Aromatic and Cystine Side-Chain Circular Dichroism in Proteins

  • Robert W. Woody
  • A. Keith Dunker


The contributions of aromatic side chains to the near-UV CD spectra of proteins are widely recognized and utilized as sensitive probes of protein conformation and ligand binding. The analysis of the near-UV CD spectra of proteins has been reviewed by Strickland (1974), Kahn (1979), and Drake (1993). Applications to studies of ligand binding were reviewed by Greenfield (1975). Our own computer-aided literature searches indicate that well over 600 papers have reported usage of near-UV CD spectra in recent years. Space and time limitations preclude a comprehensive review of these studies. In the limited review presented here, we have attempted to provide a sense of the range of the applications, with no claim that the “best” or “most useful” papers have been selected.


Circular Dichroism Circular Dichroism Spectrum Difference Spectrum Protein Secondary Structure Cyclic Dipeptide 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Albinsson, B., and Nordén, B., 1992, Excited-state properties of the indole chromophore. Electronic transition moment directions from linear dichroism measurements: Effect of methyl and methoxy substituents, J. Phys. Chem. 96: 6204–6212.CrossRefGoogle Scholar
  2. Altamirano, M. M., Plumbridge, J. A., and Calcagno, M. L., 1992, Identification of two cysteine residues forming a pair of vicinal thiols of glucosamine-6-phosphate deaminase from Escherichia coliand a study of their functional role by site-directed mutagenesis, Biochemistry 31: 1153–1158.PubMedCrossRefGoogle Scholar
  3. Altamirano, M. M., Hernandez-Arana, A., Tello-Solis, S., and Calcagno, M. L., 1994, Spectrochemical evidence for the presence of a tyrosine residue in the allosteric site of glucosamine-6-phosphate deaminase from Escherichia coli, Eur. J. Biochem. 220: 409–413.PubMedCrossRefGoogle Scholar
  4. Ananthanarayanan, V. S., and Ahmad, F., 1977, Evidence from rotatory measurements for an intermediate state in the guanidine hydrochloride denaturation of ß-lactoglobulin, Can. J. Biochem. 55: 239–243.CrossRefGoogle Scholar
  5. Anteunis, M. J. O., 1978, The cyclic dipeptides: Proper model compounds in peptide research, Bull. Soc. Chim. Belg. 87: 627–650.CrossRefGoogle Scholar
  6. Arakawa, T., and Kenney, W. C., 1988, Secondary structure of interleukin-2(A1a125) in unfolded state, Int. J. Pept. Protein Res. 31: 468–473.PubMedCrossRefGoogle Scholar
  7. Arakawa, T., Hsu, Y.-R., Schiffer, S. G., Tsai, L. B., Curless, C., and Fox, G. M., 1989, Characterization of a cysteine-free analog of recombinant human basic fibroblast growth factor, Biochem. Biophys. Res. Commun. 161: 335–341.PubMedCrossRefGoogle Scholar
  8. Arnold, G. E., Day, L. A., and Dunker, A. K., 1992, Tryptophan contributions to the unusual circular dichroism of fd bacteriophage, Biochemistry 31: 7948–7956.PubMedCrossRefGoogle Scholar
  9. Auer, H. E., 1973, Far-ultraviolet absorption and circular dichroism spectra of L-tryptophan and some derivatives, J. Am. Chem. Soc. 95: 3003–3011.PubMedCrossRefGoogle Scholar
  10. Babu, Y. S., Sack, J. S., Greenhough, T. J., Bugg, C. E., Means, A. R., and Cook, W. J., 1985, Three-dimensional structure of calmodulin, Nature 315: 37–40.PubMedCrossRefGoogle Scholar
  11. Baldwin, R. L., 1986, Seeding protein folding, Trends Biochem. Sci. 11: 6–9.CrossRefGoogle Scholar
  12. Baldwin, R. L., 1993, Pulsed hydrogen—deuterium exchange studies of folding intermediates, Curr. Opin. Struct. Biol. 3: 84–91.CrossRefGoogle Scholar
  13. Barrick, D., and Baldwin, R. L., 1993, The molten globule intermediate of apomyoglobin and the process of protein folding, Protein Sci. 2: 869–876.PubMedCrossRefGoogle Scholar
  14. Baskaran, R., and Rao, M. R. S., 1990, Interaction of spermatid-specific protein TP2 with nucleic acids, in vitro, J. Biol. Chem. 265: 21039–21047.PubMedGoogle Scholar
  15. Baum, J., Dobson, C. M., Evans, P. A., and Hanley, C., 1989, Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guinea pig a-lactalbumin, Biochemistry 28: 7–13.PubMedCrossRefGoogle Scholar
  16. Bayley, P. M., Nielsen, E. B., and Schellman, J. A., 1969, The rotatory properties of molecules containing two peptide groups: Theory, J. Phys. Chem. 73: 228–243.PubMedCrossRefGoogle Scholar
  17. Becerra, S. P., Clore, G. M., Gronenborn, A. M., Karlström, A. R., Stahl, S. J., Wilson, S. H., and Wingfield, P. T., 1990, Purification and characterization of the RNase H domain of HIV-1 reverse transcriptase expressed in recombinant Escherichia coli, FEBS Lett. 270: 76–80.PubMedCrossRefGoogle Scholar
  18. Beltramini, M., Bubacco, L., Salvato, B., Casella, L., Gullotti, M., and Garofani, S., 1992, The aromatic circular dichroism spectcrum as a probe for conformational changes in the active site environment of hemocyanins, Biochim. Biophys. Acta 1120: 24–32.PubMedCrossRefGoogle Scholar
  19. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., 1977, The protein data bank: A computer-based archival file for macromolecular structures, J. Mol. Biol. 112: 535–542.PubMedCrossRefGoogle Scholar
  20. Bianchi, E., Venturini, S., Pessi, A., Tramontano, A., and Sollazzo, M., 1994, High level expression and rational mutagenesis of a designed protein, the minibody. From an insoluble to a soluble molecule, J. Mol. Biol. 236: 649–659.PubMedCrossRefGoogle Scholar
  21. Biltonen, R., Lumry, R., Madison, V., and Parker, H., 1965, Studies of the chymotrypsinogen family, III. The optical rotatory dispersion of a-chymotrypsin, Proc. Natl. Acad. Sci. USA 54: 1018–1025.PubMedCrossRefGoogle Scholar
  22. Birktoft, J. J., and Blow, D. M., 1972, Structure of tosyl-a.-chymotrypsin. V. The atomic structure at 2 A resolution, J. Mol. Biol. 68: 187–240.PubMedCrossRefGoogle Scholar
  23. Björk, I., and Ylinenjärvi, K., 1989, Interaction of chicken cystatin with inactivated papains, Biochem. J. 260: 61–68.PubMedGoogle Scholar
  24. Björk, I., and Ylinenjärvi, K., 1990, Interaction between chicken cystatin and the cysteine proteinases actinidin, chymopapain A, and ficin, Biochemistry 29: 1770–1776.PubMedCrossRefGoogle Scholar
  25. Blow, D. M., Fersht, A. R., and Winter, G., eds., 1986, Design, construction and properties of novel protein molecules, Philos. Trans. R. Soc. London A Ser. 317: 291–451.Google Scholar
  26. Bode, W., Engh, R., Musil, D., Thiele, U., Huber, R., Karshikov, A., Brzin, J., Kos, J., and Turk, V., 1988, The 2.0 A x-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases, EMBO J. 7: 2593–2599.PubMedGoogle Scholar
  27. Böhm, G., Muhr, R., and Jaenicke, R., 1992, Quantitative analysis of protein far UV circular dichroism spectra by neural networks, Protein Eng. 5: 191–195.PubMedCrossRefGoogle Scholar
  28. Bolotina, I. A., and Lugauskas, V. Y., 1985, Determination of the secondary structure of proteins from the circular dichroism spectra. IV. Consideration of the contribution of aromatic amino acid residues to the circular dichroism spectra of proteins in the peptide region, Mol. Biol. (Moscow)(Engl. transl.) 19: 1154–1166.Google Scholar
  29. Borkakoti, N., Moss, D. S., and Palmer, R. A., 1982, Ribonuclease A: Least-squares refinement of the structure at 1.45 A resolution, Acta Crystalogr. Sect. B 38: 2210–2217.CrossRefGoogle Scholar
  30. Boyd, D. B., 1972, Conformational dependence of the electronic energy levels in disulfides, J. Am. Chem. Soc. 94: 8799–8804.CrossRefGoogle Scholar
  31. Brahms, S., and Brahms, J., 1980, Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism, J. Mol. Biol. 138: 149–178.PubMedCrossRefGoogle Scholar
