Skip to main content
SpringerLink
Log in

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

  • Chapter
Prediction of Protein Structure and the Principles of Protein Conformation

Abstract

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that is simplifies the description of a system: it focuses attention onto potentially critical features, and it will be superseded by better models that explain more.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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Agard, D. A., and Stroud, R. M., 1982, Linking regions between helices in bacteriorhodopsin revealed, Biophys. J. 37:589–602.

    PubMed  CAS  Google Scholar 

  • Amzel, L. M., and Poljak, R. J., 1979, Three-dimensional structure of immunoglobins, Annu. Rev. Biochem. 48:961–997.

    Article  PubMed  CAS  Google Scholar 

  • Argos, P., Rao, J. K. M., and Hargrave, P. A., 1982, Structural prediction of membrane-bound proteins, Eur. J. Biochem. 128:565–575.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Bourne, H. R., 1986, GTP-binding proteins: One molecular machine can transduce diverse signals, Nature 321: 814.

    Article  PubMed  CAS  Google Scholar 

  • Branden, C.-I., 1980, Relation between structure and function of α/ß-proteins, Q. Rev. Biophys. 13:317–338.

    Article  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Choe, S., 1987, Structural Study of Channel-Forming Proteins, Ph.D. Thesis, University of California, Berkeley.

    Google Scholar 

  • Chou, P. Y., and Fasman, G. D., 1974, Prediction of protein conformation, Biochemistry 13:222–245.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Dunnill, P., 1968, The use of helical net-diagrams to represent protein structures, Biophys. J. 8:865–875.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Eisenberg, D., Weiss, R. M., Terwilliger, T. C., and Wilcox, W., 1982b, Hydrophobic moments and protein structure, Faraday Symp. Chem. Soc. 17:109–120.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Engelman, D. M., and Zaccai, G., 1980, Bacteriorhodopsin is an inside-out protein, Proc. Natl. Acad. Sci. U.S.A. 77:5894–5898.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Fothergill, L. A., and Harkins, R. N., 1982, The amino acid sequence of yeast phosphoglycerate mutase, Proc. R. Soc. London [Biol.] 215:19–44.

    Article  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Gilman, A. G., 1984, G proteins and dual control of adenylate cyclase, Cell 36:577–579.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Halliday, K., 1984, Regional homology in GTP-binding proto-oncogene products and elongation factors, J. Cyclic Nucleotide Res. 9:435–448.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Henderson, R., and Unwin, P. N. T., 1975, Three-dimensional model of purple membrane obtained by electron microscopy, Nature 257:28–32.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Hopp, T. P., 1986, Protein surface analysis. Methods for identifying antigenic determinants and other interaction sites, J. Immunol. Methods 88:1–18.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Katre, N. V., and Stroud, R. M., 1981, A probable linking sequence between two transmembrane components of bacteriorhodopsin, FEBS Lett. 136: 170–174.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Kuhn, L. A., and Leigh, J. S., Jr., 1985, A statistical technique for predicting membrane protein structure, Biochim. Biophys. Acta 828:351–361.

    Article  PubMed  CAS  Google Scholar 

  • Kyte, J., and Doolittle, R. F., 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157:105–132.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Lim, V. I., 1974, Algorithms for prediction of α-helical and ß structural regions in globular proteins, J. Mol. Biol. 88:873–894.

    Article  PubMed  CAS  Google Scholar 

  • Lindstrom, J., Criado, M., Hochschwender, S., Fox, J. L., and Sarin, V., 1984, Immunochemical tests of acetylcholine receptor subunit models, Nature 311:573–575.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • McLachlan, A. D., 1971, Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome C551, J. Mol. Biol. 61:409–424.

    Article  PubMed  CAS  Google Scholar 

  • McLachlan, A. D., and Kam, J., 1983, Periodic features in the amino acid sequence of nematode myosin rod, J. Mol. Biol. 164:605–626.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Moller, W., and Amons, R., 1985, Phosphate-binding sequences in nucleotide-binding proteins, FEBS Lett. 186:1–7.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Nathans, J., and Hogness, D. S., 1983, Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin, Cell 34:807–814.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Ohlendorf, D. H., and Matthews, B. W., 1983, Structural studies of protein-nucleic acid interactions, Annu. Rev. Biophys. Bioeng. 12:259–284.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Popot, J.-L., and Changeux, J.-P., 1984, Nicotinic receptor of acetylcholine: Structure of an oligomeric integral membrane protein, Physiol. Rev. 64:1162–1239.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Rose, G. D., Gierasch, L. M., and Smith, J. A., 1985, Turns in peptides and proteins, Adv. Protein Chem. 37: 1–109.

    Article  PubMed  CAS  Google Scholar 

  • Rose, Z. B., 1980, The enzymology of 2,3-bisphosphoglycerate, Adv. Enzymol. 51:211–253.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Roth, R. A., and Koshland, M. E., 1981, Role of disulfide interchange enzyme in immunoglobulin synthesis, Biochemistry 20:6594–6599.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Schulz, G. E., Elzinga, M., Marx, F., and Schirmer, R. H., 1974, Three dimensional structure of adenyl kinase, Nature 250:120–123.

    Article  PubMed  CAS  Google Scholar 

  • Skalnik, D. G., and Simoni, R. D., 1985, The nucleotide sequence of syrian hamster HMG-CoA reductase cDNA, DNA 4:439–443.

    Article  PubMed  CAS  Google Scholar 

  • Stroud, R. M., and Finer-Moore, J., 1985, Acetylcholine receptor structure, function, and evolution, Annu. Rev. Cell Biol. 1:317–351.

    Article  PubMed  CAS  Google Scholar 

  • Stryer, L., 1986, Cyclic GMP cascade of vision, Annu. Rev. Neurosci. 9:87–119.

    Article  PubMed  CAS  Google Scholar 

  • Stryer, L., and Bourne, H. R., 1986, G proteins: A family of signal transducers, Annu. Rev. Cell. Biol. 2:391–419.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Wang, A. C., Wang, I. Y., and Fudenberg, H. H., 1977, Immunoglobulin structure and genetics, J. Biol. Chem. 252:7192–7199.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Wistow, G. J., Katial, A., Craft, C., and Shinohara, T., 1986, Sequence analysis of bovine retinal S-antigen, FEBS Lett. 196:23–28.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of California, San Francisco, 94143, California, USA

    Janet Finer-Moore, J. Fernando Bazan & Robert M. Stroud

  2. Genentech, Inc., South San Francisco, California, 94080, USA

    John Rubin

Authors
  1. Janet Finer-Moore
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. Fernando Bazan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John Rubin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Robert M. Stroud
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts, 02254, USA

    Gerald D. Fasman

Rights and permissions

Reprints and permissions

Copyright information

© 1989 Plenum Press, New York

About this chapter

Cite this chapter

Finer-Moore, J., Bazan, J.F., Rubin, J., Stroud, R.M. (1989). Identification of Membrane Proteins and Soluble Protein Secondary Structural Elements, Domain Structure, and Packing Arrangements by Fourier-Transform Amphipathic Analysis. In: Fasman, G.D. (eds) Prediction of Protein Structure and the Principles of Protein Conformation. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-1571-1_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-4613-1571-1_19

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4612-8860-2

  • Online ISBN: 978-1-4613-1571-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation