashima, K. and Termini, J., 1986, bacteriorhodopsin: Fourier-transform infrared difference methods for studies of protonation of carboxyl groups, Methods Enzymol. 127:649–662.
  PubMed CAS Google Scholar
• Dong, A., Huang, P., and Caughey, W. S., 1990, Protein secondary structure in water from second-derivative amide I infrared spectra, Biochemistry 29:3303–3308.
  PubMed CAS Google Scholar
• Dong, A., Huang, P., and Caughey, W. S., 1992, Redox-dependent changes in ß-extended chain and turn structures of cytochrome c in water solution determined by second derivative amide I infrared spectra, Biochemistry 31:182–189.
  PubMed CAS Google Scholar
• Döring, O., and Böttger, M., 1992, Effect of D2O on maize plasmalemma ATPase and electron transport coupled proton pumping, Biochem. Biophys. Res. Commun. 182:870–876.
  PubMed Google Scholar
• Dousseau, F., Therrien, M., and Pézolet, M., 1989, On hte spectral subtraction of water from the FT-IR spectra of aqueous solutions of proteins, Appl. Spectroscopy 40:538–542.
  Google Scholar
• Downer, N. W., Bruckman, T. J., and Hazzard, J., 1986, Infrared spectroscopic study of photoreceptor membrane and purple membrane: Protein secondary structure and hydrogen deuterium exchange, J. Biol. Chem. 261:3640–3647.
  PubMed CAS Google Scholar
• Dunker, A. K., 1982, Proton motive force tranducer and its role in proton pumps, proton engine, tabacco mosaic virus assembly and hemoglobin allosterism, J. Theor. Biol. 97:95–127.
  PubMed CAS Google Scholar
• 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.
  PubMed CAS Google Scholar
• El Antri, S., Sire, O., and Alpert, B., 1990, Relationship between protein/solvent proton exchange and progressive conformation and fluctuation changes in hemoglobin, Eur. J. Biochem. 191:163–168.
  PubMed CAS Google Scholar
• Engelhard, M., Gerwert, K., Hess, B., Kreutz, W., and Siebert, F., 1985, Light-driven protonation changes of internal aspartic acids of bacteriorhodopsin: An investigation by static and time-resolved infrared difference spectroscopy using (4-13C) Aspartic acid labeled purple membrane, Biochemistry 24:400–407.
  PubMed CAS Google Scholar
• Englander, S. W., and Kallenbach, N. R., 1984, Hydrogen exchange and structral dynamics of protein and nucleic acids, Quarterly Review Biophysics 16:521–655.
  Google Scholar
• Fabian, H., Nauman, D., Misselwitz, R., Ristau, O., Gerlach, D., and Weife, H., 1992, Secondary structure of streptokinase in aqueous solution: A Fourier transform infrared spectroscopic study, Biochemistry 31:3532–3538.
  Google Scholar
• Fettiplace, R., and Haydon, D. A., 1980, Water permeability of lipid membranes, Physiol. Rev. 60:510–550.
  PubMed CAS Google Scholar
• Fink, D. J., and Gendreau, R. M., 1984, Quantitative surface studies of protein adsorption by infrared spectroscopy: corrections for bulk concentrations, Anal. Biochem. 139:140–148.
  PubMed CAS Google Scholar
• Fink, D. J., Hutson, T. B., Chittur, K. K., and Genderau, R. M., 1987, Quantitative surface studies of protein adsorption by infrared spectroscopy. II. Quantification of adsorbed and bulk proteins, Anal. Biochem. 165:147–154.
  PubMed CAS Google Scholar
• Finkelstein, A., 1987, Water Movement trough Lipid Bilayers, Pores, and Plasma Membranes. Theory and reality, John Wiley&Sons, New York.
  Google Scholar
• Fraser, P. E., Nguyen, J. T., Surewicz, W. K., and Kirschner, D. A., 1991, pH-dependent structural transitions of Alzheimer amyloid peptides, Biophys. J. 60:1190–1201.
  PubMed CAS Google Scholar
• Fraser, P. E., Nguyen, J. T., Surewicz, W. K., and Mantsch, H. H., 1991, pH-dependent structural transitions of Alzheimer amyloid peptides, Biophys. J. 60:1190–1201.
  PubMed CAS Google Scholar
• Frauenfelder, H., and Gratton, E., 1986, Protein dynamics and hydration, Methods Enzymol. 127:207–216.
