Advertisement

The Development of the Prediction of Protein Structure

  • Gerald D. Fasman
Chapter

Abstract

The tenet of structural biology that function follows form had its seeds in the monograph by C. B. Anfinsen, The Molecular Basis of Evolution (Anfinsen, 1959), wherein he stated “Protein chemists naturally feel that the most likely approach to the understanding of cellular behavior lies in the study of structure and function of protein molecules.” The achievement of protein crystallography over the past 30 years has confirmed this view whereby the description of the structure and function of proteins is now frequently understood at the atomic level.

References

  1. Abercrombie, D. M., and Khorana, H. G., 1986, Regeneration of native bacteriorhodopsin following acetylation of ∈-amino groups of Lys-30,-40 and-41, J. Mol. Biol. 261:4875–4880.Google Scholar
  2. Allen, G., Trinnaman, B. I., and Green, N. M., 1980, The primary structure of the calcium ion-transporting adenosine triphosphatase protein of rabbit skeletal sarcoplasmic reticulum, Biochem. J. 187: 591–616.PubMedGoogle Scholar
  3. Allison, I. P., McIntyre, B. W., and Bloch, D., 1982, Tumor-specific antigen of murine T-lymphoma defined with monclonal antibody, J. Immunol. 129:2293–2300.PubMedGoogle Scholar
  4. Ananthanaryanan, V. S., and Bandekar, I., 1976, Application of one-dimensional Isling model to the secondary structure in globular proteins: Predicted ß-regions, Int. J. Peptide Protein Res. 8:615–623.CrossRefGoogle Scholar
  5. Ananthanaryanan, V. S., Brahmachari, S. K., and Paltabiraman, N., 1984, Proline-containing ß-turns in peptides and proteins: Analysis of structural data on globular proteins, Arch. Biochem. Biophys. 232:482–495.CrossRefGoogle Scholar
  6. Anderer, F. A., 1963, Recent studies on the structure of tobacco mosaic virus, Adv. Protein Chem. 13:1–35.Google Scholar
  7. Anderson, W., Burt, S., and Loew, G., 1979, Energy-conformation studies of frequency of ß-turns in tetrapeptide sequences, Int. J. Peptide Protein Res. 14:402–408.CrossRefGoogle Scholar
  8. Anfinsen, C. B., 1959, The Molecular Basis of Evolution, John Wiley & Sons, New York.Google Scholar
  9. Anfinsen, C. B., 1973, Principles that govern the folding of protein chains, Science 181:233–230.CrossRefGoogle Scholar
  10. Anfinsen, C. B., Haber, E., Sela, M., and White, F. H., 1961, The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain, Proc. Natl. Acad. Sci. U.S.A. 47:1309–1314.PubMedCrossRefGoogle Scholar
  11. Arden, B., Klotz, J. L., Siu, G., and Hood, L., 1985, Diversity and structure of genes of the α family of mouse T-cell antigen receptor, Nature 316:783–787.PubMedCrossRefGoogle Scholar
  12. Argos, P., 1987a, Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis, J. Mol. Biol. 197:331–348.PubMedCrossRefGoogle Scholar
  13. Argos, P., 1987b, A sensitive procedure to compare amino acid sequences, J. Mol. Biol. 193:385–396.PubMedCrossRefGoogle Scholar
  14. Argos, P., and Mohana-Rao, J. K., 1985, Relationships between exons and the predicted structure of mem-brane-bound proteins, Biochim. Biophys. Acta 827:283–297.CrossRefGoogle Scholar
  15. Argos, P., and Palau, J., 1982, Amino acid distribution in protein secondary structures, Int. J. Peptide Protein Res. 19:380–393.CrossRefGoogle Scholar
  16. Argos, P., Schwarz, J., and Schwarz, J., 1976, An assessment of protein secondary structure prediction methods based on amino acid sequence, Biochem. Biophys. Acta 439:261–273.PubMedGoogle Scholar
  17. Argos, P., Rossman, M., and Johnson, J. E., 1977, A four-helical super-secondary structure, Biochem. Biophys. Res. Commun. 75:83–86.PubMedCrossRefGoogle Scholar
  18. Argos, P., Hanei, M., and Garavito, R. M., 1978, The Chou-Fasman secondary structure prediction method with an extended data base, FEBS Lett. 93:19–24.PubMedCrossRefGoogle Scholar
  19. Argos, P., Mohana-Rao, J. K., and Hargrave, P. A., 1982, Structural prediction of membrane-bound proteins, Eur. J. Biochem. 128:565–575.PubMedCrossRefGoogle Scholar
  20. Arzamazova, N. M., Arystarkhova, E. A., Shafieva, G. I., Nazimov, I. V., Aldanova, N. A., and Modyanov, N. N., 1985, Primary structure of the α-subunit of Na+ + K+-ATPase. I. Analysis of hydrophilic fragments of the polypeptide chains, Bioorg. Khim. 11:1598–1601.PubMedGoogle Scholar
  21. Aubert, J.-P., and Loucheaux-Lefebvre, M.-H., 1976, Conformational study of α1-acid glycoprotein, Arch. Biochem. Biophys. 175:400–409.PubMedCrossRefGoogle Scholar
  22. Aubert, J.-P., Biserte, G., and Loucheux-Lefebvre, M. H., 1976, Carbohydrate-peptide linkage in glycoproteins, Arch. Biochem. Biophys. 175:410–418.PubMedCrossRefGoogle Scholar
  23. Aubert, J.-P., Helbecque, N., and Loucheux-Lefebvre, M.-H., 1981, Circular dichroism studies of synthetic Asn-X-Ser/Thr-containing peptides: Structure of glycosylation relationship, Arch. Biochem. Biophys. 208: 20–29.PubMedCrossRefGoogle Scholar
  24. Bacon, D. J., and Anderson, W. F., 1986, Multiple sequence alignment, J. Mol. Biol. 191:153–161.PubMedCrossRefGoogle Scholar
  25. Baldwin, R. L., 1980, The mechanism of folding of ribonucleases A and S, in Protein Folding (R. Jaenicke, ed.), Elsevier Amsterdam, pp. 369–384.Google Scholar
  26. Barker, W. C., Hunt, L. T., Orcutt, B. C., George, D. G., Yeh, L. S., Chen, H. R., Blomquist, M. C., Johnson, G. C., Seibel-Ross, E. I., and Ledky, R. S., 1984, Report of the National Biomedical Research Foundation, Georgetown University, Washington.Google Scholar
  27. Barkovsky, E. V., 1982, Prediction of the secondary structure of globular proteins by their amino acid sequence, Acta Biol. Med. Germ. 41:751–758.Google Scholar
  28. Barkovsky, E. V., and Bandarin, V. A., 1979, Secondary structure prediction of globular proteins from their amino acid sequence, Bioorg. Khim. 5:24–34.Google Scholar
  29. Barlow, D. J., and Thornton, J. M., 1983, Ion-pairs in proteins, J. Mol. Biol. 168:867–885.PubMedCrossRefGoogle Scholar
  30. Barth, R. K., Kim, B. S., Lan, N. C., Hunkapiller, T., Sobieck, N., Winoto, A., Gershenfeld, H., Okada, C., Hansburg, D., Weissman, I. L., and Hood, L., 1985, The murine T-cell receptor uses a limited repertoire of expressed Vß gene segments, Nature 316:517–523.PubMedCrossRefGoogle Scholar
  31. Barton, G. J., and Sternberg, M. J. E., 1987a, Evaluation and improvements in the automatic alignment of protein sequences, Protein Eng. 1:89–94.PubMedCrossRefGoogle Scholar
  32. Barton, G. J., and Sternberg, M. J. E., 1987b, A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparison, J. Mol. Biol. 198:327–337.PubMedCrossRefGoogle Scholar
