Identification of Membrane Proteins and Soluble Protein Secondary Structural Elements, Domain Structure, and Packing Arrangements by Fourier-Transform Amphipathic Analysis

  • Janet Finer-Moore
  • J. Fernando Bazan
  • John Rubin
  • Robert M. Stroud


The value of a model is that is simplifies the description of a system: it focuses attention onto potentially critical features, and it will be superseded by better models that explain more. Above all it suggests critical and focused experimental tests designed to refine the model, eliminate inconsistency, and uncover function.


Acetylcholine Receptor Membrane Domain Amphipathic Helix Phosphoglycerate Mutase Hydrophobic Moment 
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.


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  1. Adelman, J. P., Mason, A. J., Hayflick, J. S., and Seeburg, P. H., 1986, Isolation of the gene and hypothalamic cDNA for the common precursor of gonadotropin-releasing hormone and prolactin release-inhibiting factor in human and rat, Proc. Natl. Acad. Sci. U.S.A. 83:179–183.PubMedCrossRefGoogle Scholar
  2. Agard, D. A., and Stroud, R. M., 1982, Linking regions between helices in bacteriorhodopsin revealed, Biophys. J. 37:589–602.PubMedGoogle Scholar
  3. Amzel, L. M., and Poljak, R. J., 1979, Three-dimensional structure of immunoglobins, Annu. Rev. Biochem. 48:961–997.PubMedCrossRefGoogle Scholar
  4. Argos, P., Rao, J. K. M., and Hargrave, P. A., 1982, Structural prediction of membrane-bound proteins, Eur. J. Biochem. 128:565–575.PubMedCrossRefGoogle Scholar
  5. Basson, M. E., Thorsness, M., Finer-Moore, J., Stroud, R. M., and Rine, J., 1988, Structural and functional conservation between yeast and human 3-hydroxy-3-methylglutaryl coenzyme A reductases, the rate-limiting enzyme of sterol biosynthesis, Molecular and Cellular Biology, 8:3797–3808.PubMedGoogle Scholar
  6. Bazan, J. F., Fletterick, R. J., and Pilkis, S. J., 1988, Evolution of a bifunctional enzyme: 6-Phosphofructo-2,6-bisphosphate, Proc. Natl. Acad. Sci., submitted.Google Scholar
  7. Bishop, J. M., and Varmus, H. E., 1985, Functions and origins ofretroviral transforming genes, in: Molecular Biology of Tumor Viruses (R. Weiss, R. Teich, H. Varmus, and J. Coffin, eds.), Cold Spring Harbor Laboratory Press, New York, pp. 249–356.Google Scholar
  8. Blundell, T. L., Pitts, J. E., Tickle, I. J., Wood, S. P., and Wu, C.-W., 1981, X-ray analysis (1.4-Å resolution) of avian pancreatic polypeptide: Small globular protein hormone, Proc. Natl. Acad. Sci. U.S.A. 78:4175–4179.PubMedCrossRefGoogle Scholar
  9. Bourne, H. R., 1986, GTP-binding proteins: One molecular machine can transduce diverse signals, Nature 321: 814.PubMedCrossRefGoogle Scholar
  10. Branden, C.-I., 1980, Relation between structure and function of α/ß-proteins, Q. Rev. Biophys. 13:317–338.CrossRefGoogle Scholar
  11. Brown, M. S., and Goldstein, J. L., 1980, Multivalent feedback regulation of HMG CoA reductase, a control mechanism coordinating isoprenoid synthesis and cell growth, J. Lipid Res. 21:505–517.PubMedGoogle Scholar
  12. Chang, E. L., Yager, P., Williams, R. W., and Dalziel, A. W., 1983, The secondary structure of reconstituted acetylcholine receptor as determined by Raman spectroscopy, Biophys. J. 41:65a.Google Scholar
  13. Chin, D. J., Gil, G., Russell, D. W., Liscum, L., Luskey, K. L., Basu, S. K., Okayama, H., Berg, P., Goldstein, J. L., and Brown, M. S., 1984, Nucleotide sequence of 3-hydroxy-3-methyl-glutaryl coenzyme A reductase, a glycoprotein of endoplasmic reticulum, Nature 308:613–617.PubMedCrossRefGoogle Scholar
  14. Choe, S., 1987, Structural Study of Channel-Forming Proteins, Ph.D. Thesis, University of California, Berkeley.Google Scholar
  15. Chou, P. Y., and Fasman, G. D., 1974, Prediction of protein conformation, Biochemistry 13:222–245.PubMedCrossRefGoogle Scholar
  16. Claudio, T., Ballivet, M., Patrick, J., and Heinemann, S., 1983, Nucleotide and deduced amino acid sequences of Torpedo calilornica acetylcholine receptor α subunit, Proc. Natl. Acad. Sci. U.S.A. 80:1111–1115.PubMedCrossRefGoogle Scholar
  17. Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J., 1983, Secondary structure assignment for α/ß proteins by a combinatorial approach, Biochemistry 22:4894–4904.PubMedCrossRefGoogle Scholar
  18. Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J., 1986, Tum prediction in proteins using a pattern-matching approach, Biochemistry 25:266–275.PubMedCrossRefGoogle Scholar
  19. Colosia, A. D., Lively, M., El-Maghrabi, M. R., and Pilkis, S. J., 1987, Isolation ofa cDNA clone for rat liver 6-phosphofructo 2-kinase/fructose 2,6-bisphosphatase, Biochem. Biophys. Res. Commun. 143:1092–1098.PubMedCrossRefGoogle Scholar
  20. Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A., and DeLisi, C., 1987, Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins, J. Mol. Biol. 195:659–685.PubMedCrossRefGoogle Scholar
  21. Creighton, T. E., Hillson, D. A., and Freedman, R. B., 1980, Catalysis by protein-disulphide isomerase of the unfolding and refolding of proteins with disulphide bonds, J. Mol. Biol. 142:43–62.PubMedCrossRefGoogle Scholar
  22. Deisenhofer, J., Epp, O., Miki, K., Huber, R., and Michel, H., 1985, Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution, Nature 318:618–624.CrossRefGoogle Scholar
  23. Dever, T. E., Glynias, M. J., and Merrick, W. C., 1987, GTP-binding domain: Three consensus sequence elements with distinct spacing, Proc. Natl. Acad. Sci. U.S.A. 84:1814–1818.PubMedCrossRefGoogle Scholar
  24. Devillers-Thiery, A., Giraudat, J., Bentaboulet, M., and Changeux, J.-P., 1983, Complete mRNA coding sequence of the acetylcholine binding α-subunit from Torpedo marmorata: A model for the transmembrane organization of the polypeptide chain, Proc. Natl. Acad. Sci. U.S.A. 80:2067–2071.PubMedCrossRefGoogle Scholar
  25. Drew, H. R., III, and Travers, A. A., 1985, Structural junctions in DNA: The influence of flanking sequence on nuclease digestion specificities, Nucleic Acids Res. 13:4445–4467.PubMedCrossRefGoogle Scholar
  26. Dunn, S. M. J., Conti-Tronconi, B. M., and Raftery, M. A., 1986, Acetylcholine receptordimers are stabilized by extracellular disulfide bonding, Biochem. Biophys. Res. Commun. 139:830–837.PubMedCrossRefGoogle Scholar
  27. Dunnill, P., 1968, The use of helical net-diagrams to represent protein structures, Biophys. J. 8:865–875.PubMedCrossRefGoogle Scholar
  28. Edman, J. C., Ellis, L., Blacher, R. W., Roth, R. A., and Rutter, W. J., 1985, Sequence of protein disulphide isomerase and implications of its relationship to thioredoxin, Nature 317:267–270.PubMedCrossRefGoogle Scholar
  29. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1982a, The helical hydrophobic moment: A measure of the amphiphilicity of a helix, Nature 299:371–374.PubMedCrossRefGoogle Scholar
  30. Eisenberg, D., Weiss, R. M., Terwilliger, T. C., and Wilcox, W., 1982b, Hydrophobic moments and protein structure, Faraday Symp. Chem. Soc. 17:109–120.CrossRefGoogle Scholar
  31. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1984a, The hydrophobic moment detects periodicity in protein hydrophobicity, Proc. Natl. Acad. Sci. U.S.A. 81:140–144.PubMedCrossRefGoogle Scholar
  32. Eisenberg, D., Schwarz, E., Komaromy, M., and Wall, R., 1984b, Analysis of membrane and surface protein sequences with the hydrophobic moment plot, J. Mol. Biol. 179:125–142.PubMedCrossRefGoogle Scholar