  PubMed CAS Google Scholar
• Frey, S., and Tamm, L. K., 1991, Orientation of melittin in phospholipid bilayers. A polarized attenuated total reflection infrared spectroscopy study, Biophys. J. 60:922–930.
  PubMed CAS Google Scholar
• Fringeli, U. P., 1981, A new crystalline phase of L-a-dipalmitoylphosphatidylcholine monohydrate, Biophys. J. 34:173–187.
  PubMed CAS Google Scholar
• Fringeli, U. P., and Günthard, H. H., 1981, Infrared membrane spectroscopy, in: Membrane Spectroscopy, (E. Grell ed.) pp 270–332, Springer-Verlag, Berlin.
  Google Scholar
• Fringeli, U. P., Apell, H. J., Fringeli, M., Lauger, P., 1989, Polarized infrared absorption of Na+/K+-ATPase studied by attenuated total reflection spectroscopy, Biochim Biophys Acta. 984:301–312.
  PubMed CAS Google Scholar
• Fritsch, J., Zundel, G., Hayd, A., and Maurer, M., 1984, Proton polarizability of hydrogen-bonded chains: an ab initio SCF calculation with a model related to the conducting system in bacteriorhodopsin, Chem. Phys. Lett. 107:65–69.
  CAS Google Scholar
• Gallagher, W., Tao, F., and Woodward, C., 1992, Comparison of hydrogen exchange rates for bovine pancreatic trypsin inhibitor in crystals and in solution, Biochemistry 31:4673–4680.
  PubMed CAS Google Scholar
• Gerwert, K., Souvigner, G., and Hess, B., 1990, Simultaneous monitoring of light-induced changes in protein side-group protonation, chromophore isomerization, and backbone motion of bacteriorhodopsin by time-resolved Fourier-transform infrared spectroscopy, Proc. Natl. Acad. Sci. U.S.A. 87:9774–9778.
  PubMed CAS Google Scholar
• Goormaghtigh, E., and Ruysschaert, J. M., 1990, Polarized attenuated total reflection spectroscopy as a tool to investigate the conformation and orientation of membrane components, in: Molecular Description of Biological Membranes by Computer-Aided Confromationazl Analysis (R. Brasseur, ed.), Vol. I, p. 285–329, CRC Press Inc., Boca Raton, Florida.
  Google Scholar
• 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.
  PubMed CAS Google Scholar
• Goormaghtigh, E., Cabiaux, V., De Meutter, J., Rosseneu, M., and Ruysschaert, J. M., 1993, Secondary structure of the particle associating domain of apolipoprotein B-100 in low-density lipoprotein by attenuated total reflection infrared spectroscopy, Biochemistry 32:6104–6110.
  PubMed CAS Google Scholar
• Goormaghtigh, E., De Meutter, J., Vanloo, B., Brasseur, R., Rosseneu, M., and Ruysschaert, J. M., 1989, Evaluation of the secondary structure of apo B100 in low density lipoprotein (LDL) by infrared spectroscopy, Biochim. Biophys. Acta 1006:147–150.
  PubMed CAS Google Scholar
• Goormaghtigh, E., Ruysschaert, J. M., and Scarborough, G. A., 1988, High-yield incorporation of the Neurospora plasma membrane H+ ATPase into proteoliposomes: Lipid requirement and secondary structure of the enzyme by IR spectroscopy, Prog. Clin. Biol. Res. 273:51–56.
  PubMed CAS Google Scholar
• Graziani, Y., and Livne, A., 1972, Water permeability of bilayer lipid membranes: Sterol-lipid interactions, J. Membr. Biol. 7:275–284.
  CAS Google Scholar
• Gregory, R. B., and Lumry, R., 1985, Hydrogen-exchange evidence for distinct structural classes in globular proteins, Biopolymers 24:301–326.
  PubMed CAS Google Scholar
• Halvorson, H. R., 1992, Padé-Laplace algorithm for sum of exponentials: selecting appropriate exponential model and initial estimates for exponential fitting, Methods Enzymol. 210:54–67.
  Google Scholar
• Haris, P. I., Coke, M., and Chapman, D., 1989, Fourier transform infrared spectroscopic investigation of rhodopsin structure and its comparison with bacteriorhodopsin, Biochim. Biophys. Acta 995:160–167.