  33. Bash, P. A., Singh, V. C., Langridge, R., and Kollman, P. A., 1987, Free energy calculations by computer simulation, Science 236:564–568.PubMedCrossRefGoogle Scholar
  34. Bashford, D., Chothia, C., and Lesk, A. M., 1987, Determinants of a protein fold. Unique features of the globin amino acid sequences, J. Mol. Biol. 196:199–216.PubMedCrossRefGoogle Scholar
  35. Bazan, J. F., Fletterick, R. J., McKinley, M. P., and Pruisner, S. B., 1987, Predicted secondary structure and membrane topology of the scrapie prion protein, Protein Eng. 1:125–135.PubMedCrossRefGoogle Scholar
  36. Beasty, A. M., and Matthews, C. R., 1985, Characterization of an early intermediate in the folding of the α-subunit of tryptophan synthase by a hydrogen exchange measurement, Biochemistry 24:3547–3553.PubMedCrossRefGoogle Scholar
  37. Beecher, B., and Cassim, J. Y., 1976, Effects of light adaption on the purple membrane of Halobacterium halobium, Biophys. J. 16:1183–1200.CrossRefGoogle Scholar
  38. Beeley, J. G., 1976, Location of the carbohydrate groups on ovomucoid, Biochem. J. 159:335–345.PubMedGoogle Scholar
  39. Beeley, J. G., 1977, Peptide chain conformation and the glycosylation of glycoproteins, Biochem. Biophys. Res. Commun. 76:1051–1055.PubMedCrossRefGoogle Scholar
  40. Bentley, G., Dodson, E., Dodson, G., Hodgkin, D., and Mercola, D., 1976, Structure of insulin in 4-zinc insulin, Nature 261: 166–168.PubMedCrossRefGoogle Scholar
  41. Billeter, M., Havel, T. F., and Kuntz, I. D., 1987a, A new approach to the problem of docking two molecules: The ellipsoid algorithm, Biopolymers 26:777–793.PubMedCrossRefGoogle Scholar
  42. Billeter, M., Havel, T. F., and Wüthrich, K., 1987b, The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization, J. Comput. Chem. 8:132–141.CrossRefGoogle Scholar
  43. Bird, C. R., Koller, B., Auffret, A. D., Huttly, A. K., Howe, C. J., Dyer, T. A., and Gray, J. C., 1985, The wheat chloroplast gene for CF0 subunit I of ATP synthase contains a large intron, EMBO J. 4:1381–1388.PubMedGoogle Scholar
  44. Black, S. D., and Glorioso, J. C., 1986, MSEQ: A microcomputer-based approach to the analysis, display, and prediction of protein structure, Biol. Techniques 4:448–460.Google Scholar
  45. Blagdon, D. E., and Goodman, G., 1975, Mechanisms of protein and polypeptide helix initiation, Biopolymers 14:241–245.PubMedCrossRefGoogle Scholar
  46. Blake, C. C. F., 1979, Exons encode protein functional units, Nature 277:598.PubMedCrossRefGoogle Scholar
  47. Bloomer, A. C., Champness, J. N., Bricogne, G., Staden, R., and Klug, A., 1978, Protein disk of tobacco mosaic virus at 2.8 Å resolution showing the interactions within and between units, Nature 276:362–368.PubMedCrossRefGoogle Scholar
  48. Blout, E. R., 1962, The dependence of the conformation of polypeptides and proteins upon amino acid composition, in: Polyamino Acids, Polypeptides, and Proteins (M. Stahman, ed.), University of Wisconsin Press, Madison, pp. 275–279.Google Scholar
  49. Blow, D. M., Irwin, M. J., and Nyborg, J., 1977, The peptide chain of tyrosyl t-RNA synthetase: No evidence for a super-secondary structure of four-α-helices, Biochem. Biophys. Res. Commun. 76:728–734.PubMedCrossRefGoogle Scholar
  50. Blundell, T. L., and Johnson, L. N., 1976, Protein Crystallography, Academic Press, New York.Google Scholar
  51. Blundell, T. L., and Sternberg, M. J. E., 1985, Computer-aided design in protein engineering, Trends Biotechnol. 3:228–235.CrossRefGoogle Scholar
  52. Blundell, T., Singh, J., Thornton, J., Burley, S. K., and Petsko, G. A., 1986a, Aromatic interactions, Science 234:1005.CrossRefGoogle Scholar
  53. Blundell, T. L., Barlow, D., Sibanda, B. L., Thornton, T. M., Taylor, W., Tickle, I. J., Sternberg, M. J. E., Pitts, J. E., Haneef, I., and Hemmings, A. M., 1986b, Three-dimensional aspects of the design of new protein molecules, Phil. Trans. R. Soc. Lond. [A] 317:333–344.CrossRefGoogle Scholar
  54. Blundell, T. L., Sibanda, B. L., Sternberg, M. J. E., and Thornton, J. M., 1987, Knowledge-based prediction of protein structures and the design of novel molecules, Nature 326:347–352.PubMedCrossRefGoogle Scholar
  55. Bonner, T. I., Buckley, N. J., Young, A. C., and Brann, M. R., 1987, Identification of a family of muscarinic acetylcholine receptor genes, Science 237:527–532.PubMedCrossRefGoogle Scholar
  56. Boswell, D. R., and McLachlan, A. D., 1984, Sequence comparison by exponentially-damped alignment, Nucleic Acids Res. 12:457–464.PubMedCrossRefGoogle Scholar
  57. Bourgeois, S., and Pfahl, M., 1976, Repressors, Adv. Protein Chem. 30:1–99.PubMedCrossRefGoogle Scholar
  58. Brandhuber, B. J., Boone, T., Kenney, W. C., and McKay, D. B., 1987, Three-dimensional structure of interleukin-2, Science 283: 1707–1709.CrossRefGoogle Scholar
  59. Brandl, C., Green, N. M., Korczak, B., and MacLennan, D. H., 1986, Two Ca2+ ATPase genes: Homologies and mechanistic implications of deduced amino acid sequences, Cell 44:597–607.PubMedCrossRefGoogle Scholar
  60. Briggs, M. S., and Gierasch, L. M., 1984, Exploring the conformational role of signal sequences: Synthesis and conformational analysis of λ receptor protein wild type and mutant signal peptides, Biochemistry 23:3111–3114.PubMedCrossRefGoogle Scholar
  61. Brisson, A., and Unwin, P. N. T., 1985, Quaternary structure of the acetylcholine receptor, Nature 315:474–477.PubMedCrossRefGoogle Scholar
  62. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983, CHARMM: A program for macromolecular energy minimization and dynamics calculations, J. Comput. Chem. 4:187–217.CrossRefGoogle Scholar
  63. Bruccoleri, R. E., and Karplus, M., 1987, Prediction of the folding of short polypeptide segments by uniform conformational sampling, Biopolymers 26:137–168.PubMedCrossRefGoogle Scholar
  64. Bunting, J. R., Athey, T. W., and Cathou, R. E., 1972, Backbone folding of immunoglobulin light and heavy chains: A comparison of predicted ß-bend positions, Biochim. Biophys. Acta 285:60–71.PubMedGoogle Scholar
  65. Burgess, A. W., and Scheraga, H. A., 1975, Assessment of some problems associated with the prediction of the three-dimensional structure of a protein from its amino acid sequence, Proc. Nat. Acad. Sci. U.S.A. 72: 1221–1225.CrossRefGoogle Scholar
  66. Burgess, A. W., Ponnuswamy, P. K., and Scheraga, H. A., 1974, Analysis of conformations of amino acid residues and prediction of backbone topography in proteins, Israel J. Chem. 12:239–286.Google Scholar