  33. El-Maghrabi, M. R., and Pilkis, S. J., 1984, Rat liver 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase: A review of relationships between the two activities of the enzyme, J. Cell. Biochem. 26:1–17.PubMedCrossRefGoogle Scholar
  34. El-Maghrabi, M. R., Pate, T. M., Murray, K. J., and Pilkis, S. J., 1984a, Differential effects of proteolysis and protein modification on the activities of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, J. Biol. Chem. 259:13096–13103.PubMedGoogle Scholar
  35. El-Maghrabi, M. R., Pate, T. M., Pilkis, J., and Pilkis, S. J., 1984b, Effect of sulfhydryl modification on the activities of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, J. Biol. Chem. 259:13104–13110.PubMedGoogle Scholar
  36. El-Maghrabi, M. R., Pate, T. M., D’Angelo, G., Correia, J. J., Lively, M. O., and Pilkis, S. J., 1987, Rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase: Identification of essential sulfhydryl residues in the primary sequence of the enzyme, J. Biol. Chem. 262:11714–11720.PubMedGoogle Scholar
  37. Emr, S., Vassarotti, A., Garrett, J., Geller, B., Takeda, M., and Douglas, M. G., 1986, The amino temrinus of the yeast F1-A TPase ß-subunit precursor functions as a mitochondrial import signal, J. Cell Biol. 102:523–533.PubMedCrossRefGoogle Scholar
  38. Engelman, D. M., and Zaccai, G., 1980, Bacteriorhodopsin is an inside-out protein, Proc. Natl. Acad. Sci. U.S.A. 77:5894–5898.PubMedCrossRefGoogle Scholar
  39. Engelman, D. M., Henderson, R., McLachlan, A. D., and Wallace, B. A., 1980, Path of the polypeptide in bacteriorhodopsin, Proc. Natl. Acad. Sci. U.S.A. 77:2023–2027.PubMedCrossRefGoogle Scholar
  40. Engelman, D. M., Goldman, A., and Steitz, T. A., 1982, The identification of helical segments in the polypeptide chain of bacteriorhodopsin, Methods Enzymol. 88:81–88.CrossRefGoogle Scholar
  41. Faust, J. R., Luskey, K. L., Chin, D. J., Goldstein, J. L., and Brown, M. S., 1982, Regulation of synthesis and degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase by low density lipoprotein and 25-hydroxycholesterol in UT-1 cells, Proc. Natl. Acad. Sci. U.S.A. 79:5205–5209.PubMedCrossRefGoogle Scholar
  42. Finer-Moore, J., and Stroud, R. M., 1984, Amphipathic analysis and possible formation of the ion channel in an acetylcholine receptor, Proc. Natl. Acad. Sci. U.S.A. 81:155–159.PubMedCrossRefGoogle Scholar
  43. Fothergill, L. A., and Harkins, R. N., 1982, The amino acid sequence of yeast phosphoglycerate mutase, Proc. R. Soc. London [Biol.] 215:19–44.CrossRefGoogle Scholar
  44. Freedman, R. B., Brockway, B. E., and Lambert, N., 1984, Protein disulphide-isomerase and the formation of native disulphide bonds, Biochem. Soc. Trans. 12:929–932.PubMedGoogle Scholar
  45. Garnier, J., Osguthorpe, D. J., and Robson, B., 1978, Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins, J. Mol. Biol. 120:97–120.PubMedCrossRefGoogle Scholar
  46. Gilman, A. G., 1984, G proteins and dual control of adenylate cyclase, Cell 36:577–579.PubMedCrossRefGoogle Scholar
  47. Gray, P. W., Leung, D. W., Pennica, D., Yelverton, E., Najarian, R., Simonsen, C. C., Derynck, R., Sherwood, P. J., Wallace, D. M, Berger, S. L., Levinson, A. D., and Goeddel, D. V., 1982, Expression of human immune interferon cDNA in E. coli and monkey cells, Nature 295:503–508.PubMedCrossRefGoogle Scholar
  48. Grenningloh, G., Rienitz, A., Schmitt, B., Methfessel, C., Zensen, M., Beyreuther, K., Gundelfinger, E. D., and Betz, H., 1987, The strychnine-binding subunit of the glycine receptor shows homology with nicotinic acetylcholine receptors, Nature 328:215–220.PubMedCrossRefGoogle Scholar