  PubMed CAS Google Scholar
• Haris, P. I., Lee, D. C. and Chapman D. 1986, A Fourier transform infrared investigation of the structural differences between ribonuclease A and ribonuclease S, Biochim. Biophys. Acta 874:255–265.
  PubMed CAS Google Scholar
• Harrick, N. J., 1967, Internal Reflection Spectroscopy, John Wiley&Sons, New York.
  Google Scholar
• Heimburg, T., and Marsh, D., 1993, Investigation of secondary and tertiary structural changes of cytochrome c in complex with anionic lipids using amide hydrogen exchange measurements: An FTIR study, Biophys. J. 65:2408–2417.
  PubMed CAS Google Scholar
• Hodgmann, C. D., (ed.), 1952, Hanbook of Chemistry and Physics, pp. 2147–2148, Chemical Rubber, Cleveland, Ohio.
  Google Scholar
• Hofer, P., and Fringeli, U. P., 1979, Structural investigation of biological material in aqueous environment by means of infrared-ATR spectroscopy, Biophys. Struct. Mech. 6:67–80.
  PubMed CAS Google Scholar
• Holloway, P. W., and Buchheit, C., 1990, Topography of the membrane-binding domain of cytochrome b5 in lipids by Fourier-transform infrared spectroscopy, Biochemistry 29:9631–9637.
  PubMed CAS Google Scholar
• Kackson, M., Haris, P. I., and Chapman, D., 1991, Fourier-transform infrared spectroscopic studies of Ca2+-binding proteins, Biochemistry 30:9681–9686.
  Google Scholar
• Kakalis, L. T., and Baianu, I. C., 1988, Oxygen-17 and deuterium nuclear magnetic relaxation studies of lysozyme hydratation in solution: Field dispersion, concentration, pH/pD and protein activity dependences, Arch. Biochem. Biophys. 267:829–841.
  PubMed CAS Google Scholar
• Kauppinen, J. K., Moffat, D. J., Mantsch, H. H., and Cameron, D. G., 1981a, Fourier self-deconvolution: A method for resolving intrinsically overlapped bands, Appl. Spectrosc. 35:271–276.
  CAS Google Scholar
• Kim, K. S., and Woodward, C. K., 1993, Protein internal flexibility and global stability: Effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor, Biochemistry 32:9609–9613.
  PubMed CAS Google Scholar
• Kim, K. S., Fuchs, J. A., and Woodward, C. K., 1993, Hydrogen exchange identifies native-state motional domains important in protein folding, Biochemistry 32:9600–9608.
  PubMed CAS Google Scholar
• Kleffel, B., Garavito, R. M., Baumeister, W., and Rosenbusch, J. P., 1985, Secondary structure of a channel-forming protein: Porin from E. coli outer membranes, EMBO J. 4:1589–1592.
  PubMed CAS Google Scholar
• Knox, D. G., and Rosenberg, A., 1980, Fluctuations of protein structure as expressed in the distribution of hydrogen exchange rate constants, Biopolymers 19:1049–1068.
  PubMed CAS Google Scholar
• Korenstein, R., and Hess, B., 1977, Hydration effects on the photocycle of bacteriorhodopsin in thin layers of purple membrane, Nature 270:184–186.
  PubMed CAS Google Scholar
• Krasov, W. H., Han, L. R., and Munger, J. C., 1988, Measurements of 2H2O by IR absorbance in doubly labeled H2O studies of energy expenditure, Am. J. Physiol. 253: R174–R177.
  Google Scholar
• Kristof, W., and Zundel, G., 1982, Proton transfer and polarizability of hydrogen bonds formed between cysteine and lysine residues, Biopolymers 21:25–42.
  CAS Google Scholar
• Laiken, S., and Printz, M. P., 1970, Kinetic class analysis of hydrogen-exchange data, Biochemistry 9:1547–1553.
  PubMed CAS Google Scholar
• Lenk, T. J., Ratner, B. D., Gendreau, R. M., and Chittur, K. K., 1989, IR spectral changes of bovine serum albumin upon surface adsorption, J. Biomed. Mater. Res. 23:549–569.
  PubMed CAS Google Scholar
• Lin, S-L., Eisenstein, L., Govindjee, R., Konno, K., and Nakanishi, K., 1987, Deprotonation of tyrosines in bacteriorhodopsin as studied by Fourier transform infrared spectroscopy with deuterium and nitrate labeling, Biochemistry 26:8327–8331.