  67. Burley, S. K., and Petsko, G. A., 1985, Aromatic-aromatic interaction: A mechanism of protein stabilization, Science 229:23–28.PubMedCrossRefGoogle Scholar
  68. Burley, S. K., and Petsko, G. A., 1986, Amino-aromatic interactions in proteins, FEBS Lett. 203:139–143.PubMedCrossRefGoogle Scholar
  69. Busetta, B., and Hospital, M., 1981, Improving the accuracy of secondary structure predictions, Biochemie 63: 951–954.CrossRefGoogle Scholar
  70. Busetta, B., and Hospital, M., 1982, An analysis of the prediction of secondary structures, Biochim. Biophys. Acta 701:111–118.CrossRefGoogle Scholar
  71. Cantor, C. R., and Jukes, T. H., 1966, The repetition of homologous sequences in the polypeptide chains of certain cytochromes and globins, Proc. Natl. Acad. Sci. U.S.A. 56:177–184.PubMedCrossRefGoogle Scholar
  72. Capaldi, R. A., and Vanderkooi, G., 1972, The low polarity of many membrane proteins, Proc. Natl. Acad. Sci. U.S.A. 69:930–932.PubMedCrossRefGoogle Scholar
  73. Catterall, W. A., 1984, The molecular basis of neuronal excitability, Science 223:653–661.PubMedCrossRefGoogle Scholar
  74. Chakravarty, P. K., Mathur, K. B., and Dhar, M. M., 1973, The synthesis of a decapeptide with glycosidase activity, Experientia 29:786–788.CrossRefGoogle Scholar
  75. Chang, E. L., Yager, P., Williams, R. W., and Dalziel, A. W., 1983, The secondary structure of reconstituted acetylcholine receptors as determined by Raman spectroscopy, Biophys. J. 41:65a.Google Scholar
  76. Charton, M., and Charton, B. I., 1983, The dependence of the Chou-Fasman parameters on amino acid side-chain structure, J. Theor. Biol. 102:121–134.PubMedCrossRefGoogle Scholar
  77. Chothia, C., 1973, Conformation of twisted ß-pleated sheets in proteins, J. Mol. Biol. 75:295–302.PubMedCrossRefGoogle Scholar
  78. Chothia, C., 1974, Hydrophobic bonding and accessible surface area in proteins, Nature 248:338–339.PubMedCrossRefGoogle Scholar
  79. Chothia, C., 1975, Structural invariants in protein folding, Nature 254:303–308.CrossRefGoogle Scholar
  80. Chothia, C., 1976, The nature of accessible and buried surfaces in proteins, J. Mol. Biol. 105:1–14.PubMedCrossRefGoogle Scholar
  81. Chothia, C., 1984, Principles that determine the structure of proteins, Annu. Rev. Biochem. 53:537–572.PubMedCrossRefGoogle Scholar
  82. Chothia, C., and Janin, J., 1975, Principles of protein-protein recognition, Nature 256:705–708.PubMedCrossRefGoogle Scholar
  83. Chothia, C., and Janin, J., 1982, Orthogonal packing of ß-sheets in proteins, Biochemistry 21:3955–3965.PubMedCrossRefGoogle Scholar
  84. Chothia, C., and Lesk, A. M., 1982a, Evolution of proteins formed by ß-sheets. I. The core of the immuno-globulin domains, J. Mol. Biol. 160:325–342.PubMedCrossRefGoogle Scholar
  85. Chothia, C., and Lesk, A. M., 1982b, Evolution of proteins formed by ß-sheets. II. Plastocyanin and azurin, J. Mol. Biol. 160:303–323.CrossRefGoogle Scholar
  86. Chothia, C., and Lesk, A. M., 1986, The relation between the divergence of sequence and structure in proteins, EMBO J. 5:823–826.PubMedGoogle Scholar
  87. Chothia, C., Levitt, M., and Richardson, D., 1977, Structure of proteins: Packing of α-helices and pleated sheets, Proc. Natl. Acad. Sci. U.S.A. 74:4130–4134.PubMedCrossRefGoogle Scholar
  88. Chothia, C., Levitt, M., and Richardson, D., 1981, Helix to helix packings in proteins, J. Mol. Biol. 145:215–250.PubMedCrossRefGoogle Scholar
  89. Chothia, C., Novotny, J., Bruccoleri, R., and Karplus, M., 1985, Domain association in immunoglobulin molecules. the packing of variable domains, J. Mol. Biol. 186:651–663.PubMedCrossRefGoogle Scholar
  90. Chou, P. Y., 1979, New approaches to protein structural analysis and conformational predictions, in: CECM Protein Folding Workshop, Université de Paris-Sud, Orsay, France.Google Scholar
  91. Chou, P. Y., 1980, Amino acid compositions of four structural classes of proteins, in: Abstracts, Second Chemical Congress of the North American Continent, Las Vegas.Google Scholar
  92. Chou, P. Y., and Fasman, G. D., 1973, Structural and functional role of Leu residues in proteins, J. Mol. Biol. 74:263–281.PubMedCrossRefGoogle Scholar
  93. Chou, P. Y., and Fasman, G. D., 1974a, Conformational parameters for amino acids in helical, ß-sheet, and random coil regions calculated from proteins, Biochemistry 13:211–222.PubMedCrossRefGoogle Scholar
  94. Chou, P. Y., and Fasman, G. D., 1974b, Prediction of protein conformation, Biochemistry 13:222–245.PubMedCrossRefGoogle Scholar
  95. Chou, P. Y., and Fasman, G. D., 1975, The conformation of glucagon: Predictions and consequences, Biochemistry 14:2536–2541.PubMedCrossRefGoogle Scholar
  96. Chou, P. Y., and Fasman, G. D., 1977a, Secondary structural prediction of proteins from their amino acid sequence, Trends Biochem. Sci. 2:128–132.CrossRefGoogle Scholar
  97. Chou, P. Y., and Fasman, G. D., 1977b, ß-Turns in proteins, J. Mol. Biol. 115:135–175.PubMedCrossRefGoogle Scholar
  98. Chou, P. Y., and Fasman, G. D., 1977c, Prediction of protein secondary structure, in: Fifth American Peptide Symposium (M. Goodman and J. Meienhofer, eds.), John Wiley & Sons, New York, pp. 284–287.Google Scholar
  99. Chou, P. Y., and Fasman, G. D., 1978a, Prediction of the secondary structure of proteins from their amino acid sequence, Adv. Enzymol. 47:45–148.PubMedGoogle Scholar
  100. Chou, P. Y., and Fasman, G. D., 1978b, Empirical predictions of protein conformation, Annu. Rev. Biochem. 47:251–276.PubMedCrossRefGoogle Scholar
  101. Chou, P. Y., and Fasman, G. D., 1979a, Prediction of ß-turns, Biophys. J. 26:367–384.PubMedCrossRefGoogle Scholar
  102. Chou, P. Y., and Fasman, G. D., 1979b, Conservation of chain reversal regions in proteins, Biophys. J. 26: 385–400.PubMedCrossRefGoogle Scholar
  103. Chou, P. Y., Adler, A. J., and Fasman, G. D., 1975, Conformational prediction and circular dichroism studies on the lac repressor, J. Mol. Biol. 96:29–45.PubMedCrossRefGoogle Scholar
  104. Chou, K.-C., Pottle, M., Nemethy, G., Veda, Y., and Scheraga, H. A., 1982, Structure of ß-sheets, J. Mol. Biol. 162:89–112.PubMedCrossRefGoogle Scholar
  105. Claudio, T., Ballivet, M. Patrick, J., and Heinemann, S., 1983, Nucleotide and deduced amino acid sequences of Torpedo californica acetylcholine receptor γ-subunit, Proc. Natl. Acad. Sci. U.S.A. 80: 1111–1115.PubMedCrossRefGoogle Scholar
  106. Cohen, C., and Parry, D. A. D., 1986, α-Helical coiled-coils: A widespread motif in proteins, Trends Biochem. Sci. 11:245–248.CrossRefGoogle Scholar