  49. Gunsalus, R. P., and Yanofsky, C., 1980, Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor, Proc. Natl. Acad. Sci. U.S.A. 77:7117–7121.PubMedCrossRefGoogle Scholar
  50. Halliday, K., 1984, Regional homology in GTP-binding proto-oncogene products and elongation factors, J. Cyclic Nucleotide Res. 9:435–448.Google Scholar
  51. Han, C.-H., and Rose, Z. B., 1979, Active site phosphohistidine peptides from red cell bisphosphoglycerate synthase and yeast phosphoglycerate mutase, J. Biol. Chem. 254:8836–8840.PubMedGoogle Scholar
  52. Hardy, L. W., Finer-Moore, J. S., Montfort, W. R., Jones, M. O., Santi, D. V., and Stroud, R. M., 1987, Atomic structure of thymidylate synthase: Target for rational drug design, Science 235:448–455.PubMedCrossRefGoogle Scholar
  53. Hass, L. T., Place, A. R., Miller, K. B., and Powers, D. A., 1980, The isolation and characterization of an active site phosphohistidine peptide from human erythrocyte bisphosphoglycerate synthase, Biochem. Biophys. Res. Commun. 95:1570–1576.PubMedCrossRefGoogle Scholar
  54. Heil, A., Muller, G., Noda, L. H., Pinder, T., Schirmer, I., Schirmer, R. H., and von Zabem, I., 1974, The amino acid sequence of porcine adenylate kinase from skeletal muscle, Eur. J. Biochem. 43:131–144.PubMedCrossRefGoogle Scholar
  55. Henderson, R., and Unwin, P. N. T., 1975, Three-dimensional model of purple membrane obtained by electron microscopy, Nature 257:28–32.PubMedCrossRefGoogle Scholar
  56. Holmgren, A., Soderberg, B. O., Eklund, H., and Branden, C. I., 1975, Three-dimensional structure of Escherichia coli thioredoxin-S2 to 2.8 Å resolution, Proc. Natl. Acad. Sci. U.S.A. 72:2305–2309.PubMedCrossRefGoogle Scholar
  57. Hopp, T. P., 1986, Protein surface analysis. Methods for identifying antigenic determinants and other interaction sites, J. Immunol. Methods 88:1–18.PubMedCrossRefGoogle Scholar
  58. Hurley, J. B., Simon, M. I., Teplow, D. B., Robishaw, J. D., and Gilman, A. G., 1984, Homologies between signal transducing G proteins and ras gene products, Science 226:860–862.PubMedCrossRefGoogle Scholar
  59. Itoh, H., Kozasa, T., Nagata, S., Nakamura, S., Katada, T., Vi, M., Iwai, S., Ohtsuka, E., Kawasaki, H., Suzuki, K., and Kaziro, Y., 1986, Molecular cloning and sequence determination of cDNAs for α subunits of the guanine nucleotide-binding proteins Gs, Gi, and Go from rat brain, Proc. Natl. Acad. Sci. U.S.A. 83: 3776–3780.PubMedCrossRefGoogle Scholar
  60. Joulin, V., Peduzzi, J., Romeo, P.-H., Rosa, R., Valentin, C., Dubart, A., Lapeyre, B., Blouquit, Y., Garel, M.-C., Goossens, M., Rosa, J., and Cohen-Solal, M., 1986, Molecular cloning and sequencing of the human erythrocyte 2,3-bisphosphoglycerate mutase eDNA: Revised amino acid sequence, EMBO J. 5: 2275–2283.PubMedGoogle Scholar
  61. Jurnak, F., 1985, Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene products, Science 230:32–36.PubMedCrossRefGoogle Scholar
  62. Kabsch, W., and Sander, C., 1984, On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations, Proc. Natl. Acad. Sci. U.S.A. 81:1075–1078.PubMedCrossRefGoogle Scholar
  63. Kaiser, E. T., and Kezdy, F. J., 1983, Secondary structures of proteins and peptides in amphiphilic environments (a review), Proc. Natl. Acad. Sci. U.S.A. 80:1137–1143.PubMedCrossRefGoogle Scholar
  64. Katre, N. V., and Stroud, R. M., 1981, A probable linking sequence between two transmembrane components of bacteriorhodopsin, FEBS Lett. 136: 170–174.CrossRefGoogle Scholar
  65. Khorana, H. G., Gerber, G. E., Herlihy, W. C., Gray, C. P., Anderegg, R. J., Nihei, K., and Biemann, K., 1979, Amino acid sequence of bacteriorhodopsin, Proc. Natl. Acad. Sci. U.S.A. 76:5046–5050.PubMedCrossRefGoogle Scholar