  32. Brazhnikov, E. V., Chirgadze, Y. N., Dolgikh, D. A., and Ptitsyn, O. B., 1985, Noncooperative temperature melting of a globular protein without specific tertiary structure: Acid form of bovine carbonic anhydrase B, Biopolymers 24: 1899–1907.PubMedCrossRefGoogle Scholar
  33. Brems, D. N., Brown, P. L., and Becker, G. W., 1990, Equilibrium denaturation of human growth hormone and its cysteine-modified forms, J. Biol. Chem. 265: 5504–5511.PubMedGoogle Scholar
  34. Brown, J. E., and Klee, W. A., 1971, Helix—coil transition of isolated amino terminus of ribonuclease, Biochemistry 10: 470–476.PubMedCrossRefGoogle Scholar
  35. Buck, M., Radford, S. E., and Dobson, C. M., 1993, A partially folded state of hen egg white lysozyme in trifluoroethanol: Structural characterization and implications for protein folding, Biochemistry 32: 669–678.PubMedCrossRefGoogle Scholar
  36. Burger, D., Cox, J. A., Comte, M., and Stein, E. A., 1984, Sequential conformational changes in calmodulin upon binding of calcium, Biochemistry 23: 1966–1971.CrossRefGoogle Scholar
  37. Burley, S. K., and Petsko, G. A., 1985, Aromatic—aromatic interaction: A mechanism of protein structure stabilization, Science 229: 23–28.PubMedCrossRefGoogle Scholar
  38. 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.CrossRefGoogle Scholar
  39. Bychkova, V. E., and Ptitsyn, O. B., 1993, The molten globule in vitro and in vivo, Chemtracts Biochem. Mol. Biol. 4: 133–163.Google Scholar
  40. Bychkova, V. E., Pain, R. H., and Ptitsyn, O. B., 1988, The `molten globule’ state is involved in the translocation of proteins across membranes? FEBS Lett. 238: 231–234.PubMedCrossRefGoogle Scholar
  41. Bychkova, V. E., Berni, R., Rossi, G. L., Kutyshenko, V. P., and Ptitsyn, O. B., 1992, Retinol-binding protein is in the molten globule state at low pH, Biochemistry 31: 7566–7571.PubMedCrossRefGoogle Scholar
  42. Cantor, C. R., and Timasheff, S. N., 1982, Optical spectroscopy of proteins, in: The Proteins(H. Neurath and R. L. Hill, eds.), 3rd ed., Vol. 5, pp. 145–306.Google Scholar
  43. Carmack, M., and Neubert, L. A., 1967, Circular dichroism and the absolute configuration of the chiral disulfide group, J. Am. Chem. Soc. 89: 7134–7136.CrossRefGoogle Scholar
  44. Chaffotte, A. F., Cadieux, C., Guillou, Y., and Goldberg, M. E., 1992, A possible initial folding intermediate: The C-terminal proteolytic domain of tryptophan synthase 13 chain folds in less than 4 milliseconds into a condensed state with non-native-like secondary structure, Biochemistry31:4303–4308. Chen, A. K., and Woody, R. W., 1971, A theoretical study of the optical rotatory properties of polytyrosine, J. Am. Chem. Soc. 93: 29–37.Google Scholar
  45. Chen, M., Chen, L., and Fromm, H. J., 1994, Replacement of glutamic acid 29 with glutamine leads to a loss of cooperativity for AMP with porcine fructose-1,6-bisphosphatase, J. Biol. Chem. 269: 5554–5558.PubMedGoogle Scholar
  46. Chen, Y.-H., Yang, J. T., and Martinez, H. M., 1972, Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion, Biochemistry 11: 4120–4131.PubMedCrossRefGoogle Scholar
  47. Cismowski, M. J., and Huang, P. C., 1991, Effect of cysteine replacements at positions 13 and 50 on metallothionein structure, Biochemistry 30: 6626–6632.PubMedCrossRefGoogle Scholar
  48. Clack, B. A., and Gray, D. M., 1989, A CD determination of the a-helix contents of the coat proteins of four filamentous bacteriophages: fd, IKe, Pfl, and Pß, Biopolymers 28: 1861–1873.PubMedCrossRefGoogle Scholar
  49. Clements, J. M., Bawden, L. J., Boxidge, R. E., Catlin, G., Cook, A. L., Craig, S., Drummond, A. H., Edwards, R. M., Fallon, A., Green, D. R., Hellewell, P. G., Kirwin, P. M., Nayee, P. D., Richardson, S. J., Brown, D., Chahwala, S. B., Snarey, M., and Winslow, D., 1991, Two PDGF-B chain residues, arginine 27 and isoleucine 30, mediate receptor binding and activation, EMBO J. 10: 4113–4120.PubMedGoogle Scholar
  50. Coleman, D. L., and Blout, E. R., 1968, The optical activity of the disulfide bond in L-cystine and some derivatives of L-cystine, J. Am. Chem. Soc. 90: 2405–2416.PubMedCrossRefGoogle Scholar
  51. Colquhoun, D., and Sakmann, B., 1981, Fluctuations in the microsecond time range of the current through single acetylcholine receptor ion channels, Nature 294: 464–466.PubMedCrossRefGoogle Scholar
  52. Comb, D. G., and Roseman, S., 1958, Glucosamine metabolism. IV. Glucosamine-6-phosphate deaminase, J. Biol. Chem. 233: 807–827.Google Scholar
  53. Cowan, S. W., Newcomer, M. E., and Jones, T. A., 1990, Crystallographic refinement of human serum retinol binding protein at 2 A resolution, Protein Struct. Funct. Genet. 8: 44–61.CrossRefGoogle Scholar
  54. Craig, S., Pain, R. H., Schmeissner, U., Virden, R., and Wingfield, P. T., 1989, Determination of the contributions of individual aromatic residues to the CD spectrum of IL-13 using site directed mutagenesis, Int. J. Pept. Protein Res. 33: 256–262.PubMedCrossRefGoogle Scholar
  55. Cramer, W. A., Cohen, F. S., Merrill, A. R., and Song, H. Y., 1990, Structure and dynamics of the colicin El channel, Mol. Microbiol. 4: 519–526.PubMedCrossRefGoogle Scholar
  56. Crouch, T. H., and Klee, C. B., 1980, Positive cooperative binding of calcium to bovine brain calmodulin, Biochemistry 19: 3692–3698.PubMedCrossRefGoogle Scholar
  57. Davis, J. M., Narachi, M. A., Alton, N. K., and Arakawa, T., 1987, Structure of human tumor necrosis factor a derived from recombinant DNA, Biochemistry 26: 1322–1326.PubMedCrossRefGoogle Scholar
  58. Day, L. A., 1973, Circular dichroism and ultraviolet absorption of a deoxyribonucleic acid-binding protein of filamentous bacteriophage, Biochemistry 12: 5329–5339.PubMedCrossRefGoogle Scholar
  59. Day, L. A., and Wiseman, R. L., 1978, A comparison of DNA packaging in the virions of fd, Xf, and Pfl, in: The Single-Stranded DNA Phages( D. T. Denhardt, D. Dressler, and D. S. Ray, eds.), pp. 605–625, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY.Google Scholar
  60. Deber, C. M., Khan, A. R., Li, Z., Joensson, C., Glibowicka, M., and Wang, J., 1993, Val —* Ala mutations selectively alter helix—helix packing in the transmembrane segment of phage M13 coat protein, Proc. Natl. Acad. Sci. USA 90: 11648–11652.PubMedCrossRefGoogle Scholar
  61. Del Bene, J., and Jaffé, H. H., 1968, Use of the CNDO method in spectroscopy. I. Benzene, pyridine, and the diazenes, J. Chem. Phys. 48: 1807–1813.CrossRefGoogle Scholar
  62. Dolgikh, D. A., Gilmanshin, R. I., Brazhnikov, E. V., Bychkova, V. E., Semisotnov, G. V., Venyaminov, S. Y., and Ptitsyn, O. B., 1981, a-Lactalbumin: Compact state with fluctuating tertiary structure? FEBS Lett. 136: 311–315.Google Scholar
  63. Dolgikh, D. A., Abaturov, L. V., Bolotina, I. A., Brazhnikov, E. V., Bushuev, V. N., Bychkova, V. E., Gilmanshin, R. I., Lebedev, Y. O., Semisotnov, G. V., Tiktopulo, E. I., and Ptitsyn, O. B., 1985, Compact state of a protein molecule with pronounced small-scale mobility: Bovine a-lactalbumin, Eur. Biophys. J. 13: 109–121.PubMedCrossRefGoogle Scholar
  64. Donovan, J. W., 1969, Ultraviolet absorption by proteins, in: Physical Principles and Techniques inProtein Chemistry, Part A ( S. J. Leach, ed.), pp. 101–170, Academic Press, New York.Google Scholar
  65. Drake, A. F., 1993, Spectroscopic assignments in the CD spectra of proteins and peptides, Proc. 5 th Int. Conf. CD, Pingree Park, CO, pp. 21 - 46.Google Scholar
  66. Dryden, D., and Weir, M. P., 1991, Evidence for an acid-induced molten-globule state in interleukin2: A fluorescence and circular dichroism study, Biochim. Biophys. Acta 1078: 94–100.PubMedCrossRefGoogle Scholar