  107. Cohen, F. E., and Kuntz, I. D., 1987, Prediction of the three-dimensional structure of human growth hormone, Proteins 1:162–166.CrossRefGoogle Scholar
  108. Cohen, F. E., and Sternberg, M. J. E., 1980a, The use of chemically derived distant constants in the prediction of protein structure with myoglobin as an example, J. Mol. Biol. 137:9–22.PubMedCrossRefGoogle Scholar
  109. Cohen, F. E., and Sternberg, M. J. E., 1980b, On the prediction of protein structure: The significance of the root-mean-square deviation, J. Mol. Biol. 138:321–333.PubMedCrossRefGoogle Scholar
  110. Cohen, F. E., Richmond, J. T., and Richards, F. M. J., 1979, Protein folding: Evaluation of some simple rules for the assembly of helices into tertiary structure with myoglobin as an example, J. Mol. Biol. 132:275–288.PubMedCrossRefGoogle Scholar
  111. Cohen, F. E., Sternberg, M. J. E., and Taylor, W. R., 1980, Analysis and prediction of protein ß-sheet structures by a combinatorial approach, Nature 285:378–382.PubMedCrossRefGoogle Scholar
  112. Cohen, F. E., Sternberg, M. J. E., and Taylor, W. R., 1981, Analysis of the tertiary structure of protein sandwiches, J. Mol. Biol. 148:253–272.PubMedCrossRefGoogle Scholar
  113. Cohen, F. E., Sternberg, M. J. E., and Taylor, W. R., 1982, Analysis and prediction of the packing of α-helices against a ß-sheet in the tertiary structure of globular proteins, J. Mol. Biol. 156:821–862.PubMedCrossRefGoogle Scholar
  114. 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
  115. Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J., 1986a, Turn prediction in proteins using a pattern matching approach, Biochemistry 25:266–275.PubMedCrossRefGoogle Scholar
  116. Cohen, F. E., Kosen, P. A., Kuntz, I. D., Epstein, C. B., Cardelli, T. C., and Smith, K. A., 1986b, Structure activity studies of interleukin-2, Science 234:349–356.PubMedCrossRefGoogle Scholar
  117. Conboy, J., Kan, Y. W., Shohet, S. B., and Mohandas, N., 1986, Molecular cloning of protein 4.1, a major structural element of the human erythrocyte membrane skeleton, Proc. Natl. A cad. Sci. U.S.A. 83:9512–9516.CrossRefGoogle Scholar
  118. Cook, D. A., 1967, The relation between amino acid sequence and protein conformation, J. Mol. Biol. 29:167–171.PubMedCrossRefGoogle Scholar
  119. Cornette, J. L., Cease, K. B., Margalit, J. 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
  120. Corrigan, A. J., and Huang, P. C., 1982, A BASIC microcomputer program for plotting the secondary structure of proteins, Comput. Prog. Biomed. 15:163–168.CrossRefGoogle Scholar
  121. Crawford, I. P., Niermann, T., and Kirshner, K., 1987, Predictions of secondary structure by evolutionary comparison: Application to the α-subunit of tryptophan synthase, Proteins 1:118–129.CrossRefGoogle Scholar
  122. Crawford, J. L., Lipscomb, W. N., and Schellman, C. G., 1973, The reverse turn as a polypeptide conformation in globular proteins, Proc. Natl. Acad. Sci. U.S.A. 70:538–542.PubMedCrossRefGoogle Scholar
  123. Creighton, T. E., 1978, Experimental studies of protein folding and unfolding, Prog. Biophys. Mol. Biol. 33: 231–297.PubMedCrossRefGoogle Scholar
  124. Creighton, T. E., 1979, Electrophoretic analysis of the unfolding of proteins by urea, J. Mol. Biol. 129:235–264.PubMedCrossRefGoogle Scholar
  125. Criado, M., Hochschwender, S., Sarin, V., Fox, J. L., and Lindstrom, J., 1985, Evidence for unpredicted transmembrane domains in acetylcholine receptor subunits, Proc. Nat. Acad. Sci. U.S.A. 82:2004–2008.CrossRefGoogle Scholar
  126. Crick, F. H. C., 1953, The packing of α-helices: Simple coiled coils, Acta Crystallogr. 6:689–697.CrossRefGoogle Scholar
  127. Crippen, G. M., 1977a, A statistical approach to the calculation of conformation of proteins. 1. Theory, Macromolecules 10:21–25.PubMedCrossRefGoogle Scholar
  128. Crippen, G. M., 1977b, A statistical approach to the calculation of conformation of proteins. 2. The reoxidation of reduced trypsin inhibitor, Macromolecules 10:25–28.PubMedCrossRefGoogle Scholar
  129. Crippen, G., M., 1977c, A novel approach to the calculation of conformation: Distance geometry, J. Compo Physiol. 26:449–452.Google Scholar
  130. Crippen, G. M., 1978, The tree structural organization of proteins, J. Mol. Biol. 126:315–332.PubMedCrossRefGoogle Scholar
  131. Crippen, G. M., and Kuntz, I. D., 1978, A survey of atom packing in globular proteins, Int. J. Peptide Protein Res. 12:47–56.CrossRefGoogle Scholar
  132. Davies, B. D., and Tai, R. C., 1980, The mechanism of protein secretion across membranes, Nature 283:433–438.CrossRefGoogle Scholar
  133. Davies, D. R., 1964, A correlation between amino acid composition and protein structure J. Mol. Biol. 9:605–609.PubMedCrossRefGoogle Scholar
  134. Dayhoff, M. O., 1972, Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington.Google Scholar
  135. Dayhoff, M. O., 1978, Atlas of Protein Sequence and Structure. Supplement 3, National Biomedical Research Foundation, Washington.Google Scholar
  136. Dayhoff, M. O., Barker, W. C., and Hunt, L. T., 1983, Establishing homologies in protein sequences, Methods Enzymol. 91:524–545.PubMedCrossRefGoogle Scholar
  137. DeGrado, W. F., Kezdy, E. J., and Kaiser, E. T., 1981, Design, synthesis and characterization of a cytotoxic peptide with melittin-like activity, J. Am. Chem. Soc. 103:679–681.CrossRefGoogle Scholar
  138. de Groot, R. J., Luytjes, W., Horzinek, M. C., van der Zeijst, B. A. M., Spaan, W. J. M., and Lenstra, J. A., 1987, Evidence for a coiled-coil structure in spike proteins of coronaviruses, J. Mol. Biol. 196:963–966.PubMedCrossRefGoogle Scholar
  139. Deisenhofer, J., Epp, O., Mikki, K., Huber, R., and Michel, H., 1984, X-ray structural analysis of a membrane protein complex electron density map at 3 Å resolution and a model of the chromophores of the photosynthetic reaction centre from Rhodopseudomonas viridis, J. Mol. Biol. 180:385–398.PubMedCrossRefGoogle Scholar
  140. Deisenhofer, J., Epp, O., Mikki, K., Huber, R., and Michel, H., 1985, Structure of the protein subunits in the photoreaction centre of Rhodopseudomonas viridis at 3Å resolution, Nature 318:618–624.CrossRefGoogle Scholar
  141. Deléage, G., and Roux, B., 1987, An algorithm for protein secondary structure prediction based on class prediction, Protein Eng. 1:289–294.PubMedCrossRefGoogle Scholar
  142. Deléage, G., Tinland, B., and Roux, B., 1987, A computerized version of the Chou and Fasman method for predicting the secondary structure of proteins, Anal. Biochem. 165:200–207.CrossRefGoogle Scholar