  PubMed CAS Google Scholar
• Loh, S. N., and Markley, J. L., 1994, Hydrogen bonding in proteins as studied by amide hydrogen D/H fractionation factors: Application to staphylococcal nuclease, Biochemistry 33:1029–1036.
  PubMed CAS Google Scholar
• MacDonald, G. M., and Barry, B. A., Difference FT-IR study of a novel biochemical preparation of photosystem II. Biochemistry 31:9848-9856.
  Google Scholar
• Maeda, A., Ohkita, Y. J., Sasaki, J., Shichida, Y., and Yoshizawa, T., 1993, Water structural changes in lumirhodopsin, metarhodopsin I, and metarhodopsin II upon photolysis of bovin rhodopsin: Analysis by Fourier-transform infrared spectroscopy, Biochemistry 32:12033–12038.
  PubMed CAS Google Scholar
• Maeda, A., Sasaki, J., Shichida, Y., and Yoshizawa, T., 1992, Water structural changes in the bacteriorhodopsin photocycle: Analysis by Fourier transform infrared spectroscopy, Biochemistry 31:462–467.
  PubMed CAS Google Scholar
• Marrero, H., and Rothschild, K. J., 1987, Conformational changes in bacteriorhodopsin studied by infrared attenuated total reflection, Biophys. J. 5:629–635.
  Google Scholar
• Mellier, A., and Diaf, A., 1988, Infrared study of phospholipid hydration. Main phase transition of saturated phosphatidylcholine/ water multilamellar samples, Chem. Phys. Lipids 46:51–56.
  CAS Google Scholar
• Merz, H., and Zundel, G., 1986, Thermodynamics of proton transfer in carboxylic acid-retinal Schiff base hydrogen bonds with large proton polarizability, Biochem. Biophys. Res. Commun. 138:819–825.
  PubMed CAS Google Scholar
• Michel-Villaz, M., Saibil, H. R., and Chabre, M., 1979, Orientation of rhodopsin a-helices in retinal rod outer segment membranes studied by infrared linear dichroïsm, Proc. Natl. Acad. Sci. U.S.A. 76:4405–4408.
  PubMed CAS Google Scholar
• Mitchell, R. C., Haris, P. I., Fallowfield, C., Keeling, D. J., and Chapman, D., 1988, Fourier-transform infrared spectroscopy studies on gastric H+/K+-ATPase, Biochim. Biophys. Acta 947:31–38.
  Google Scholar
• Moh, P. P., Fiamingo, F. G., and Alben, J., 1987, Conformational sensitivity of beta-93 cystein SH to ligation of hemoglobin observed by FT-IR spectroscopy, Biochemistry 26:6243–6249.
  PubMed CAS Google Scholar
• Molday, R. S., Englander, S. W., and Kallen, R. G., 1972, Primary structure effects on peptide group hydrogen exchange, Biochemistry 11:150–158.
  PubMed CAS Google Scholar
• Muga, A., Mantsch, H. H., and Surewitcz, W. K., 1991, Membrane binding induces destabilization of cytochrome c structure, Biochemistry 30:7219–7224.
  PubMed CAS Google Scholar
• Nabedryk, E., and Breton, J., 1981, Orientation of intrinsic proteins in photosynthetic membranes: Polarized infrared spectroscopy of chloroplasts and chromatophores, Biochim. Biophys. Acta 635:515–524.
  PubMed CAS Google Scholar
• Nabedryk, E., Garavito, R. M., and Breton, J., 1988, The orientation of ß-sheets in porin. A polarized Fourier-transform infrared spectroscopic investigation, Biophys. J. 53:671–676.
  PubMed CAS Google Scholar
• Nedelec, J-F., Alfsen, A., and Lavialle, F., 1989, Comparative study of myelin proteolipid apoprotein solvation by multilayer membranes of synthetic DPPC and biological lipid extract from bovine brain. An FT-IR investigation, Biochimie 71:145–171.
  PubMed CAS Google Scholar
• Okamura, E., Umemura, J., and Takenaka, T., 1990, Orientation studies of hydrated dipalmitoylphosphatidylcholine multibilayers by polarized FTIR-ATR spectroscopy, Biochim. Biophys. Acta 1025:94–98.
  PubMed CAS Google Scholar
• Ormos, P., 1991, Infrared spectroscopic demonstration of a conformational change in bacte-riorhodopsin involved in proton pumping, Proc. Natl. Acad. Sci. U.S.A. 88:473–477.