  66. Kistler, J., Stroud, R. M., Klymkowsky, M. W., Lalancette, R. A., and Fairclough, R. H., 1982, Structure and function of an acetylcholine receptor, Biophys. J. 37:371–381.PubMedCrossRefGoogle Scholar
  67. Kuhn, L. A., and Leigh, J. S., Jr., 1985, A statistical technique for predicting membrane protein structure, Biochim. Biophys. Acta 828:351–361.PubMedCrossRefGoogle Scholar
  68. Kyte, J., and Doolittle, R. F., 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157:105–132.PubMedCrossRefGoogle Scholar
  69. La Cour, T. F. M., Nyborg, J., Thirup, S., and Clark, B. F. C., 1985, Structural details of the binding of guanosine diphosphate to elongation factor Tu from E. coli as studied by x-ray crystallography, EMBO J. 4:2385–2388.PubMedGoogle Scholar
  70. Lewis, C. A., and Stevens, C. F., 1983, Acetylcholine receptor channel ionic selectivity: Ions experience an aqueous environment, Proc. Natl. Acad. Sci. U.S.A. 80:6110–6113.PubMedCrossRefGoogle Scholar
  71. Lim, V. I., 1974, Algorithms for prediction of α-helical and ß structural regions in globular proteins, J. Mol. Biol. 88:873–894.PubMedCrossRefGoogle Scholar
  72. Lindstrom, J., Criado, M., Hochschwender, S., Fox, J. L., and Sarin, V., 1984, Immunochemical tests of acetylcholine receptor subunit models, Nature 311:573–575.PubMedCrossRefGoogle Scholar
  73. Liscum, L., Cummings, R. D., Anderson, R. G. W., DeMartino, G. N., Goldstein, J. L., and Brown, M. S., 1983, 3-Hydroxy-3-methylglutaryl-CoA reductase: A transmembrane glycoprotein of the endoplasmic reticulum with N-linked “high-mannose” oligosaccharides, Proc. Natl. Acad. Sci. U.S.A. 80:7165–7169.PubMedCrossRefGoogle Scholar
  74. Liscum, L., Finer-Moore, J., Stroud, R. M., Luskey, K. L., Brown, M. S., and Goldstein, J. L., 1985, Domain structure of 3-hydroxy-3-methylglutaryl coenzyme A reductase, a glycoprotein of the endoplasmic reticulum, J. Biol. Chem. 260:522–530.PubMedGoogle Scholar
  75. Lively, M. O., El-Maghrabi, M. R., Pilkis, J., D’Angelo, G., Colosia, A. D., Ciavola, J., Fraser, B. A., and Pilkis, S. J., 1988, Complete amino acid sequence of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, J. Biol. Chem. 263:839–849.PubMedGoogle Scholar
  76. Lochrie, M. A., Hurley, J. B., and Simon, M. I., 1985, Sequence of the a subunit of photoreceptor G protein: Homologies between transducin, ras, and elongation factors, Science 228:96–99.PubMedCrossRefGoogle Scholar
  77. Luskey, K. L., and Stevens, B., 1985, Human 3-hydroxy-3-methylglutaryl coenzyme A reductase. Conserved domains responsible for catalytic activity and sterol-regulated degradation, J. Biol. Chem. 260: 10271–10277.PubMedGoogle Scholar
  78. Maizel, J. V., and Lenk, R. P., 1981, Enhanced graphic matrix analysis of nucleic acid and protein sequences, Proc. Natl. Acad. Sci. U.S.A. 78:7665–7669.PubMedCrossRefGoogle Scholar
  79. Masters, S. B., Stroud, R. M., and Bourne, H. R., 1986, Family of G protein a chains: Amphipathic analysis and predicted structure of functional domains, Protein Eng. 1:47–54.PubMedCrossRefGoogle Scholar
  80. McCarthy, M. P., Earnest, J. P., Young, E. F., Choe, S., and Stroud, R. M., 1986, The molecular neurobiology of the acetylcholine receptor, Annu. Rev. Neurosci. 9:383–413.PubMedCrossRefGoogle Scholar
  81. McClarin, J. A., Frederick, C. A., Wang, B.-C., Greene, P., Boyer, H. W., Grable, J., and Rosenberg, J. M., 1986, Structure of the DNA-Eco R1 endonuclease recognition complex at 3 Å resolution, Science 234: 1526–1541.PubMedCrossRefGoogle Scholar
  82. McCrea, P., Popot, J.-L., and Engelman, D., 1986, Accessibility of the acetylcholine receptor δ chain C-terminus to hydrophilic reagents in reconstituted vesicles, Biophys. J. 49:355a.Google Scholar