  143. Dencher, N. A., and Heyn, M. P., 1978, Formation and properties of bacteriorhodopsin monomers in the non-ionic detergents octyl-ß-glucoside and Triton X-100, FEBS Lett. 96:322–396.PubMedCrossRefGoogle Scholar
  144. DeSantis, P., Giglio, E., Liquori, A. M., and Ripamonti, A., 1965, Van der Waals interaction and the stability of helical polypeptide chains, Nature 206:456–458.CrossRefGoogle Scholar
  145. DesJarlais, R. L., Sheridan, R. P., Dixon, J. S., Kuntz, I. D., and Venkataraghavan, R., 1986, Docking flexible ligands to macromolecular receptors by molecular shape, J. Med. Chem. 29:2149–2153.PubMedCrossRefGoogle Scholar
  146. Devereaux, J., Haeben, P., and Smithies, O., 1984, A comprehensive set of sequence analysis programs for the VAX, Nucleic Acids Res. 17:387–395.CrossRefGoogle Scholar
  147. Devillers-Thiery, A., Giraudet, J., Bentaboulet, M., and Changeux, J.-P., 1983, Complete mRNA coding sequence of the acetylcholine binding α-subunit of Torpedo marmorata acetylcholine receptor: A model for transmembrane organization of the polypeptide chain, Proc. Natl. Acad. Sci. U.S.A. 80: 2067–2071.PubMedCrossRefGoogle Scholar
  148. Dickerson, R. E., Takano, T., Eisenberg, D., Kallai, O. B., Samson, L., and Cooper, A., 1971, Ferricytochrome c: General features of the horse and bonito proteins at 2.8 Å resolution, J. Bioi. Chem. 246: 1511–1535.Google Scholar
  149. Dill, K. A., 1985, Theory for the folding and stability of globular proteins, Biochemistry 24:1501–1509.PubMedCrossRefGoogle Scholar
  150. Dixon, R. A., Kobilka, B. K., Strader, D. J., Benovic, J. L., Dohlman, H. G., Frielle, T., Bolanowski, M. A., Bennet, C. D., Rands, E., Diehl, R. E., Mumford, R. A., Slater, E. E., Sigal, I. S., Caron, M. G., Lefkowitz, R. J., and Strader, C. D., 1986, Cloning of the gene and eDNA mammalian ß-adrenergic receptor and homology with rhodopsin, Nature 321:75–79.PubMedCrossRefGoogle Scholar
  151. Dohlman, H. G., Caron, M. G., and Lefkowitz, R. L., 1987, A family of receptors coupled to guanine nucleotide regulatory proteins, Biochemistry 26:2657–2664.PubMedCrossRefGoogle Scholar
  152. Drexler, K. E., 1980, Molecular engineering: An approach to the development of general capabilities for molecular manipulation, Proc. Natl. Acad. Sci. U.S.A. 78:5275–5278.CrossRefGoogle Scholar
  153. Dufton, M. J., and Hider, R. C., 1977, Snake toxin secondary structure predictions. Structure activity relationships, J. Mol. Biol. 115:177–193.PubMedCrossRefGoogle Scholar
  154. Duncan, T. M., Parsonage, D., and Senior, A. E., 1986, Structure of the nucleotide-binding domain in the ß-subunit of Escherichia coli F1-ATPase, FEBS Lett. 208:1–6.PubMedCrossRefGoogle Scholar
  155. Dunhill, P., 1968, The use of helical net-diagrams to represent protein structures, Biophys. J. 8:865–875.CrossRefGoogle Scholar
  156. Ecker, J. G., and Kupferschmid, M., 1982, Report OR, Rensselaer Polytechnic, Troy, NY.Google Scholar
  157. Edelman, G. M., Cunningham, B. A., Reeke, G. N., Jr., Becker, J. W., Waxdall, M. J., and Wang, J. L., 1972, The covalent and three-dimensional structure of concanavalin A, Proc. Natl. Acad. Sci. U.S.A. 69: 2580–2584.PubMedCrossRefGoogle Scholar
  158. 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 relation to thioredoxin, Nature 317:267–270.PubMedCrossRefGoogle Scholar
  159. Edmonds, D. T., 1985, The α-helix dipole in membranes: A new gating mechanism for ion channels, Eur. Biophys. J. 13:31–35.PubMedCrossRefGoogle Scholar
  160. Edsall, J. Y., and McKenzie, H. A., 1983, Water and proteins II. The location and dynamics of water in protein systems and its relation to their stability and properties, Adv. Biophysics 16:53–183.CrossRefGoogle Scholar
  161. Edwards, M. S., Sternberg, M. J. E., and Thornton, J. M., 1987, Structure and sequence patterns in the loops of ßαß units, Protein Eng. 1:173–181.PubMedCrossRefGoogle Scholar
  162. Efimov, A. V., 1977, Stereochemistry of the packing of α-helices and the ß-structure in a compact globule, Dokl. Akad. Nauk SSSR 235:699–702.PubMedGoogle Scholar
  163. Efimov, A. V., 1979, Packing of α-helices in globular proteins. Layer-structure of globular hydrophobic cores, J. Mol. Biol. 134:23–46.PubMedCrossRefGoogle Scholar
  164. Efimov, A. V., 1982a, Role of constrictions in formation of protein structures containing four helical regions, Mol. Biol. 16:271–281.Google Scholar
  165. Efimov, A. V., 1982b, Super-secondary structures of ß-proteins, Mol. Biol. 16:799–806.Google Scholar
  166. Efimov, A. V., 1984, A novel super-secondary structure of proteins and the relation between the structure and amino acid sequence, FEBS Lett. 166:33–38.PubMedCrossRefGoogle Scholar
  167. Efimov, A. V., 1985, Standard conformations of polypeptide chains in irregular regions of proteins, Mol. Biol. 20:350–360.Google Scholar
  168. Efimov, A. V., 1986a, Standard structures in protein molecules. I. α-ß Hairpins, Mol. Biol. 20:329–339.Google Scholar
  169. Efimov, A. V., 1986b, Standard structures in protein molecules. II. ß-α Hairpins, Mol. Biol. 20:340–345.Google Scholar
  170. Eisenberg, D., 1984, Three-dimensional structure of membrane surface proteins, Annu. Rev. Biochem. 53:595–623.PubMedCrossRefGoogle Scholar
  171. Eisenberg, D., Weiss, R. M., Terwilliger, T. C., and Wilcox, W., 1982a, Hydrophobic moments and protein structure, Faraday Symp. Chem. Soc. 17:109–120.CrossRefGoogle Scholar
  172. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1982b, The helical hydrophobic moment: A measure of the amphilicity of a helix, Nature 299:371–374.PubMedCrossRefGoogle Scholar
  173. Eisenberg, D., Schwartz, E., Komaromy, M., and Wall, R., 1984a, Analysis of membrane and surface protein sequences with the hydrophobic moment plot, J. Mol. Biol. 179:125–142.PubMedCrossRefGoogle Scholar
  174. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1984b, The hydrophobic moment detects periodicity in protein hydrophobicity, Proc. Natl. Acad. Sci. U.S.A. 81:140–144.PubMedCrossRefGoogle Scholar
  175. Elleman, T. C., Azad, A. A., and Ward, C. W., 1982, Neuraminidase gene from early Asian strain human influenza virus, A/RI/5-/57(H2N2), Nucleic Acids Res. 10:7005–7015.PubMedCrossRefGoogle Scholar
  176. Emr, S. D., and Silhavy, T. J., 1983, Importance of secondary structure in the signal sequence for protein secretion, Proc. Natl. Acad. Sci. U.S.A. 80:4599–4603.PubMedCrossRefGoogle Scholar