  PubMed CAS Google Scholar
• Ormos, P., Chu, K., and Mourant, J., 1992, Infrared study of the L, M, and N intermediates of bacteriorhodopsin using the photoreaction of M, Biochemistry 31:6933–6937.
  PubMed CAS Google Scholar
• Pastrana, B., Mautone, A. J., and Mendelsohn, R., 1991, Fourier-transform infrared studies of secondary structure and orientation of pulmonary surfactant SP-C and its effects on the dynamic surface properties of phospholipid? Biochemistry 30:10058–10064.
  PubMed CAS Google Scholar
• Petrelski, S. J., Byler, D. M., and Liebman, M. N., 1991, Comparison of various molecular forms of bovine trypsin: correlation of infrared spectra with X-ray crystal structures, Biochemistry 30:133–143.
  Google Scholar
• Petrelski, S. J., Tedeschi, N., Arakawa, T., and Carpenter, J. F., 1993, Dehydration-induced conformational transitions in protein and their inhibition by stabilizers, Biophys. J. 65:661–671.
  Google Scholar
• Pidgeon, C., Apostol, G., and Markovich, R., 1989, Fourier-transform infrared assay of liposomal lipids, Anal. Biochem. 181:28–32.
  PubMed CAS Google Scholar
• Poole, P. L., and Finney, J. L., 1984, Sequential hydration of dry proteins: a direct difference IR investigation of sequence homologs lysozyme and a-lactalbumin, Biopolymers 23:1647–1666.
  PubMed CAS Google Scholar
• Powell, J. R., Wasacz, F. M., and Jakobsen, R. J., 1986, An algorithm for the reproducible spectral subtraction of water from the FTIR spectra of proteins in dilute solutions and adsorbed mono-layers, Appl. Spectrosc. 40:339–344.
  CAS Google Scholar
• Provencher, S.W., 1976, A Fourier method for the analysis of exponential decay curves, Biophys. J. 16:27–41.
  PubMed CAS Google Scholar
• Provencher, S.W., 1982, A constrained regularization method for inverting data represented by linar algebraic or integral equations, Computer Phys. Commun. 27:213–227.
  Google Scholar
• Provencher, S. W., 1982, CONTIN: A general purpose constrained regularization program for inverting noisy linear algebraic and integral equations, Computer Phys. Commun. 27:229–242.
  Google Scholar
• Provencher, S. W., and Dovi, V. G., 1979, Direct analysis of continuous relaxation spectra, J. Biochem. Biophys. Methods 1:313–318.
  PubMed CAS Google Scholar
• Rashin, A. A., 1987, Correlation between the calculated local stability and hydrogen exchange rates in proteins, J. Mol. Biol. 198:339–349.
  PubMed CAS Google Scholar
• Rath, P., Bouché, O., Merril, A. R., Cramer, W. A., and Rotschild, K. J., 1991, Fourier-transform infrared evidence for a predominantly a-helical structure of the membrane bound channel forming COOH-terminal peptide of colicin El, Biophys. J. 59:516–522.
  PubMed CAS Google Scholar
• Reilly, K. E., Becka, R., Thomas, G. J., 1992, Deuterium exchange of operator 8CH groups as a Raman probe of repressor recognition: interactions of wild-type and mutant G repressors with operator OL1, Biochemistry 31:3118–3125.
  PubMed CAS Google Scholar
• Roepe, P. D., Ahl, P. L., Herzfeld, J., Lugtenburg, J., and Rothschild, K. J., 1988, Tyrosine protonation changes in bacteriorhodopsin: A Fourier transform infrared study of BR548 and its primary photoproduct, J. Biol. Chem. 263:5110–5117.
  PubMed CAS Google Scholar
• Rosenberg, A., 1986, Use of hydrogen exchange kinetics in the study of the dynamic properties of biological membranes, Methods Enzymol. 127:630–648.
  PubMed CAS Google Scholar
• Rothschil, K. J., Sanches, R., Hsiao, T. L., and Clark, N. A., 1980, A spectroscopic study of rhodopsin alpha-helix orientation, Biophys. J. 31:53–64.
  Google Scholar
• Rothschild, K. J., and Clark, N. A., 1979, Polarized infrared spectroscopy of oriented purple membrane, Biophys. J. 5.25: 473–488.