  83. McLachlan, A. D., 1971, Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome C551, J. Mol. Biol. 61:409–424.PubMedCrossRefGoogle Scholar
  84. McLachlan, A. D., and Kam, J., 1983, Periodic features in the amino acid sequence of nematode myosin rod, J. Mol. Biol. 164:605–626.PubMedCrossRefGoogle Scholar
  85. McLachlin, A. D., and Stewart, M., 1976, The 14-fold periodicity in α-tropomyosin and the interaction with actin, J. Mol. Biol. 103:271–298.CrossRefGoogle Scholar
  86. Medynski, D. C., Sullivan, K., Smith, D., Van Dop, C., Chang, F. H., Fung, B. K. K., Seeburg, P. H., and Bourne, H. R., 1985, Amino acid sequence of the α subunit of transducin deduced from the cDNA sequence, Proc. Natl. Acad. Sci. U.S.A. 82:4311–4315.PubMedCrossRefGoogle Scholar
  87. Michel, H., Weyer, K. A., Gruenberg, H., Dunger, I., Oesterhelt, D., and Lottspeich, F., 1986, The ‘light’ and ‘medium’ subunits of the photosynthetic reaction centre from Rhodopseudomonas viridis: Isolation of the genes, nucleotide and amino acid sequence, EMBO J. 5:1149–1158.PubMedGoogle Scholar
  88. Miller, J., McLachlan, A. D., and Klug, A., 1985, Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes, EMBO J. 4:1609–1614.PubMedGoogle Scholar
  89. Moller, W., and Amons, R., 1985, Phosphate-binding sequences in nucleotide-binding proteins, FEBS Lett. 186:1–7.PubMedCrossRefGoogle Scholar
  90. Moore, W. M., Holliday, L. A., Puett, D., and Brady, R. N., 1974, On the conformation of the acetylcholine receptor protein from Torpedo nobiliana, FEBS Lett. 45:145–149.PubMedCrossRefGoogle Scholar
  91. Murray, K. J., El-Maghrabi, M. R., Kountz, P. D., Lukas, T. J., Soderling, T. R., and Pilkis, S. J., 1984, Amino acid sequence of the phosphorylation site of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, J. Biol. Chem. 259:7673–7681.PubMedGoogle Scholar
  92. Nathans, J., and Hogness, D. S., 1983, Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin, Cell 34:807–814.PubMedCrossRefGoogle Scholar
  93. Nikolics, K., Mason, A. J., Szonyi, E., Ramachandran, J., and Seeburg, P. H., 1985, A prolactin-inhibiting factor within the precursor for human gonadotropin-releasing hormone, Nature 316:511–517.PubMedCrossRefGoogle Scholar
  94. Noda, M., Takahashi, H., Tanabe, T., Toyosato, M., Furutani, Y., Hirose, T., Asai, M., Inayama, S., Miyata, T., and Numa, S., 1982, Primary structure of α-subunit precursor of Torpedo californica acetylcholine receptor deduced from a cDNA sequence, Nature 299:793–797.PubMedCrossRefGoogle Scholar
  95. Noda, M., Takahashi, H., Tanabe, T., Toyosato, M., Kikyotani, S., Hirose, T., Asai, M., Takashima, H., Inayama, S., Miyata, T., and Numa, S., 1983a, Primary structures of ß and δ-subunit precursors of Torpedo californica acetylcholine receptor deduced from cDNA sequences, Nature 301:251–255.PubMedCrossRefGoogle Scholar
  96. Noda, M., Takahashi, H., Tanabe, T., Toyosato, M., Kikyotani, S., Furutani, Y., Hirose, T., Takashima, H., Inayama, S., Miyata, T., and Numa, S., 1983b, Structural homology of Torpedo californica acetylcholine receptor subunits, Nature 302:528–532.PubMedCrossRefGoogle Scholar
  97. Ohlendorf, D. H., and Matthews, B. W., 1983, Structural studies of protein-nucleic acid interactions, Annu. Rev. Biophys. Bioeng. 12:259–284.PubMedCrossRefGoogle Scholar
  98. Ovchinnikov, Yu. A., Abdulaev, N. G., Feigina, M. Yu., Kiseiev, A. V., and Lobanov, N. A., 1979, The structural basis of the functioning of bacteriorhodopsin: An overview, FEBS Lett. 100:219–224.PubMedCrossRefGoogle Scholar
  99. Perutz, M. F., Kendrew, J. C., and Watson, H. C., 1965, Structure and function of haemoglobin. II. Some relations between polypeptide chain configuration and amino acid sequence, J. Mol. Biol. 13:669–678.CrossRefGoogle Scholar