  67. Dufton, M. J., and Hider, R. C., 1983, Conformational properties of the neurotoxins and cytotoxins isolated from elapid snake venoms, CRC Crit. Rev. Biochem. 14: 113–171.PubMedCrossRefGoogle Scholar
  68. Dunker, A. K., 1994, P22 phage capsids under pressure, Biophys. J. 66: 1269–1271.PubMedCrossRefGoogle Scholar
  69. Dunker, A. K., Ensign, L. D., Arnold, G. E., and Roberts, L. M., 1991, Proposed molten globule intermediates in fd phage penetration and assembly, FEBS Lett. 292: 275–278.PubMedCrossRefGoogle Scholar
  70. Eftink, M. R., Helton, K. J., Beavers, A., and Ramsay, G. D., 1994, The unfolding of Trpaporepressor as a function of pH: Evidence for an unfolding intermediate, Biochemistry 33: 10220–10228.PubMedCrossRefGoogle Scholar
  71. Egusa, S., Sisido, M., and Imanishi, Y., 1985, One-dimensional aromatic crystals in solution. 4. Ground-and excited-state properties of poly(L-1-pyrenylalanine) studied by chiroptical spectroscopy including circularly polarized fluorescence and fluorescence-detected circular dichroism, Macromolecules 18: 882–889.CrossRefGoogle Scholar
  72. Elöve, G. A., Chaffotte, A. F., Roder, H., and Goldberg, M. E., 1992, Early steps in cytochrome cfolding probed by time-resolved circular dichroism and fluorescence spectroscopy, Biochemistry 31: 6876–6883.PubMedCrossRefGoogle Scholar
  73. Elwell, M. L., and Schellman, J. A., 1977, Stability of phage T4 lysozymes. I. Native properties and thermal stability of wild type and two mutant lysozymes, Biochim. Biophys. Acta. 494: 367–383.PubMedCrossRefGoogle Scholar
  74. Epand, R. M., Gawish, A., Iqbal, M., Gupta, K. B., Chen, C. H., Segrest, J. P., and Anantharamaiah, G. M., 1987, Studies of synthetic peptide analogs of the amphipathic helix, J. Biol. Chem. 262: 9389–9396.PubMedGoogle Scholar
  75. Evans, P. A., and Radford, S. E., 1994, Probing the structure of folding intermediates, Curr. Opin. Struct. Biol. 4: 100–106.CrossRefGoogle Scholar
  76. Fernando, T., and Royer, C. A., 1992, Unfolding of trprepressor studied using fluorescence spectroscopic techniques, Biochemistry 31: 6683–6691.PubMedCrossRefGoogle Scholar
  77. Fleischhauer, J., Grötzinger, J., Kramer, B., Krüger, P., Wollmer, A., Woody, R. W., and Zobel, E., 1994, Calculation of the cd spectrum of cyclo(L-Try-L-Tyr) based on a molecular dynamics simulation, Biophys. Chem. 49: 141–152.PubMedCrossRefGoogle Scholar
  78. Forsén, S., Vogel, H. J., and Drakenburg, T., 1986, Biophysical studies of calmodulin, Calcium Cell Funct. 6: 113–157.Google Scholar
  79. Freer, S. T., Kraut, J., Robertus, J. D., Wright, H. T., and Xuong, N. H., 1970, Chymotrypsinogen: 2.5Â crystal structure, comparison with «-chymotrypsin, and implications for zymogen activation, Biochemistry 9: 1997–2009.PubMedCrossRefGoogle Scholar
  80. Freskgârd, P.-O., Mârtensson, L.-G., Jonasson, P., Jonsson, B.-H., and Carlsson, U., 1994, Assignment of the contribution of the tryptophan residues to the circular dichroism spectrum of human carbonic anhydrase II, Biochemistry 33: 14281–14288.PubMedCrossRefGoogle Scholar
  81. Gajdusek, D. C., 1988, Transmissible and nontransmissible dementias: Distinction between primary cause and pathogenetic mechanisms in Alzheimer’s disease and aging, Mt. Sinai J. Med. 55: 3–5.PubMedGoogle Scholar
  82. Gierasch, L. M., and King, J. A., eds., 1990, Protein Folding: Deciphering the Second Half of the Genetic Code, American Association for the Advancement of Science Press, Washington, DC.Google Scholar
  83. Gittelman, M. S., and Matthews, C. R., 1990, Folding and stability of trpaporepressor from Escherichia coli, Biochemistry 29: 7011–7020.PubMedCrossRefGoogle Scholar
  84. Goel, R., Beard, W. A., Kumar, A., Casas-Finet, J. R., Strub, M.-P., Stahl, S. J., Lewis, M. S., Bebenek, K., Becerra, S. P., Kunkel, T. A., and Wilson, S. H. 1993, Structure/function studies of HIV-1 reverse transcriptase: Dimerization-defective mutant L289K, Biochemistry 32: 13012–13018.PubMedCrossRefGoogle Scholar
  85. Goto, Y., and Fink, A. L., 1989, Conformational states of ß-lactamase: Molten-globule states at acidic and alkaline pH with high salt, Biochemistry 28: 945–952.PubMedCrossRefGoogle Scholar
  86. Goux, W. J., and Hooker, T. M., Jr., 1980a, Chiroptical properties of proteins. I. Near-ultraviolet circular dichroism of ribonuclease S, J. Am. Chem. Soc. 102: 7080–7087.CrossRefGoogle Scholar
  87. Goux, W. J., and Hooker, T. M., Jr., 1980b, The chiroptical properties of proteins. II. Near-ultraviolet circular dichroism of lysozyme, Biopolymers 19: 2191–2208.PubMedCrossRefGoogle Scholar
  88. Goux, W. J., Kadesch, T. R., and Hooker, T. M., Jr., 1976, Contribution of side-chain chromophores to the optical activity of proteins: Model compound studies. IV. The indole chromophore of yohimbinic acid, Biopolymers 15: 977–997.PubMedCrossRefGoogle Scholar
  89. Green, N. M., and Melamed, M. D., 1966, Optical rotatory dispersion, circular dichroism, and far-ultraviolet spectra of avidin and streptavidin, Biochem. J. 100: 614–621.PubMedGoogle Scholar
  90. Greenfield, N. J., 1975, Enzyme—ligand complexes: Spectroscopic studies, CRC Crit. Rev. Biochem. 3: 71–110.PubMedCrossRefGoogle Scholar
  91. Greenfield, N., and Fasman, G. D., 1969, Computed circular dichroism spectra for the evaluation of protein conformation, Biochemistry 8: 4108–4116.PubMedCrossRefGoogle Scholar
  92. Grishina, I. B., 1994, Aromatic circular dichroism in globular proteins. Applications to protein structure and folding, Ph.D. thesis, Colorado State University.Google Scholar
  93. Grishina, I. B., and Woody, R. W., 1994, Contributions of tryptophan side chains to the circular dichroism of globular proteins: Exciton couplets and coupled oscillators, Discuss. Faraday Soc. 99: 245–262.CrossRefGoogle Scholar
  94. Guy, H. R., 1984, A structural model of the acetylcholine receptor channel based on partition energy and helix packing calculations, Biophys. J. 45: 249–261.PubMedCrossRefGoogle Scholar
  95. Halper, J. P., Latovitzki, N., Bernstein, H., and Beychok, S., 1971, Optical activity of human lysozyme, Proc. Natl. Acad. Sci. USA 68: 517–522.PubMedCrossRefGoogle Scholar
  96. Haynie, D. T., and Freire, E., 1993, Structural energetics of the molten globule state, Proteins Struct. Funct. Genet. 16: 115–140.PubMedCrossRefGoogle Scholar
  97. Herron, J. N., He, X. M., Mason, M. L., Voss, E. W., Jr., and Edmundson, A. B., 1989, Three-dimensional structure of a fluorescein—Fab complex crystallized in 2-methyl-2,4-pentanediol, Proteins Struct. Funct. Genet. 5: 271–280.PubMedCrossRefGoogle Scholar
  98. Himmelwright, R. S., Eickman, N. C., LuBien, C. D., and Solomon, E. I., 1980, Chemical and spectroscopic comparison of the binuclear copper active site of mollusc and arthropod hemocyanins, J. Am. Chem. Soc. 102: 5378–5388.CrossRefGoogle Scholar
  99. Hodgkin, D. C., 1974, Insulin, its chemistry and biochemistry, Proc. R. Soc. (London) Ser. A338:251–275. Hooker, T. M., Jr., and Schellman, J. A., 1970, Optical activity of aromatic chromophores. I. o, m, and p-tyrosine, Biopolymers 9: 1319–1348.Google Scholar
  100. Horwitz, J., and Strickland, E. H., 1971, Absorption and circular dichroism spectra of ribonuclease-S at 77° K, J. Biol. Chem. 246: 3749–3752.PubMedGoogle Scholar
  101. Horwitz, J., Strickland, E. H., and Billups, C., 1970, Analysis of the vibrational structure in the near-ultraviolet circular dichroism and absorption spectra of tyrosine derivatives and ribonuclease-A at 77° K, J. Am. Chem. Soc. 92: 2119–2129.PubMedCrossRefGoogle Scholar
  102. Hu, D., and Eftink, M. R., 1993, Interaction of indoleacrylic acid with trpaporepressor from Escherichia coli, Arch. Biochem. Biophys. 305: 588–594.PubMedCrossRefGoogle Scholar