  177. Engelman, D. M., and Steitz, T., 1981, The spontaneous insertion of proteins into and across membranes: The helical hairpin hypothesis, Cell 23:411–422.PubMedCrossRefGoogle Scholar
  178. Engelman, D. M., and Steitz, T. A., 1984, On the folding and insertion of globular membrane proteins, in: The Protein Folding Problem (D. Wetlaufer, ed.), Westview Press, Boulder, CO, pp. 87–113.Google Scholar
  179. Engelman, D. M., and Zaccai, G., 1980, Bacteriorhopdopsin is an inside-out protein, Proc. Natl. Acad. Sci. U.S.A. 77:5894–5898.PubMedCrossRefGoogle Scholar
  180. 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
  181. Engelman, D. M., Goldman, A., and Steitz, T., 1986, The identification of helical segments in the polypeptide chain of bacteriorhodopsin, Methods Enzymol. 88:81–88.CrossRefGoogle Scholar
  182. Engelman, D. M., Steitz, T. A., and Goldman, A., 1986, Identifying non-polar transbilayer helices in amino acid sequences of membrane proteins, Annu. Rev. Biophys. Biophys. Chem. 15:321–353.PubMedCrossRefGoogle Scholar
  183. Epand, R. M., 1971, Studies on the conformation of glucagon, Can. J. Biol. Chem. 49:166–169.Google Scholar
  184. Erni, B., and Zanolari, B., 1986, Glucose-permease of the bacterial phosphotransferase system, J. Biol. Chem. 261:16398–16403.PubMedGoogle Scholar
  185. Esipova, N. G., and Tumanyan, Y. G., 1972, Factors determining the formation of the tertiary structure of globular protein, Mol. Biol. 6:840–850.Google Scholar
  186. Fasman, G. D., 1980, Prediction of protein conformation from the primary structure, Ann. N. Y. Acad. Sci. 348: 147–159.CrossRefGoogle Scholar
  187. Fasman, G. D., 1982, Prediction of the secondary structure of proteins, in: From Cyclotrons to Cytochromes. Essays in Molecular Biology and Chemistry (N. O. Kaplan and A. Robinson, eds.), Academic Press, New York, pp. 455–468.Google Scholar
  188. Fasman, G. D., 1985, A critique of the utility of the prediction of protein secondary structure. International Symposium on Biomolecular Structure and Interactions, J. Biosci. 8:15–23.CrossRefGoogle Scholar
  189. Fasman, G. D., 1987, The road from poly-α-amino acids to the prediction of protein conformation. Biopolymers and biotechnology symposium in honor of Prof. Ephraim Katzir on his 70th birthday, Biopolymers 26: 559–579.CrossRefGoogle Scholar
  190. Fasman, G. D., and Chou, P. Y., 1974, Prediction of protein conformation: Consequences and aspirations, in: Peptides, Polypeptides, and Proteins (E. R. Blout, F. A. Bovey, M. Goodman, and N. Lotan, eds.), John Wiley & Sons, New York, pp. 114–125.Google Scholar
  191. Fasman, G. D., Chou, P. Y., and Adler, A. J., 1976, Prediction of the conformation of the histones, Biophys. J. 16:1201–1238.PubMedCrossRefGoogle Scholar
  192. Fasman, G. D., Chou, P. Y., and Adler, A. J., 1977, Histone conformation: Predictions and experimental studies, in: The Molecular Biology of the Mammalian Genetic Apparatus—I, (P. O. P. Ts’o, ed.), Elsevier-Exerpta Medica/North Holland, Amsterdam, pp. 1–52.Google Scholar
  193. Finer-Moore, J., and Stroud, R. M., 1984, Amphipathic analysis and possible formation of the ion channel in acetylcholine receptor, Proc. Natl. Acad. Sci. U.S.A. 81: 155–159.PubMedCrossRefGoogle Scholar
  194. Finkelstein, A. Y., Ptitsyn, O. B., and Bendsko, P., (1970), Coiling and topology on the anti-parallel ß-structure, Biofisika 24:21–26.Google Scholar
  195. Finney, J. L., Gellatly, B. J., Golton, I. C., and Goodfellow, J., 1980, Solvent effects and polar interactions in the structural stability and dynamics of globular proteins, Biophys. J. 32: 17–23.PubMedCrossRefGoogle Scholar
  196. Fishleigh, R. Y., Robson, B., Garnier, J., and Finn, P. W., 1987, Studies on rationales for an expert system approach to the interpretation of protein sequence data. Preliminary analysis of the human epidermal growth factor receptor, FEBS Lett. 214:219–225.PubMedCrossRefGoogle Scholar
  197. Fitch, W. M., 1966a, The relation between frequencies of amino acids and ordered trinucleotides, J. Mol. Biol. 16:1–8.PubMedCrossRefGoogle Scholar
  198. Fitch, W. M., 1966b, An improved method of testing for evolutionary homology, J. Mol. Biol. 16:9–16.PubMedCrossRefGoogle Scholar
  199. Fitch, W. M., 1966c, Evidence suggesting a partial, internal duplication in the ancestral gene for hemecontaining globins, J. Mol. Biol. 16:17–27.PubMedCrossRefGoogle Scholar
  200. Fitch, W. M., and Smith, T. F., 1983, Optimal sequence alignments, Proc. Natl. Acad. Sci. U.S.A. 80:1382–1386.PubMedCrossRefGoogle Scholar
  201. Fleming, P. J., Dailey, H. A., Corcoran, D., and Strittmatter, P., 1978, The primary structure of the non-polar segment of bovine cytochrome b5, J. Biol. Chem. 253:5369–5372.PubMedGoogle Scholar
  202. Flinta, C., von Heijne, G., and Johansson, J., 1983, Helical sidedness and the distribution of polar residues in trans-membrane helices, J. Mol. Biol. 168:193–196.PubMedCrossRefGoogle Scholar
  203. Foster, D. L., Boublik, M., and Kaback, H. R., 1983, Structure of the lac carrier protein of Escherichia coli, J. Biol. Chem. 258:31–34.PubMedGoogle Scholar
  204. Froimowitz, M., and Fasman, G. D., 1974, Prediction of secondary structure of proteins using the helix-coil transition theory, Macromolecules 7:583–589.PubMedCrossRefGoogle Scholar
  205. Fukushima, D. Kupferberg, J. P., Yokoyama, S., Kroon, D. J., Kaiser, E. T., and Kezdy, F. J., 1979, A synthetic amphiphilic helical docosapeptide with the surface properties of plasma apolipoprotein A-I, J. Am. Chem. Soc. 101:3703–3704.CrossRefGoogle Scholar
  206. Furois-Corbin, S., and Pullman, A., 1987, Theoretical studies of the packing of α-helices into possible transmembrane bundles: Sequences including alanines, leucines and serines, Biochim. Biophys. Acta 902: 31–45.PubMedCrossRefGoogle Scholar
  207. 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
  208. Garratt, R. C., Taylor, W. R., and Thornton, J. M., 1985, The influence of tertiary structure on secondary structure prediction. Accessibility versus predictability for ß-structure, FEBS Lett. 188:59–62.CrossRefGoogle Scholar
  209. Geisow, M. J., and Roberts, R. D. B., 1980, Amino acid preferences for secondary structure vary with protein class, Int. J. Biol. Macromol. 2:387–389.CrossRefGoogle Scholar
  210. Geisow, M. J., Fritsche, U., Hexham, J. M., Dash, B., and Johnson, T., 1986, A consensus amino acid sequence repeat in Torpedo and mammalian Ca2+-dependent membrane-binding proteins, Nature 320: 636–638.PubMedCrossRefGoogle Scholar
  211. Gelin, B., and Karplus, M., 1979, Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment, Biochemistry 18:1256–1268.PubMedCrossRefGoogle Scholar