  100. Pilkis, S. J., Fox, E., Wolfe, L., Rothbarth, L., Colosia, A., Stewart, H. B., and El-Maghrabi, M. R., 1986, Hormonal modulation of key hepatic regulatory enzymes in the gluconeogenic/glycolytic pathway, Ann. N.Y. Acad. Sci. 478:1–19.PubMedCrossRefGoogle Scholar
  101. Pilkis, S. J., Claus, T. H., Kountz, P. D., and Maghrabi, M. R., 1987, Enzymes of the fructose-6-phosphate fructose-1,6-bisphosphate substrate cycle, in: The Enzymes, Volume 28 (P. D. Boyer and E. G. Krebs, eds.), Academic Press, New York, pp. 3–45.Google Scholar
  102. Popot, J.-L., and Changeux, J.-P., 1984, Nicotinic receptor of acetylcholine: Structure of an oligomeric integral membrane protein, Physiol. Rev. 64:1162–1239.PubMedGoogle Scholar
  103. Rao, J. K. M., and Argos, P., 1986, A conformational preference parameter to predict helices in integral membrane proteins, Biochim. Biophys. Acta 869:197–214.CrossRefGoogle Scholar
  104. Ratnam, M., Sargent, P., Sarin, V., Fox, J. L., LeNguyen, D., Rivier, J., Criado, M., and Lindstrom, J., 1986, Location of antigenic determinants on primary sequences of subunits of nicotinic acetylcholine receptor by peptide mapping, Biochemistry 25:2621–2632.PubMedCrossRefGoogle Scholar
  105. Reeke, G. N., Jr., Becker, J. W., and Edelman, G. M., 1975, The covalent and three-dimensional structure of concanavalin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure, J. Biol. Chem. 250: 1525–1547.PubMedGoogle Scholar
  106. Reynolds, G., Basu, S. K., Osborne, T. F., Chin, D. J., Gil, G., Brown, M. S., Goldstein, J. L., and Luskey, K. L., 1984, HMG CoA reductase: A negatively regulated gene with unusual promoter and 5′ untranslated regions, Cell 38:275–286.PubMedCrossRefGoogle Scholar
  107. Rhodes, D., and Klug, A., 1986, An underlying repeat in some transcriptional control sequences corresponding to half a double helical turn of DNA, Cell 46:123–132.PubMedCrossRefGoogle Scholar
  108. Robishaw, J. D., Russell, D. W., Harris, B. A., Smigel, M. D., and Gilman, A. G., 1986, Deduced primary structure of the α subunit of the GTP-binding stimulatory protein of adenylate cyclase, Proc. Natl. Acad. Sci. U.S.A. 83:1251–1255.PubMedCrossRefGoogle Scholar
  109. Rose, G. D., Gierasch, L. M., and Smith, J. A., 1985, Turns in peptides and proteins, Adv. Protein Chem. 37: 1–109.PubMedCrossRefGoogle Scholar
  110. Rose, Z. B., 1980, The enzymology of 2,3-bisphosphoglycerate, Adv. Enzymol. 51:211–253.PubMedGoogle Scholar
  111. Ross, M. J., Klymkowsky, M. W., Agard, D. A., and Stroud, R. M., 1977, Structural studies of a membrane-bound acetylcholine receptor from Torpedo californica, J. Mol. Biol. 116:635–659.PubMedCrossRefGoogle Scholar
  112. Roth, R. A., and Koshland, M. E., 1981, Role of disulfide interchange enzyme in immunoglobulin synthesis, Biochemistry 20:6594–6599.PubMedCrossRefGoogle Scholar
  113. Schevitz, R. W., Otwinowski, Z., Joachimiak, A., Lawson, C. L., and Sigler, P. B., 1985, The three-dimensional structure of trp repressor, Nature 317:782–786.PubMedCrossRefGoogle Scholar
  114. Schiffer, M., and Edmundson, A. B., 1967, Use of helical wheels to represent the structures of proteins and to identify segments with helical potential, Biophys. J. 7:121–135.PubMedCrossRefGoogle Scholar
  115. Schofield, P. R., Darlison, M. G., Fujita, N., Burt, D. R., Stephenson, F. A., Rodriguez, H., Rhee, L. M., Ramachandran, J., Reale, V., Glencorse, T. A., Seeburg, P. H., and Barnard, E. A., 1987, Sequence and functional expression of the GABA receptor shows a ligand-gated receptor super-family, Nature 328:221–227.PubMedCrossRefGoogle Scholar
  116. Schulz, G. E., Elzinga, M., Marx, F., and Schirmer, R. H., 1974, Three dimensional structure of adenyl kinase, Nature 250:120–123.PubMedCrossRefGoogle Scholar