  Google Scholar
• Rothschild, K. J., Bousché, O., Braiman, M. S., Hasselbacher, C. A., and Spudich, J. L., 1988, Fourier-transform infrared study of the halorhodopsin chloride pump, Biochemistry 27:2420–2424.
  PubMed CAS Google Scholar
• Rothschild, K. J., Braiman, M. S., He, Y-W., Marti, T., and Khorana, H. G., 1990, Vibrational spectroscopy of bacteriorhodopsin mutants: Evidence for the interaction of aspartic acid 212 with tyrosine 185 and possible role in the proton pump mechanism, J. Biol. Chem. 265:16985–16991.
  PubMed CAS Google Scholar
• Rothschild, K. J., He, Y-W., Gray, D., Roepe, P. D., Pelletier, S. L., Brown, R. S., and Herzfeld, J., 1989, Fourier transform infrared evidence for proline structural changes during the bacteriorhodopsin photocycle, Proc. Natl. Acad. Sci. U.S.A. 86:9832–9835.
  PubMed CAS Google Scholar
• Rothschild, K. J., Roepe, P., Lugtenburg, J., and Pardoen, J. A., 1984, Fourier transform infrared evidence for Schiff base alteration in the first step of the bacteriorhodopsin photocycle, Biochemistry 23:6103–6109.
  PubMed CAS Google Scholar
• Sami, M., and Dempsey, C., 1988, Hydrogen exchange from the transbilayer hydrophobic peptide of glycophorin reconstituted in lipid bilayers, F.E.B.S. Lett. 240:211–215.
  CAS Google Scholar
• Sanchez-Ruiz, J. M., and Martinez-Carrion, M., 1988, A Fourier-transform infrared spectroscopic study of the phosphoserine residues in hen egg phosvitin and ovalbumin, Biochemistry 27:3338–3342.
  PubMed CAS Google Scholar
• Sarver, R. W., and Krueger, W. C., 1993, Infrared investigation of proteins deposited on polyethylene films, Anal. Biochem. 519-525.
  Google Scholar
• Sarver, R. W., and Kruerger, W. C., 1991, Protein secondary structure from Fourier-transform infrared spectroscopy: A database analysis, Anal. Biochem. 194:89–100.
  PubMed CAS Google Scholar
• Schinkel, J. E., Downer, N. W., and Rupley, J. A., 1985, Hydrogen exchange of lysozyme powders. Hydration dependence of internal motions, Biochemistry 24:352–366.
  PubMed CAS Google Scholar
• Schlereth, D., Fernandez, V. M., and Mäntele, W., 1993, Protein conformational changes in tetra-heme cytochromes detected by FTIR spectroelectrochemistry: Desulfovibrio desulfuricans Norway 4 and Desulfovibrio gigas cytochromes c3, Biochemistry 32:9199–9208.
  PubMed CAS Google Scholar
• Simhony, S., Katzir, A., and Kosower, E. M., 1988, Fourier-transform infrared spectra of organic compounds in solution and as thin films obtained by using an attenuated total internal reflectance fiber-optic cell, Anal. Chem. 60:1908–1910.
  CAS Google Scholar
• Simhony, S., Kosower, E. M., and Katzir, A., 1986, Novel attenuated total internal reflectance spectroscopic cell using infrared fibers for aqueous solutions, Appl. Phys. Lett. 49:253–254.
  CAS Google Scholar
• Simhony, S., Kosower, E. M., and Katzir, A., 1987, Fourier-transform infrared spectra of aqueous protein mixtures using a novel attenuated total internal reflectance cell with infrared fibers, Biochem. Biophys. Res. Commun. 142:1059–1063.
  PubMed CAS Google Scholar
• Simhony, S., Schnitzer, I., Katzir, A., and Kosower, E. M., 1988, Evanescent wave infrared spectroscopy of liquids using silver halide optical fibers, J. Appl. Phys. 64:3732–3734.
  CAS Google Scholar
• Strauss, H. L., 1986, Vibrational methods for water structure in non polar media, Methods Enzymol. 127:106–113.
  PubMed CAS Google Scholar
• Swedberg, S. A., Pesek, J. J., and Fink, A. L., 1990, Attenuated total reflection Fourier-transform infrared analysis of an acyl-enzyme intermediate of a-chymotrypsin, Anal. Biochem. 186:153–158.
  PubMed CAS Google Scholar
• Tamm, L. K., 1988, Lateral diffusion and microscope studies on a monoclonal antibody specifically bound to supported phospholipid bilayers, Biochemistry 27:1450–1457.