  103. Hu, D. D., and Eftink, M. R., 1994, Thermodynamic studies of the interaction of trp aporepressor with tryptophan analogs, Biophys. Chem. 49: 233–239.PubMedCrossRefGoogle Scholar
  104. Huber, R., Epp, O., Steigemann, W., and Formanek, H., 1971, The atomic structure of erythrocruorin in the light óf the chemical sequence and its comparison with myoglobin, Eur. J. Biochem. 19: 42–50.PubMedCrossRefGoogle Scholar
  105. Ikeda, K., and Hamaguchi, K., 1969, The binding of N-acetylglucosamine to lysozyme. Studies on circular dichroism, J. Biochem. (Tokyo) 66: 513–520.Google Scholar
  106. Ikeda, K., and Hamaguchi, K., 1972, A tryptophyl circular dichroic band at 305 mµ of hen egg-white lysozyme, J. Biochem. (Tokyo) 71: 265–273.Google Scholar
  107. Ikehara, K., Utiyama, H., and Kurata, M., 1975, Studies on the structure of filamentous bacteriophage fd. II. All-or-none disassembly in guanidine-HC1 and sodium dodecyl sulfate, Virology 66: 306–315.PubMedCrossRefGoogle Scholar
  108. Imoto, T., Johnson, L. N., North, A. C. T., Phillips, D. C., and Rupley, J. A., 1972, Vertebrate lysozymes, in: The Enzymes(P. D. Boyer, ed.), 3rd ed., Vol. 7, pp. 665–868, Academic Press, New York.Google Scholar
  109. Jeng, M.-F, Englander, S. W., Elöve, G. A., Wand, J., and Roder, H., 1990, Structural description of acid-denatured cytochrome cby hydrogen exchange and 2D NMR, Biochemistry29: 10433–10437.PubMedCrossRefGoogle Scholar
  110. Jennings, P. A., and Wright, P. E., 1993, Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin, Science 262: 892–896.PubMedCrossRefGoogle Scholar
  111. Jirgensons, B., 1973, Optical Activity of Proteins and Other Macromolecules, 2nd ed., Springer-Verlag, Berlin.Google Scholar
  112. Joachimiak, A., Kelley, R. L., Gunsalus, R. P., Yanofsky, C., and Sigler, P. B., 1983, Purification and characterization of trpaporepressor, Proc. Natl. Acad. Sci. USA 80: 668–672.PubMedCrossRefGoogle Scholar
  113. Johnson. W. C., Jr., 1988, Secondary structure of proteins through circular dichroism spectroscopy, Annu. Rev. Biophys. Biophys. Chem. 17: 145–166.CrossRefGoogle Scholar
  114. Johnson, W. C., Jr., and Tinoco, I., Jr., 1972, Circular dichroism of polypeptide solutions in the vacuum ultraviolet, J. Am. Chem. Soc. 94: 4389–4390.PubMedCrossRefGoogle Scholar
  115. Kahn, P. C., 1979, The interpretation of near-ultraviolet circular dichroism, Methods Enzymol. 61: 339378.Google Scholar
  116. Kéry, V., Bystríckÿ, S., Sevcík, J., and Zelinka, J., 1986, Circular dichroism of the guanyloribonuclease Sa and its complex with guanosine 3’-phosphate, Biochim. Biophys. Acta 869: 75–80.CrossRefGoogle Scholar
  117. Khorasanizadeh, S., Peters, I. D., Butt, T. R., and Roder, H., 1993, Folding and stability of a tryptophancontaining mutant of ubiquitin, Biochemistry 32: 7054–7063.PubMedCrossRefGoogle Scholar
  118. Kim, P. S., and Baldwin, R. L., 1990, Intermediates in the folding reactions of small protein, Annu. Rev. Biochem. 59: 631–660.PubMedCrossRefGoogle Scholar
  119. Kistler, J., Stroud, R. M., Klymkowski, M. W., Lalancette, R. A., and Fairclough, R. H., 1982, Structure and function of an acetylcholine receptor, Biophys. J. 37: 371–383.PubMedCrossRefGoogle Scholar
  120. Kitamoto, T., Tateishi, J., Tashima, T., Takeshita, I., Barry, R. A., DeArmond, S. J., and Prusiner, S. B., 1986, Amyloid plaques in Creutzfeldt-Jakob disease stain with prion protein antibodies, Ann. Neurol. 20: 204–208.PubMedCrossRefGoogle Scholar
  121. Kuramitsu, S., Ikeda, K., Hamaguchi, K., Fujio, H., Amano, T., Miwa, S., and Nishina, T., 1974, Ionization constants of Glu 35 and Asp 52 in hen, turkey, and human lysozyme, J. Biochem. (Tokyo) 76: 671–683.Google Scholar
  122. Kuramitsu, S., Ikeda, K., and Hamaaguchi, K., 1975, Participation of the catalytic carboxyls, Asp 52 and Glu 35, and Asp 101 in the binding of substrate analogs to hen lysozyme, J. Biochem. (Tokyo) 77: 291–301.Google Scholar
  123. Kuroda, Y., Kidokoro, S., and Wada, A., 1992, Thermodynamic characterization of cytochrome cat low pH. Observation of the molten globule state and of the cold denaturation process, J. Mol. Biol. 223: 1139–1153.PubMedCrossRefGoogle Scholar
  124. Kuwajima, K., 1977, A folding model of a-lactalbumin deduced from the three-state denaturation mechanism, J. Mol. Biol. 114: 241–258.PubMedCrossRefGoogle Scholar
  125. Kuwajima, K., 1989, The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure, Proteins Struct. Funct. Genet. 6: 87–103.PubMedCrossRefGoogle Scholar
  126. Kuwajima, K., Nitta, K., Yoneyama, M., and Sugai, S., 1976, Three-state denaturation of a-lactalbumin by guanidine hydrochloride, J. Mol. Biol. 106: 359–373.PubMedCrossRefGoogle Scholar
  127. Kuwajima, K., Hiraoka, Y., Ikeguchi, M., and Sugai, S., 1985, Comparison of the transient folding intermediates in lysozyme and a-lactalbumin, Biochemistry 24: 874–881.PubMedCrossRefGoogle Scholar
  128. Kuwajima, K., Yamaya, H., Miwa, S., Sugai, S., and Nagamura, T., 1987, Rapid formation of secondary structure framework in protein folding studied by stopped flow CD, FEBS Lett. 221: 115–118.PubMedCrossRefGoogle Scholar
  129. Kuwajima, K., Sakuraoka, A., Fueki, S., Yoneyama, M., and Sugai, S., 1988, Folding of carp parvalbumin studied by equilibrium and kinetic circular dichroism spectra, Biochemistry 27: 7419–7428.CrossRefGoogle Scholar
  130. Kuwajima, K., Garvey, E. P., Finn, B. E., Matthews, C. R., and Sugai, S., 1991, Transient intermediates in the folding of dihydrofolate reductase as detected by far-ultraviolet circular dichroism spectroscopy, Biochemistry 30: 7693–7703.PubMedCrossRefGoogle Scholar
  131. Lakey, J. H., Massotte, D., Heitz, F., Dasseux, J.-L., Faucon, J.-F., Parker, M. W., and Pattus, F., 1991, Membrane insertion of the pore-forming domain of colicin A. A spectroscopic study, Eur. J. Biochem. 196: 599–607.PubMedCrossRefGoogle Scholar
  132. Lane, A. N., and Jardetzky, 0., 1987, Unfolding of the trp repressor from Escherichia colimonitored by fluorescence, circular dichroism and nuclear magnetic resonance, Eur. J. Biochem. 164: 389–396.PubMedCrossRefGoogle Scholar
  133. Legrand, M., and Viennet, R., 1965, Dichroïsme circulaire optique. XV. Étude de quelques acides aminés, Bull. Soc. Chim. Fr. 1965: 679–681.Google Scholar
  134. Levinthal, C., 1968, Are there pathways for protein folding? J. Chim. Phys. 65: 44–45.Google Scholar
  135. Lin, K., Li, L., Correia, J. J., and Pilkis, S. J., 1992, Arg-257 and Arg-307 of 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase bind the C-2 phospho group of fructose-2,6-bisphosphate in the fructose2,6-bisphosphatase domain, J. Biol. Chem. 267: 19163–19171.PubMedGoogle Scholar
  136. Lindahl, P., Alriksson, E., Jörnvall, H., and Björk, I., 1988, Interaction of the cysteine proteinase inhibitor chicken cystatin with papain, Biochemistry 27: 5074–5082.PubMedCrossRefGoogle Scholar
  137. Linderberg, J., and Michl, J., 1970, On the inherent optical activity of organic disulfides, J. Am. Chem. Soc. 92: 2619–2625.CrossRefGoogle Scholar
  138. Linse, S., Helmersson, A., and Forsén, 1991, Calcium binding to calmodulin and its globular domains, J. Biol. Chem. 266: 8050–8054.PubMedGoogle Scholar
  139. Lüthi-Peng, Q., and Winkler, F. K., 1992, Large spectral changes accompany the conformational transition of human pancreatic lipase induced by acylation with the inhibitor tetrahydrolipstatin, Eur. J. Biochem. 205: 383–390.PubMedCrossRefGoogle Scholar
  140. McConn, J., Fasman, G. D., and Hess, G. P., 1969, Conformation of the high pH form of chymotrypsin, J. Mol. Biol. 39: 551–562.Google Scholar