  117. Skalnik, D. G., and Simoni, R. D., 1985, The nucleotide sequence of syrian hamster HMG-CoA reductase cDNA, DNA 4:439–443.PubMedCrossRefGoogle Scholar
  118. Stroud, R. M., and Finer-Moore, J., 1985, Acetylcholine receptor structure, function, and evolution, Annu. Rev. Cell Biol. 1:317–351.PubMedCrossRefGoogle Scholar
  119. Stryer, L., 1986, Cyclic GMP cascade of vision, Annu. Rev. Neurosci. 9:87–119.PubMedCrossRefGoogle Scholar
  120. Stryer, L., and Bourne, H. R., 1986, G proteins: A family of signal transducers, Annu. Rev. Cell. Biol. 2:391–419.PubMedCrossRefGoogle Scholar
  121. Sullivan, K. A., Liao, Y.-C., Alborzi, A., Beiderman, B., Chang, F.-H., Masters, S. B., Levinson, A. D., and Bourne, H. R., 1986, Inhibitory and stimulatory G proteins of adenylate cyclase: cDNA and amino acid sequences of the α chains, Proc. Natl. Acad. Sci. U.S.A. 83:6687–6691.PubMedCrossRefGoogle Scholar
  122. Sumikawa, K., Houghton, J., Smith, J. G., Bell, L., Richards, B. M., and Barnard, E. A., 1982, The molecular cloning and characterization of cDNA coding for the α subunit of the acetylcholine receptor, Nucleic Acids Res. 10:5809–5822.PubMedCrossRefGoogle Scholar
  123. Tanabe, T., Nukada, T., Nishikawa, Y., Sugimoto, K., Suzuki, H., Takahashi, H., Noda, M., Haga, T., Ichiyama, A., Kangawa, K., Minamino, N., Matsuo, H., and Numa, S., 1985, Primary structure of the α-subunit of transducin and its relationship to ras proteins, Nature 315:242–245.PubMedCrossRefGoogle Scholar
  124. Tauler, A., El-Maghrabi, M. R., and Pilkis, S. J., 1987, Functional hemology of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatllse, phosphoglycerate mutase, and 2,3-bisphosphoglycerate mutase, J. Biol. Chem. 262:16808–16815.PubMedGoogle Scholar
  125. Turnell, W., Sarra, R., Glover, I. D., Baum, J. O., Caspi, D., Baltz, M. L., and Pepys, M. B., 1986, Secondary structure prediction of human SAA1. Presumptive identification of calcium and lipid binding sites, Mol. Biol. Med. 3:387–407.PubMedGoogle Scholar
  126. Vassarotti, A., Stroud, R., and Douglas, M., 1987, Independent mutations at the amino terminus of a protein act as surrogate signals for mitochondrial import, EMBO J. 6:705–711.PubMedGoogle Scholar
  127. Wang, A. C., Wang, I. Y., and Fudenberg, H. H., 1977, Immunoglobulin structure and genetics, J. Biol. Chem. 252:7192–7199.PubMedGoogle Scholar
  128. Winn, S. I., Watson, H. C., Harkins, R. N., and Fothergill, L. A., 1981, Structure and activity of phosphoglycerate mutase, Phil. Trans. R. Soc. Land. [Biol.] 293:121–130.CrossRefGoogle Scholar
  129. Wistow, G. J., Katial, A., Craft, C., and Shinohara, T., 1986, Sequence analysis of bovine retinal S-antigen, FEBS Lett. 196:23–28.PubMedCrossRefGoogle Scholar
  130. Yatsunami, K., and Khorana, G., 1985, GTPase of bovine rod outer segments: The amino acid sequence of the α subunit as derived from the cDNA sequence, Proc. Natl. Acad. Sci. U.S.A. 82:4316–4320.PubMedCrossRefGoogle Scholar
  131. Young, E. F., Ralston, E., Blake, J., Ramachandran, J., Hall, Z. W., and Stroud, R. M., 1985, Topological mapping of acetylcholine receptor: Evidence for a model with five transmembrane segments and a cytoplasmic COOH-terminal peptide, Proc. Natl. Acad. Sci. U.S.A. 82:626–630.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1989

Authors and Affiliations

  • Janet Finer-Moore
    • 1
  • J. Fernando Bazan
    • 1
  • John Rubin
    • 2
  • Robert M. Stroud
    • 1
  1. 1.Department of Biochemistry and BiophysicsUniversity of CaliforniaSan FranciscoUSA
  2. 2.Genentech, Inc.South San FranciscoUSA

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