  PubMed CAS Google Scholar
• Tamm, L. K., and McConnel, H. M., 1985, Supported phospholipid bilayers, Biophys. J. 47:105–113.
  PubMed CAS Google Scholar
• Tamm, L. K., and Tatulian, S. A., 1993, Orientation of functional and nonfunctional PTS permease signal sequences in lipid bilayers. A polarized attenuated total reflection infrared study, Biochemistry 32:7720–7726.
  PubMed CAS Google Scholar
• Tiede, D. M., 1985, Incorporation of membrane proteins into interfacial films: Model membranes for electrical and structural characterisation, Biochim. Biophys. Acta 811:357–359.
  PubMed CAS Google Scholar
• Tonge, P., Moore, R., and Wharton, C. W., 1989, Fourier-transform infra-red studies of the alkaline isomerization of mitochondrial cytochrome c and the ionization of carboxylic acids, Biochem. J. 258:599–605.
  PubMed CAS Google Scholar
• Tüchsen, E., Hayes, J. M., Ramaprased S., Copie, V., and Woodward, C., 1987, Solvent exchange of buried water and hydrogen exchange of peptide NH group hydrogen bonded to buried waters in bovine pancreatic trypsin inhibitor, Biochemistry 26:5163–5172.
  PubMed Google Scholar
• Van Thiel, M., Backer, E. D., and Pimentel, G. C., 1957, Infrared studies of hydrogen bonding of water by the matrix isolation technique, J. Chem. Phys. 27:486–490.
  Google Scholar
• Vandenbussche, G., Clercx, A., Clercx, M., Curstedt, T., Johansson, J., Jörnvall, H., and Ruysschaert, J. M., 1992b, Secondary structure and orientation of the surfactant protein SP-B in a lipid environment. A Fourier-transform infrared spectroscopy study, Biochemistry 31:9169–9176.
  PubMed CAS Google Scholar
• Vandenbussche, G., Clercx, A., Curstedt, T., Johansson, J., Jörnvall, H., and Ruysschaert, J. M., 1992a, Structure and orientation of the surfactant-associated protein C in a lipid bilayer, Eur. J. Biochem. 203:201–209.
  PubMed CAS Google Scholar
• Vasilescu, V., and Katona, E., 1986, Deuteration as a tool in investigating the role of water in the structure and function of excitable membrane, Methods Enzymol. 127:662–678.
  PubMed CAS Google Scholar
• Venyaminov, S. Y., and Kalnin, N. N., 1990a, Quantitative IR spectrophotometry of peptides compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption band, Biopolymers 30:1243–1257.
  PubMed CAS Google Scholar
• Venyaminov, S. Y., and Kalnin, N. N., 1990b, Quantitative IR spectrophotometry of peptides compounds in water (H2O) solutions. II. Amide absorption bands of polypeptides and fibrous proteins in a-, ß-and random conformations, Biopolymers 30:1259–1271.
  PubMed CAS Google Scholar
• Vincent, S.S., Star, C. J., and Levin, I. W., 1984, Infrared spectroscopic study of the pH-dependent secondary structure of brain clathrin, Biochemistry 23:625–631.
  CAS Google Scholar
• Walrafen, G. E., 1967, Raman spectral studies of the effects of temperature on water structure, J. Chem. Phys. 47:114–126.
  CAS Google Scholar
• Wlodawer, A., Walter, J., Huber, K., and Sjölin, L., 1984, Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II, J. Mol. Biol. 180:301–329.
  PubMed CAS Google Scholar
• Woodward, C. K., and Rosenberg, A., 1970, Oxidized Ruase as a protein model having no contribution to the hydrogen exchange rate from conformational restriction, Proc. Natl. Acad. Sci. U.S.A. 66:1067–1074.
  PubMed CAS Google Scholar
• Zhang, Y-P., Lewin, R. N., Hodges, R. S., and McElhaney, R. N., 1992, FTIR spectroscopic studies of the conformation and amide hydrogen exchange of a peptide model of the hydro-phobic transmembrane a-helices of membrane proteins, Biochemistry 31:11572–11578.
  PubMed CAS Google Scholar
• Zundel, G., 1986, Proton polarizability of hydrogen bonds: Infrared methods, relevance to electrochemical and biological systems, Methods Enzymol. 127:439–455.
  PubMed CAS Google Scholar

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