  212. Gerber, G. E., Anderegg, R. J., Herlihy, W. C., Gray, C. P., Bieman, K., and Khorana, H. G., 1979, Partial primary structure of bacteriorhodopsin: Sequencing methods for membrane proteins, Proc. Natl. Acad. Sci. U.S.A. 76:227–231.PubMedCrossRefGoogle Scholar
  213. Getzoff, E. D., Tainer, J. A., and Olson, A. J., 1986, Recognition and interactions controlling the assemblies of ß-barrel domains, Biophys. J. 49:191–206.PubMedCrossRefGoogle Scholar
  214. Ghelis, C., and Yon, J., 1982, Protein Folding, Academic Press, New York.Google Scholar
  215. Gibrat, J.-F., Garnier, J., and Robson, B., 1987, Further developments of protein secondary structure prediction using information theory: New parameters and consideration of residue pairs, J. Mol. Biol. 198:425–443.PubMedCrossRefGoogle Scholar
  216. Gilbert, W., 1978, Why genes in pieces? Nature 271:501.PubMedCrossRefGoogle Scholar
  217. Gilson, M. K., and Honig, B. H., 1987, Calculation of electrostatic potentials in an enzyme active site, Nature 330:84–86.PubMedCrossRefGoogle Scholar
  218. Glaeser, R. M., and Jap, B. K., 1985, Absorption flattening in the circular dichroism spectra of small membrane fragmerits, Biochemistry 24:6398–6401.PubMedCrossRefGoogle Scholar
  219. Goad, W. B., and Kanehisa, M. I., 1982, Pattern recognition in nucleic acid sequences I. A general method for finding local homologies and symmetries, Nucleic Acids Res. 10:247–263.PubMedCrossRefGoogle Scholar
  220. Gordon, D. J., and Holzworth, G., 1971, Artifacts in the measure of optical activity of membrane suspensions, Arch. Biochem. Biophys. 142:481–488.PubMedCrossRefGoogle Scholar
  221. Grantham, R., 1974, Amino acid difference formula to help explain protein evolution, Science 185: 862–864.PubMedCrossRefGoogle Scholar
  222. Gratzer, W. B., Bailey, E., and Beaven, G. H., 1967, Conformational states of glucagon, Biochem. Biophys. Res. Commun. 28:914–919.PubMedCrossRefGoogle Scholar
  223. Gray, T. M., and Matthews, B. W., 1984, Intrahelical hydrogen bonding of serine, threonine, and cysteine residues within α-helices and its relevance to membrane-bound proteins, J. Mol. Biol. 175:75–81.PubMedCrossRefGoogle Scholar
  224. Green, N. M., and Flanagan, M. T., 1976, The prediction of the conformation of membrane proteins from the sequence of amino acids, Biochem. J. 153:729–732.PubMedGoogle Scholar
  225. Grenningloh, G., Rienitz, A., Schmitt, B., Methfessel, C., Zensen, M., Beyreuther, K., Grundelfinger, 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
  226. Gribskov, M., Burgess, R. R., and Devereaux, J., 1986, PEPPLOT, a protein secondary analysis program for the UWGCG sequence analysis software package, Nucleic Acids Res. 14:327–334.PubMedCrossRefGoogle Scholar
  227. Gribskov, M., McLachlan, A. D., and Eisenberg, D., 1987, Profile analysis: Detection of distantly related proteins, Proc. Natl. Acad. Sci. U.S.A. 84:4355–4358.PubMedCrossRefGoogle Scholar
  228. Gutte, B., Daumigen, M., and Wittschieber, E., 1979, Design, synthesis and characteristics of a 34-residue polypeptide that interacts with nucleic acids, Nature 281:650–655.PubMedCrossRefGoogle Scholar
  229. Guy, H. R., 1981, Structural models of the nicotinic acetylcholine receptor and its toxin-binding sites, Cell. Mol. Neurobiol. 1:231–258.PubMedCrossRefGoogle Scholar
  230. 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
  231. Guy, H. R., 1985, Amino acid side-chain partition energies and distribution of residues in soluble proteins, Biophys. J. 47:61–70.PubMedCrossRefGoogle Scholar
  232. Guy, H. R., and Seetharamulu, P., 1986, Molecular model of the action potential sodium channel, Proc. Natl. Acad. Sci. U.S.A. 83:508–512.PubMedCrossRefGoogle Scholar
  233. Guzzo, A. Y., 1965, The influence of amino acid sequence on protein structure, Biophys. J. 5:809–822.PubMedCrossRefGoogle Scholar
  234. Haber, J. E., and Koshland, Jr., D. E., 1970, An evaluation of the relatedness of proteins based on comparison of amino acid sequences, J. Mol. Biol. 50:617–639.PubMedCrossRefGoogle Scholar
  235. Hager, K. M., Mandala, S. M., Davenport, J. W., Speicher, D. W., Benz, Jr., E. J., and Slayman, C. W., 1986, Amino acid sequences of the plasma membrane ATPase of Neurospora crassa: Deduction from genomic and c-DNA sequences, Proc. Natl. Acad. Sci. U.S.A. 83:7693–7697.PubMedCrossRefGoogle Scholar
  236. Hagler, A. T., and Honig, B., 1978, On the formation of protein tertiary structure on a computer. Proc. Natl. Acad. Sci. U.S.A. 75:554–558.PubMedCrossRefGoogle Scholar
  237. Hagler, A. T., Huler, E., and Lifson, S., 1974, Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals, J. Am. Chem. Soc. 96:5319–5327.PubMedCrossRefGoogle Scholar
  238. Hammett, L. P., 1970, Physical Organic Chemistry, 2nd ed., McGraw-Hill, New York.Google Scholar
  239. Hardman, K. D., and Ainsworth, C. F., 1972, Structure of concanavalin A at 2.4 α resolution, Biochemistry 11:4910–4919.PubMedCrossRefGoogle Scholar
  240. Harrison, S. C., 1985, Two for the price of one, Nature 313:736–737.PubMedCrossRefGoogle Scholar
  241. Havel, T. F., Kuntz, I. D., and Crippen, G. M., 1983, The theory and practice of distance geometry, Bull. Math. Biol. 45:665–720.Google Scholar
  242. Hayes, T. G., 1980, Chou-Fasman analysis of the secondary structure of F and LE interferons, Biochem. Biophys. Res. Commun. 95:872–879.PubMedCrossRefGoogle Scholar
  243. Hayward, S. B., and Stroud, R. M., 1981, Projected structure of purple membrane determined to 3.7 Å resolution by low temperature electron microscopy, J. Mol. Biol. 151:491–517.PubMedCrossRefGoogle Scholar
  244. Heber-Katz, E., Hollosi, M., Dietzschold, B., Hudecz, F., and Fasman, G. D., 1985, The T cell response to the glycoprotein D of the herpes simplex virus: The significance of antigen conformation, J. Immunol. 135: 1385–1390.PubMedGoogle Scholar
  245. Hedrick, S. M., Cohen, D. I., Nielsen, E. A., and Davis, M. M., 1984a, Isolation of cDNA clones encoding T-cell-specific membrane associated proteins, Nature 308:149–153.PubMedCrossRefGoogle Scholar
  246. Hedrick, S. M., Nielsen, E. A., Kavaler, J., Cohen, D. I., and Davis, M. M., 1984b, Sequence relationships between putative T-cell receptor polypeptides and immunoglobulins, Nature 308:153–158.PubMedCrossRefGoogle Scholar
  247. Hellberg, S., Sjostrom, M., and Wold, S., 1986, The prediction of bradykinin potentiating potency of penta peptides. An example of a peptide quantitative structure-activity relationship, Acta Chem. Scand. B40:135–140.CrossRefGoogle Scholar