  141. 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.PubMedCrossRefGoogle Scholar
  142. Mann, C. J., and Matthews, C. R., 1993, Structure and stability of an early folding intermediate of Escherichia coli trpaporepressor measured by far-UV stopped-flow circular dichroism and 8-anilino1-naphthalene sulfonate binding, Biochemistry 32: 5282–5290.PubMedCrossRefGoogle Scholar
  143. Mann, C. J., Royer, C. A., and Matthews, C. R., 1993, Tryptophan replacements in the trpaporepressor from Escherichia coli: Probing the equilibrium and kinetic folding models, Protein Sci. 2: 1853–1861.Google Scholar
  144. Manning, M. C., and Woody, R. W., 1989, Theoretical study of the contribution of aromatic side chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor, Biochemistry 28: 8609–8613.PubMedCrossRefGoogle Scholar
  145. Martin, S. R., and Bayley, P. M., 1986, The effects of Cap` and Cdr` on the secondary and tertiary structure of bovine testis calmodulin. A circular dichroism study, Biochem. J. 238: 485–490.PubMedGoogle Scholar
  146. Marvin, D. A., Hale, R. D., Nave, C., and Citterich, M. H., 1994, Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, fl, and M13), Ifl and IKe, J. Mol. Biol. 235: 260–286.PubMedCrossRefGoogle Scholar
  147. Matthews, B. W., 1993, Structural and genetic analysis of protein stability, Annu. Rev. Biochem. 62: 139–160.PubMedCrossRefGoogle Scholar
  148. Matthews, C. R., 1993, Pathways of protein folding, Annu. Rev. Biochem. 62: 653–683.PubMedCrossRefGoogle Scholar
  149. Maune, J. F., Beckingham, K., Martin, S. R., and Bayley, P. M., 1992, Circular dichroism studies on calcium binding to two series of Ca“ binding site mutants of Drosophila melanogastercalmodulin, Biochemistry 31: 7779–7786.Google Scholar
  150. Mercola, D., and Wollmer, A., 1981, The crystal structure of insulin and solution phenomena: Use of the high-resolution structure in the calculation of the optical activity of the tyrosyl residues, in: Structural Studies on Molecules of Biological Interest. A Volume in Honour of Dorothy Hodgkin( G. Dodson, J. P. Glusker, and D. Sayre, eds.), pp. 557–582, Oxford University Press (Clarendon), London.Google Scholar
  151. Merrill, A. R., Cohen, F. S., and Cramer, W. A., 1990, On the nature of the structural change of the colicin El channel peptide necessary for its translocation-competent state, Biochemistry 29: 5829–5836.Google Scholar
  152. Mitraki, A., and King, J., 1989, Protein folding intermediates and inclusion body formation, Bio-Technology 7: 690–697.CrossRefGoogle Scholar
  153. Monaco, H.L., Zanotti, G., Ottonello, S., and Berni, R., 1984, Crystallization of human plasma aporetinol-binding protein, J. Mol. Biol. 178:477–479.Google Scholar
  154. Morris, A. J., and Tolan, D. R., 1993, Site-directed mutagenesis identifies aspartate 33 as a previously unidentified critical residue in the catalytic mechanism of rabbit aldolase A, J. Biol. Chem. 268: 1095–1100.Google Scholar
  155. Nagarajan, R., and Woody, R. W., 1973, The circular dichroism of gliotoxin and related epidithiapiperazinediones, J. Am. Chem. Soc. 95: 7212–7222.PubMedCrossRefGoogle Scholar
  156. Nall, B. T., and Dill, K. A., eds., 1991, Conformations and Forces in Protein Folding, American Association for the Advancement of Science Press, Washington, DC.Google Scholar
  157. Neubig, R. R., Boyd, N. D., and Cohen, J. B., 1982, Conformations of Torpedoacetylcholine receptor associated with ion transport and desensitization, Biochemistry 21: 3460–3467.Google Scholar
  158. Newcomer, M. E., Jones, T. A., Àgvist, J., Sundelin, J., Eriksson, U., Rask, L., and Peterson, P. A., 1984, The three-dimensional structure of retinol-binding protein, EMBO J. 3: 1451–1454.PubMedGoogle Scholar
  159. Niephaus, H., Schleker, W., and Fleischhauer, J., 1985, CNDO/S-CI-Rechnungen zum Circulardichroismus von Disulfidbrücken in Proteinen im nahen UV, Z. Naturforsch. 40a: 1304–1311.Google Scholar
  160. Nozaka, M., Kuwajima, K., Nitta, K., and Sugai, S., 1978, Detection and characterization of the intermediate on the folding pathway of human a-lactalbumin, Biochemistry 17: 3753–3758.PubMedCrossRefGoogle Scholar
  161. Nozaki, Y., Chamberlain, B. K., Webster, R. E., and Tanford, C., 1976, Evidence for a major conformational change of coat protein in assembly of Fl bacteriophage, Nature 259: 335–337.PubMedCrossRefGoogle Scholar
  162. Ohgushi, M., and Wada, A., 1983, `Molten-globule state’: A compact form of globular proteins with mobile side-chains, FEBS Lett. 164: 21–24.Google Scholar
  163. Ohgushi, M., and Wada, A., 1984, Liquid-like state of side chains at the intermediate stage of protein denaturation, Adv. Biophys. 18: 75–90.PubMedCrossRefGoogle Scholar
  164. Osumi-Davis, P. A., Sreerama, N., Volkin, D. B., Middaugh, C. R., Woody, R. W., and Woody, A.-Y. M., 1994, Bacteriophage T7 RNA polymerase and its active-site mutants: Kinetic, spectroscopic and calorimetric characterization, J. Mol. Biol. 237: 5–19.PubMedCrossRefGoogle Scholar
  165. Ovchinnikov, Y. A., and Ivanov, V. T., 1982, The cyclic peptides: Structure, conformation, and function, in: The Proteins, 3rd ed., Vol. 5 ( H. Neurath and R. L. Hill, eds.), pp. 307–642, Academic Press, New York.Google Scholar
  166. Pain, R., ed., 1994, Mechanisms of Protein Folding, Oxford University Press, London.Google Scholar
  167. Pan, K.-M., Baldwin, M., Nguyen, J., Gasset, M., Serban, A., Groth, D., Melhorn, I., Huang, Z., Fletterick, R. J., Cohen, F. E., and Prusiner, S. B., 1993, Conversion of a-helices into 0-sheets features in the formation of the scrapie prion proteins, Proc. Nall. Acad. Sci. USA 90: 10962–10966.CrossRefGoogle Scholar
  168. Pancoska, P., and Keiderling, T. A., 1991, Systematic comparison of statistical analyses of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins, Biochemistry 3: 6885–6895.CrossRefGoogle Scholar
  169. Pancoska, P., Yasui, S. C., and Keiderling, T. A., 1991, Statistical analyses of the vibrational circular dichroism of selected proteins and relationship to secondary structures, Biochemistry 30: 5089–5103.PubMedCrossRefGoogle Scholar
  170. Patti, J. M., Boles, J. O., and Höök, M., 1993, Identification and biochemical characterization of the ligand binding domain of the collagen adhesin from Staphylococcus aureus, Biochemistry 32: 11428–11435.PubMedCrossRefGoogle Scholar
  171. Pattus, F., Massotte, D., Wilmsen, H. U., Lakey, J., Tsernoglou, D., Tucker, A., and Parker, M. W., 1990, Colicins: Prokaryotic killer-pores, Experientia 46: 180–192.PubMedGoogle Scholar
  172. Perczel, A., Hollósi, M., Tusnâdy, G., and Fasman, G. D., 1991, Convex constraint analysis: A natural deconvolution of circular dichroism curves of proteins, Protein Eng. 4: 669–679.PubMedCrossRefGoogle Scholar
  173. Perczel, A., Park, K., and Fasman, G. D., 1992, Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide, Anal. Biochem. 203: 83–93.PubMedCrossRefGoogle Scholar
  174. Pflumm, M. N., and Beychok, S., 1969, Optical activity of cystine-containing proteins. II. Circular dichroism spectra of pancreatic ribonuclease A, ribonuclease S, and ribonuclease S-protein, J. Biol. Chem. 244: 3973–3981.PubMedGoogle Scholar
  175. Phillips, R. S., and Gollnick, P., 1990, The environments of Trp-248 and Trp-330 in tryptophan indolelyase from Escherichia coli, FEBS Lett. 268: 213–216.PubMedCrossRefGoogle Scholar
  176. Pillet, L., Trémeau, O., Ducancel, F., Drevet, P., Zinn-Justin, S., Pinkasfeld, S., Boulain, J.-C., and Ménez, A., 1993, Genetic engineering of snake toxins, J. Biol. Chem. 268: 909–916.PubMedGoogle Scholar
  177. Platt, J. R., 1949, Classification of spectra of cata-condensed hydrocarbons, J. Chem. Phys. 17:484–495. Potekhin, S., and Pfeil, W., 1989, Microcalorimetric studies of conformational transitions of ferricytochrome cin acidic solution, Biophys. Chem. 34: 55–62.Google Scholar
  178. Pribié, R., van Stokkum, I. H. M., Chapman, D., Haris, P. I., and Bloemendal, M., 1993, Protein secondary structure from Fourier transform infrared and/or circular dichroism spectra, Anal. Biochem. 214: 366–378.CrossRefGoogle Scholar
  179. Provencher, S. W., and Glöckner, J., 1981, Estimation of globular protein secondary structure from circular dichroism, Biochemistry 20: 33–37.PubMedCrossRefGoogle Scholar
  180. Prusiner, S. B., 1993, Genetic and infectious prion diseases, Arch. Neurol. 50: 1129–1153.PubMedCrossRefGoogle Scholar
  181. Prusiner, S. B., McKinley, M. P., Bowman, K. A., Bolton, D. C., Bendheim, P. E., Groth, D. F., and Glenner, G. G., 1983, Scrapie prions aggregate to form amyloid-like birefringent rods, Cell 35: 349–358.PubMedCrossRefGoogle Scholar
  182. Ptitsyn, O. B., 1987, Protein folding: Hypotheses and experiments, J. Protein Chem. 6: 273–293.CrossRefGoogle Scholar
  183. Ptitsyn, O. B., Pain, R. H., Semisotnov, G. V., Zerovnik, E., and Razgulyaev, O. I., 1990, Evidence for a molten globule state as a general intermediate in protein folding, FEBS Lett. 262: 20–24.PubMedCrossRefGoogle Scholar
  184. Radford, S. E., Dobson, C. M., and Evans, P. A., 1992, The folding of hen lysozyme involves partially structured intermediates and multiple pathways, Nature 358: 302–307.PubMedCrossRefGoogle Scholar
  185. Rauk, A., 1984, Chiroptical properties of disulfides. Ab initio studies of dihydrogen disulfide and dimethyl disulfide, J. Am. Chem. Soc. 106: 6517–6524.CrossRefGoogle Scholar
  186. Reed, J., and Kinzel, V., 1984, Near-and far-ultraviolet circular dichroism of the catalytic subunit of adenosine cyclic 5’-monophosphate dependent protein kinase, Biochemistry 23: 1357–1362.PubMedCrossRefGoogle Scholar
  187. Rees, A. R., Sternberg, M. J. E., and Wetzel, R., eds., 1992, Protein Engineering: A Practical Approach,Oxford University Press, London.Google Scholar
  188. Richards, F. M., and Vithayathil, P. J., 1959, The preparation of subtilisin-modified ribonuclease and the separation of the peptide and protein components, J. Biol. Chem. 234: 1459–1465.PubMedGoogle Scholar
  189. Richards, F. M., and Wyckoff, H. W., 1971, Bovine pancreatic ribonuclease, in: The Enzymes, 3rd ed., Vol. 4 ( P. D. Boyer, ed.), pp. 647–806, Academic Press, New York.Google Scholar
  190. Roberts, L. M., and Dunker, A. K., 1993, Structural changes accompanying chloroform-induced contraction of the filamentous phage fd, Biochemistry 32: 10479–10488.PubMedCrossRefGoogle Scholar
  191. Roberts, G. W., Lofthouse, R., Allsop, D., Landon, M., Kidd, M., Prusiner, S. B., and Crow, T. J., 1988, CNS amyloid proteins in neurodegenerative diseases, Neurology 38: 1534–1540.PubMedCrossRefGoogle Scholar
  192. Roder, H., and Elöve, G. A., 1994, Early stages of protein folding, in: Mechanisms of Protein Folding( R. Pain, ed.), pp. 26–54, Oxford University Press, London.Google Scholar
  193. Safar, J., Roller, P. P., Gajdusek, D. C., and Gibbs, C. J., Jr., 1994, Scrapie amyloid (prion) protein has the conformational characteristics of an aggregated molten globule folding intermediate, Biochemistry 33: 8375–8383.PubMedCrossRefGoogle Scholar
  194. St. Hilaire, P. M., Boyd, M. K., and Toone, E. J., 1994, Interaction of the Shiga-like toxin type 1 B-subunit with its carbohydrate receptor, Biochemistry 33: 14452–14463.CrossRefGoogle Scholar
  195. Samal, B. B., Arakawa, T., Boone, T. C., Jones, T., Prestrelski, S. J., Narhi, L. O., Wen, J., Stearns, G. W., Crandall, C. A., Pope, J., and Suggs, S., 1995, High level expression of human leukemia inhibitory factor (LIF) from a synthetic gene in Escherichia coliand the physical and biological characterization of the protein, Biochim. Biophys. Acta 1260: 27–34.PubMedCrossRefGoogle Scholar
  196. Sancho, J., Neira, J. L., and Fersht, A. R., 1992, An N-terminal fragment of barnase has residual helical structure similar to that in a refolding intermediate, J. Mol. Biol. 224: 749–758.PubMedCrossRefGoogle Scholar
  197. Sanders, J. C., Haris, P. I., Chapman, D., Otto, C., and Hemminga, M. A., 1993, Secondary structure of M13 coat protein in phospholipids studied by circular dichroism, Raman and Fourier transform infrared spectroscopy, Biochemistry 32: 12446–12454.PubMedCrossRefGoogle Scholar
  198. Sang, B.-C., and Gray, D. M., 1989, CD measurements show that fd and IKe gene 5 proteins undergo minimal conformational changes upon binding to poly(rA), Biochemistry 28: 9502–9507.PubMedCrossRefGoogle Scholar
  199. Sarver, R. W., Jr., and Krueger, W. C., 1991, An infrared and circular dichroism combined approach to the analysis of protein secondary structure, Anal. Biochem. 199: 61–67.PubMedCrossRefGoogle Scholar
  200. Schendel, S. L., and Cramer, W. A., 1994, On the nature of the unfolded intermediate in the in vitrotransition of colicin El channel domain from the aqueous to the membrane phase, Protein Sci. 3: 2272–2279.PubMedCrossRefGoogle Scholar
  201. Schleker, W., and Fleischhauer, J., 1987, Zum Circulardichroismus von Disulfidbrticken in Proteinen, Teil 2. Vergleichende CNDO/S- and INDO-S-CI-Rechnungen, Z. Naturforsch. 42a: 361–366.Google Scholar
  202. Searcy, D. G., Montenay-Garestier, T., Laston, D. J., and Héléne, C., 1988, Tyrosine environment and phosphate binding in the archaebacterial histone-like protein HTa, Biochim. Biophys. Acta 953: 321–333.CrossRefGoogle Scholar
  203. Sears, D. W., and Beychok, S., 1973, Circular dichroism, in: Physical Principles and Techniques of Protein Chemistry, Part C ( S. J. Leach, ed.), pp. 445–593, Academic Press, New York.Google Scholar
  204. Seery, V. L., and Farrell, H. M., Jr., 1990, Spectroscopic evidence for ligand-induced conformational change in NADP’: isocitrate dehydrogenase, J. Biol. Chem. 265: 17644–17648.PubMedGoogle Scholar
  205. Shiraki, M., 1969, Circular dichroism and optical rotatory dispersion of N-acetylaromatic amino acid amides as models for proteins, Sci. Pap. Coll. Gen. Educ. Univ. Tokyo 19: 151–173.Google Scholar
  206. Shire, S. J., McKay, P., Leung, D. W., Cachianes, G. J., Jackson, E., Wood, W. I., Raghavendra, K., Khairallah, L., and Schuster, T. M., 1990, Preparation and properties of recombinant DNA derived tobacco mosaic virus coat protein, Biochemistry 29: 5119–5126.PubMedCrossRefGoogle Scholar
  207. Shortie, D., 1989, Probing the determinants of protein folding and stability with amino acid substitutions, J. Biol. Chem. 264: 5315–5318.Google Scholar
  208. Simons, E. R., and Blout, E. R., 1968, Circular dichroism of ribonuclease A, ribonuclease S, and some fragments, J. Biol. Chem. 243: 218–221.PubMedGoogle Scholar
  209. Singh, B. R., and DasGupta, B. R., 1989, Changes in the molecular topography of the light and heavy chains of type A botulinum neurotoxin following their separation, Biophys. Chem. 34: 259–267.PubMedCrossRefGoogle Scholar
  210. Singh, B. R., Song, P.-S., Eilfeld, P., and Rüdiger, W., 1989, Differential exposure of aromatic amino acids in the red-light-absorbing and far-red-light-absorbing forms of 124-kDa oat phytochrome, Eur. J. Biochem. 184: 715–721.PubMedCrossRefGoogle Scholar
  211. Singh, J., and Thornton, J. M., 1985, The interaction between phenylalanine rings in proteins, FEBS Lett. 191: 1–6.CrossRefGoogle Scholar
  212. Sisido, M., and Imanishi, Y., 1985, One-dimensional aromatic crystals in solution. 5. Empirical energy and theoretical circular dichroism calculations on helical poly(L-1-pyrenylalanine), Macromolecules 18: 890–894.CrossRefGoogle Scholar
  213. Sisido, M., Egusa, S., and Imanishi, Y., 1983a, One-dimensional aromatic crystals in solution. 1. Synthesis, conformation, and spectroscopic properties of poly(L-1-naphthylalanine), J. Am. Chem. Soc. 105: 1041–1049.CrossRefGoogle Scholar
  214. Sisido, M., Egusa, S., and Imanishi, Y., 1983b, One-dimensional aromatic crystals in solution. 2. Synthesis, conformation, and spectroscopic properties of poly(L-2-naphthylalanine), J. Am. Chem. Soc. 105: 4077–4082.CrossRefGoogle Scholar
  215. Smith, G. D., Duax, W. L., Dodson, E. J., Dodson, G. G., de Graaf, R. A. G., and Reynolds, C. D., 1982, The structure of des-Phe B1 bovine insulin, Acta Crystallogr. Sect. B 38: 3028–3032.CrossRefGoogle Scholar
  216. Smith, M., 1986, Site-directed mutagenesis, Philos. Trans. R. Soc. London Ser. A 317: 295–304.CrossRefGoogle Scholar
  217. Snow, J. W., and Hooker, T. M., Jr., 1978, The chiroptical properties of the strychnine alkaloids: Strychnine, ß-colubrine, brucine, and their dihydro derivatives, Can. J. Chem. 56: 1222–1230.CrossRefGoogle Scholar
  218. Snow, J. W., Hooker, T. M., Jr., and Schellman, J. A., 1977, The optical properties of tyrosine-containing cyclic dipeptides, Biopolymers 16: 121–142.PubMedCrossRefGoogle Scholar
  219. Sondek, J., and Shortie, D., 1990, Accommodation of single amino acid insertions by the native state of staphylococcal nuclease, Proteins Struct. Funct. Genet. 7: 299–305.PubMedCrossRefGoogle Scholar
  220. Sondek, J., and Shortie, D., 1992, Structural and energetic differences between insertions and substitutions in staphylococcal nuclease, Proteins Struct. Funct. Genet. 13: 132–140.PubMedCrossRefGoogle Scholar
  221. Song, P. S., and Kurtin, W. E., 1969, A spectroscopic study of the polarized luminescence of indoles, J. Am. Chem. Soc. 91: 4892–4906.CrossRefGoogle Scholar
  222. Sopkova, J., Gallay, J., Vincent, M., Pancoska, P., and Lewit-Bentley, A., 1994, The dynamic behavior of annexin V as a function of calcium ion binding: A circular dichroism, uv absorption, and steady-state and time-resolved fluorescence study, Biochemistry 33: 4490–4499.PubMedCrossRefGoogle Scholar
  223. Sreerama, N., and Woody, R. W., 1993, A self-consistent method for the analysis of protein secondary structure from circular dichroism, Anal. Biochem. 209: 32–44.PubMedCrossRefGoogle Scholar
  224. Sreerama, N., and Woody, R. W., 1994, Protein secondary structure from circular dichroism spectroscopy. Combining variable selection principle and cluster analysis with neural network, ridge regression, and self-consistent methods, J. Mol. Biol. 242: 497–507.PubMedGoogle Scholar
  225. Sreerama, N., Manning, M. C., and Woody, R. W., 1991, The circular dichroism of biopolymers: Aromatic side-chain CD in proteins, Proc. 4th Int. Conf. CD, Bochum, Germany, pp. 186–201.Google Scholar
  226. Stewart, J. J. P., 1990, MOPAC 5.0, Quantum Chem. Progr. Exch. 9: 581.Google Scholar
  227. Strickland, E. H., 1972, Interactions contributing to the tyrosyl circular dichroism bands of ribonucleaseS and -A, Biochemistry 11: 3465–3474.PubMedCrossRefGoogle Scholar
  228. Strickland, E. H., 1974, Aromatic contributions to circular dichroism spectra of proteins, CRC Crit. Rev. Biochem. 2: 113–175.PubMedCrossRefGoogle Scholar
  229. Strickland, E. H., and Mercola, D. A., 1976, Near-ultraviolet tyrosyl circular dichroism of pig insulin monomers, dimers, and hexamers. Dipole—dipole coupling calculations in the monopole approximation, Biochemistry 15: 3875–3884.PubMedCrossRefGoogle Scholar
  230. Sturtevant, J. M., 1994, The thermodynamic effects of protein mutations, Curr. Opin. Struct. Biol. 4: 69–78.CrossRefGoogle Scholar
  231. Sugiyama, H., Popot, J.-L., and Changeux, J.-P., 1976, Studies on the electrogenic action of acetylcholine with Torpedo marmorataelectric organ. J. Mol. Biol. 106: 485–496.PubMedCrossRefGoogle Scholar
  232. Surewicz, W. K., Mantsch, H. H., and Chapman, D., 1993, Determination of protein secondary structure by Fourier transform infrared spectróscopy: A critical assessment, Biochemistry 32: 389–394.PubMedCrossRefGoogle Scholar
  233. Susi, H., and Byler, D. M., 1986, Resolution-enhanced Fourier transform infrared spectroscopy of enzymes, Methods Enzymol. 130: 290–311.PubMedCrossRefGoogle Scholar
  234. Symons, M. C. R., and Petersen, R. L., 1978, Electron addition to the active site of Cancer magisterhaemocyanins, Biochim. Biophys. Acta 535: 247–252.PubMedCrossRefGoogle Scholar
  235. Tadaki, D. K., and Niyogi, S. K., 1993, The functional importance of hydrophobicity of the tyrosine at position 13 of human epidermal growth factor in receptor binding, J. Biol. Chem. 268: 1011410119.Google Scholar
  236. Tagliavini, F., Prelli, F., Ghiso, J., Bugiani, O., Serban, D., Prusiner, S. B., Farlow, M. R., Ghetti, B., and Frangione, B., 1991, Amyloid protein of Gerstmann-Sträussler-Scheinker disease (Indiana kindred) is an 11 kd fragment of prion protein with an N-terminal glycine at codon 58, EMBO J. 10: 513–519.PubMedGoogle Scholar
  237. Tanaka, F., Forster, L. S., Pal, P. K., and Rupley,. J. A., 1975, The circular dichroism of lysozyme, J. Biol. Chem. 250: 6977–6982.PubMedGoogle Scholar
  238. Teichberg, V. I., Kay, C. M., and Sharon, N., 1970, Separation of contributions of tryptophans and tyrosines to the ultraviolet circular dichroism spectrum of hen egg-white lysozyme, Eur. J. Biochem. 16: 55–59.PubMedCrossRefGoogle Scholar
  239. Tetin, S. Y., Mantulin, W. W., Denzin, L. K., Weidner, K. M., and Voss, E. W., Jr., 1992, Comparative circular dichroism studies of an anti–fluorescein monoclonal antibody (Mab 4–4–20) and its derivatives, Biochemistry 31: 12029 – 12034.PubMedCrossRefGoogle Scholar
  240. Tinoco, I., Jr., 1962, Theoretical aspects of optical activity. Part two: Polymers, Adv. Chem. Phys. 4: 113160.Google Scholar
  241. van der Goot, F. G., González-Manas, J. M., Lakey, J. H., and Pattus, F., 1991, A `molten globule’ membrane-insertion intermediate of the pore-forming domain of colicin A, Nature 354: 408–410.PubMedCrossRefGoogle Scholar
  242. van der Goot, F. G., Lakey, J., Pattus, F., Kay, C. M., Sorokine, O., van Dorsselaer, A., and Buckley, J. T., 1992, Spectroscopic study of the activation and oligomerization of the channel-forming toxin aerolysin: Identification of the site of proteolytic activation, Biochemistry 31: 8566–8570.PubMedCrossRefGoogle Scholar
  243. van der Goot, F. G., Pattus, F., Wong, K. R., and Buckley, J. T., 1993a, Oligomerization of the channel-forming toxin aerolysin precedes insertion into lipid bilayers, Biochemistry 32: 2636–2642.PubMedCrossRefGoogle Scholar
  244. van der Goot, F. G., Ausio, J., Wong, K. R., Pattus, F., and Buckley, J. T., 1993b, Dimerization stabilizes the pore-forming toxin aerolysin in solution, J. Biol. Chem. 268: 18272–18279.PubMedGoogle Scholar
  245. 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.PubMedCrossRefGoogle Scholar
  246. Volbeda, A., and Hol, W. G. J., 1989, Crystal structure of hexameric haemocyanin from Panulirus interruptusrefined at 3.2 A resolution, J. Mol. Biol. 209: 249–279.PubMedCrossRefGoogle Scholar
  247. Vorherr, T., James, P., Krebs, J., Enyedi, A., McCormick, D. J., Penniston, J. T., and Carafoli, E., 1990, Interaction of calmodulin with the calmodulin binding domain of the plasma membrane Ca“ pump, Biochemistry 29: 355–365.PubMedCrossRefGoogle Scholar
  248. Voss, E. W., Jr., ed., 1984, Fluorescein Hapten: An Immunological Probe, CRC Press, Boca Raton, FL. Vuilleumier, S., Sancho, J., Loewenthal, R., and Fersht, A. R., 1993, Circular dichroism studies of barnase and its mutants: Characterization of the contribution of aromatic side chains, Biochemistry 32: 10303–10313.Google Scholar
  249. Walsh, M., Stevens, F. C., Oikawa, K., and Kay, C. M., 1979, Circular dichroism studies of native and chemically modified CaZ’-dependent protein modulator, Can. J. Biochem. 57: 267–278.PubMedGoogle Scholar
  250. Waltho, J. P., Feher, V. A., Merutka, G., Dyson, H. J., and Wright, P. E., 1993, Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin, Biochemistry 32: 6337–6347.PubMedCrossRefGoogle Scholar
  251. Warme, P. K., and Morgan, R. S., 1978, A survey of amino acid side-chain interactions in 21 proteins, J. Mol. Biol. 118: 289–304.PubMedCrossRefGoogle Scholar
  252. Weidner, K. M., Denzin, L. K., and Voss, E. W., Jr., 1992, Molecular stabilization effects of interactions between anti-metatype antibodies and liganded antibody, J. Biol. Chem. 267: 10281–10288.PubMedGoogle Scholar
  253. Wendt, B., Hofmann, T., Martin, S. R., Bayley, P., Brodin, P., Grundström, T., Thulin, E., Linse, S., and Forsén, S., 1988, Effect of amino acid substitutions and deletions on the thermal stability, the pH stability and unfolding by urea of bovine calbindin D9k, Eur. J. Biochem. 175: 439–445.PubMedCrossRefGoogle Scholar
  254. White, H. D., 1988, Kinetic mechanism of calcium binding to whiting parvalbumin, Biochemistry 27: 3357–3365.PubMedCrossRefGoogle Scholar
  255. Williams, R. W., 1986, Protein secondary structure analysis using Raman amide I and amide III spectra, Methods Enzymol. 130: 311–331.PubMedCrossRefGoogle Scholar
  256. 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.PubMedCrossRefGoogle Scholar
  257. Wingfield, P. T., Stahl, S. J., Payton, M. A., Venkatesan, S., Misra, M., and Steven, A. C., 1991, HIV-1 rev expressed in recombinant Escherichia coli: Purification, polymerization, and conformational properties, Biochemistry 30: 7527–7534.PubMedCrossRefGoogle Scholar
  258. Wishart, D. S., Sykes, B. D., and Richards, F. M., 1991, Simple techniques for the quantification of protein secondary structure by ‘H NMR spectroscopy, FEBS Lett. 293: 72–80.PubMedCrossRefGoogle Scholar
  259. Wollmer, A., 1972, Konformationsanalyse von Proteinen mit Hilfe des Circulardichroismus und der optischen Rotationsdispersion, pp. 33–55, Habilitationsschrift, RWTH, Aachen.Google Scholar
  260. Wollmer, A., Fleischhauer, J., Strassburger, W., Thiele, H., Brandenburg, D., Dodson, G., and Mercola, D., 1977, Side-chain mobility and the calculation of tyrosyl circular dichroism of proteins. Implications of a test with insulin and des-Bl-phenylalanine insulin, Biophys. J. 20: 233–243.PubMedCrossRefGoogle Scholar
  261. Wollmer, A., Strassburger, W., Hoenjet, E., Glatter, U., Fleischhauer, J., Mercola, D. A., de Graaf, R. A. G., Dodson, E. J., Dodson, G. G., Smith, D. G., Brandenburg, D., and Danho, W., 1980, Correlation of structural details of insulin in the crystal and in solution, in: Insulin: Chemistry, Structure and Function of Insulin and Related Hormones(D. Brandenburg and A. Wollmer, eds.), pp. 27–35, de Gruyter, Berlin.Google Scholar
  262. Wong, K.-P., and Tanford, C., 1973, Denaturation of bovine carbonic anhydrase B by guanidine hydrochloride, J. Biol. Chem. 248: 8518–8523.PubMedGoogle Scholar
  263. Wood, S. P., Blundell, T. L., Wollmer, A., Lazarus, N. R., and Neville, R. W. J., 1975, Relation of conformation and association of insulin to receptor binding. X-ray and circular-dichroism studies on bovine and hystricomorph insulins, Eur. J. Biochem. 55: 531–542.PubMedCrossRefGoogle Scholar
  264. Woody, R. W., 1968, Improved calculation of the mr*rotational strength in polypeptides, J. Chem. Phys. 49: 4797–4806.PubMedCrossRefGoogle Scholar
  265. Woody, R. W., 1972, The circular dichroism of aromatic polypeptides: Theoretical studies of poly-Lphenylalanine and some para-substituted derivatives, Biopolymers11: 1149–1171.PubMedCrossRefGoogle Scholar
  266. Woody, R. W., 1973, Application of the Bergson model to the optical properties of chiral disulfides, Tetrahedron 29: 1273–1283.CrossRefGoogle Scholar
  267. Woody, R. W., 1977, Optical rotatory properties of biopolymers, J. Polym. Sci. Macromol. Rev. 12: 181–230.CrossRefGoogle Scholar
  268. Woody, R. W., 1978, Aromatic side-chain contributions to the far ultraviolet circular dichroism of peptides and proteins, Biopolymers 17: 1451–1467.CrossRefGoogle Scholar
  269. Woody, R. W., 1985, Circular dichroism of peptides, in: The Peptides, Vol. 7 ( V. J. Hruby, ed.), pp. 15–114, Academic Press, New York.Google Scholar
  270. Woody, R. W., 1994, Contribution of tryptophan side chains to the far-ultraviolet circular dichroism of proteins, Eur. Biophys. J. 23: 253–262.PubMedCrossRefGoogle Scholar
  271. Woody, R. W., 1995, Circular dichroism, Methods Enzymol. 246: 34–71.PubMedCrossRefGoogle Scholar
  272. Woody, R. W., and Tinoco, I., Jr., 1967, Optical rotation of oriented helices. III. Calculation of the rotatory dispersion and circular dichroism of the alpha and 310-helix, J. Chem. Phys. 46: 4927–4945.CrossRefGoogle Scholar
  273. Wu, C.-S. C., Sun, X. H., and Yang, J. T., 1990, Conformation of acetylcholine receptor in the presence of agonists and antagonists, J. Protein Chem. 9: 119–126.PubMedCrossRefGoogle Scholar
  274. Wu, L. C., Laub, P. B., Elöve, G. A., Carey, J., and Roder, H., 1993, A noncovalent peptide complex as a model for an early folding intermediate of cytochrome c, Biochemistry 32: 10271–10276.CrossRefGoogle Scholar
  275. Yamamoto, Y., and Tanaka, J., 1972, Polarized absorption spectra of crystals of indole and its related compounds, Bull. Chem. Soc. Jpn. 45: 1362–1366.CrossRefGoogle Scholar
  276. Yanari, S., and Bovey, F. A., 1960, Interpretation of the ultraviolet spectral changes of proteins, J. Biol. Chem. 235: 2818–2826.PubMedGoogle Scholar
  277. Yang, J. T., Wu, C.-S., and Martinez, H. M.,, 1986, Calculation of protein conformation from circular dichroism, Methods Enzymol. 130: 208–269.Google Scholar
  278. Yang, B., Gathy, K. N., and Coleman, M. S., 1994, Mutational analysis of residues in the nucleotide binding domain of human terminal deoxynucleotidyl transferase, J. Biol. Chem. 269:11859–11868. Yang, Y., Kuramitsu, S., Nakae, Y., Ikeda, K., and Hamaguchi, K., 1976, Interactions of a-and ß-Nacetyl-o-glucosamine with hen and turkey lysozymes, J. Biochem. (Tokyo) 80: 425–434.Google Scholar
  279. Yasui, S. C., and Keiderling, T. A., 1986, Vibrational circular dichroism of polypeptides. VI. Polytyrosine a-helical and random-coil results, Biopolymers 25: 5–15.PubMedCrossRefGoogle Scholar
  280. Yasui, S. C., Keiderling, T. A., and Katakai, R., 1987, Vibrational circular dichroism of polypeptides. X. A study of a-helical oligopeptides in solution, Biopolymers 26: 1407–1412.PubMedCrossRefGoogle Scholar
  281. Zhang, J.-G., Reid, G. E., Moritz, R. L., Ward, L. D., and Simpson, R. J., 1993, Specific covalent modification of the tryptophan residues in murine interleukin-6. Effect on biological activity and conformational stability, Eur. J. Biochem. 217: 53–59.PubMedCrossRefGoogle Scholar
  282. Zhang, R.-G., Joachimiak, A., Lawson, C. L., Schevitz, R. W., Otwinowski, Z., and Sigler, P. B., 1987, The crystal structure of trpaporepressor at 1.8 A shows how binding tryptophan enhances DNA affinity, Nature 327:591–597.SGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1996

Authors and Affiliations

  • Robert W. Woody
    • 1
  • A. Keith Dunker
    • 2
  1. 1.Department of Biochemistry and Molecular BiologyColorado State UniversityFort CollinsUSA
  2. 2.Department of Biochemistry and BiophysicsWashington State UniversityPullmanUSA

Personalised recommendations