  248. Henderson, R., and Unwin, P. N. T., 1975, Three-dimensional model of purple membrane obtained by electron microscopy, Nature 257:28–32.PubMedCrossRefGoogle Scholar
  249. Hol, W. G. J., van Duijnen, P. T., and Berendsen, H. J. C., 1978, The α-helix dipole and the properties of proteins, Nature 273:443–446.PubMedCrossRefGoogle Scholar
  250. Hol, W. G. J., Halie, L. M., and Sander, C., 1981, Dipoles of the α-helix and ß-sheet: Their role in protein folding, Nature 294:532–536.PubMedCrossRefGoogle Scholar
  251. Holmes, M. A., and Matthews, B. W., 1982, Structure of thermolysin refined at 1.6 Å resolution, J. Mol. Biol. 160:623–639.PubMedCrossRefGoogle Scholar
  252. Hones, J., Jany, K.-D., Pfleider, G., and Wagner, A. F. V., 1987, An integrated prediction of secondary, tertiary, and quaternary structure of glucose dehydrogenase, FEBS Lett. 212:193–198.PubMedCrossRefGoogle Scholar
  253. Honig, B. H., and Hubbell, W. L., 1984, Stability of “salt bridges” in membrane proteins, Proc. Natl. Acad. Sci. U.S.A. 81:5412–5416.PubMedCrossRefGoogle Scholar
  254. Honig, B. H., Ray, A., and Levinthal, C., 1976, Conformational flexibility and protein folding: Rigid structural fragments connected by flexible joints in subtilisn BPN, Proc. Natl. Acad. Sci. U.S.A. 73:1974–1978.PubMedCrossRefGoogle Scholar
  255. Honig, B. H., Hubbell, W. L., and Flewelling, R. F., 1986, Electrostatic interactions in membranes and proteins, Annu. Rev. Biophys. Biophys. Chem. 15:163–193.PubMedCrossRefGoogle Scholar
  256. Hopp, T. P., and Woods, K. R., 1981, Prediction of protein antigenic determinants from amino acid sequence, Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828.PubMedCrossRefGoogle Scholar
  257. Hruby, W., Krstenansky, J., Gysin, B., Pelton, J. T., Trivedi, D., and McKee, R. L., 1986, Conformational considerations in the design of glucagon agonists and antagonists: Examination using synthetic analogs, Biopolymers 25:S135–S155.PubMedCrossRefGoogle Scholar
  258. Huang, K.-S., Bayley, H., Liao, M.-J., London, E., and Khorana, H. G., 1981, Refolding of an integral membrane protein. Denaturation, renaturation, and reconstitution of intact bacteriorhodopsin and two proteolytic fragments, J. Biol. Chem. 256:3802–3809.PubMedGoogle Scholar
  259. Huang, K.-S., Radhakrishnan, R., Bayley, H., and Khorana, H. G., 1982, Orientation of retinal in bacteriorhodopsin as studied by cross-linking using a photosensitive analog of retinal, J. Biol. Chem. 257: 13616–13623.PubMedGoogle Scholar
  260. Huber, R., Kulka, D., Ruhlman, A., and Steigman, W., 1971, Pancreatic trypsin inhibitor (Kunitz) Part I. Structure and function, Cold Spring Harbor Symp. Quant. Biol. 36:141–150.Google Scholar
  261. Hucho, F., 1986, The nicotinic acetylcholine receptor and its ion channel, Eur. J. Biochem. 158:211–256.PubMedCrossRefGoogle Scholar
  262. Hurle, M. R., Matthews, C. R., Cohen, F. E., Kuntz, I. D., Toumadje, A., and Johnson, Jr., W. C., 1987, Prediction of the tertiary structure of the α-subunit of tryptophan synthetase, Proteins 2:210–224.PubMedCrossRefGoogle Scholar
  263. IntelliGenetics, Inc., 1981-1985. PER References Manual, IntelliGenetics, Mountain View, CA.Google Scholar
  264. Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S. J., and Scheraga, H. A., 1980, Characterization of multiple bends in proteins, Biopolymers 19:1183–1210.PubMedCrossRefGoogle Scholar
  265. Jaenicke, R., 1984, Protein folding and protein association, Angew. Chem. [Engl.] 23:395–413.CrossRefGoogle Scholar
  266. Jaenicke, R., 1987, Folding and association of proteins, Prog. Biophys. Mol. Biol. 49:117–237.PubMedCrossRefGoogle Scholar
  267. Janin, J., 1979, Surface and inside volumes in globular proteins, Nature 277:491–492.PubMedCrossRefGoogle Scholar
  268. Janin, J., and Chothia, C., 1980, Packing of α-helices onto ß-pleated sheets and anatomy of α/ß proteins, J. Mol. Biol. 143:95–128.PubMedCrossRefGoogle Scholar
  269. Jap, B. K., and Kong, S. H., 1986, Secondary structure of halorhodopsin, Biochemistry 25:502–505.PubMedCrossRefGoogle Scholar
  270. Jap, B. K., Maestre, M. F., Hayward, S. B., and Glaeser, R. M., 1983, Peptide-chain secondary structure of bacteriorhodopsin, Biophys. J. 43:81–89.PubMedCrossRefGoogle Scholar
  271. Jones, D. D., 1975, Amino acid properties and side-chain orientation in proteins: A cross correlation approach, J. Theor. Biol. 50:167–183.PubMedCrossRefGoogle Scholar
  272. Kabat, E. A., and Wu, T. T., 1973a, The influence of nearest-neighbor amino acids on the conformation of the middle amino acid in proteins: Comparison of predicted and experimental determination of ß-sheets in conconavalin A, Proc. Natl. Acad. Sci. U.S.A. 70:1473–1477.PubMedCrossRefGoogle Scholar
  273. Kabat, E. A., and Wu, T. T., 1973b, The influence of nearest-neighboring amino acid residues on aspects of secondary structure of proteins. Attempts to locate α-helices and ß-sheets, Biopolymers 12:751–774.PubMedCrossRefGoogle Scholar
  274. Kabat, E. A., Wu, T. T., Bilofsky, H., Reid-Miller, M., and Perry, H., 1983, Sequences of Immunological Interest, U.S. Dept. of Health and Human Services, Washington.Google Scholar
  275. Kabsch, W., and Sander, C., 1983a, How good are predictions of protein secondary structure? FEBS Lett. 155: 179–182.PubMedCrossRefGoogle Scholar
  276. Kabsch, W., and Sander, C., 1983b, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometric features, Biopolymers 22:2577–2637.PubMedCrossRefGoogle Scholar
  277. 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
  278. Kabsch, W., and Sander, C., 1985, Identical pentapeptides with different backbones, Nature 317:207.PubMedCrossRefGoogle Scholar
  279. Kanazawa, H., Hama, H., Rosen, B. P., and Futai, M., 1985, Deletion of seven amino acids from the γ subunit of Escherichia coli H+-ATPases causes total loss of F1 assembly on membrane, Arch. Biochem. Biophys. 241:364–370.PubMedCrossRefGoogle Scholar
  280. Karplus, M., and Weaver, D. L., 1979, Diffusion-collision model for protein folding, Biopolymers 18:1421–1437.CrossRefGoogle Scholar
  281. Karplus, P. A., and Schulz, G. E., 1985, Prediction of chain flexibility in proteins, Naturwissenschaften 72: 212–213.CrossRefGoogle Scholar
  282. Kauzmann, W., 1959, Some factors in the interpretation of protein denaturation, Adv. Protein Chem. 14: 1–63.PubMedCrossRefGoogle Scholar
  283. Kawakami, K., Noguchi, S., Noda, M., Takahashi, H., Ohta, T., Kawamura, M., Nojima, H., Nagano, K., Hirose, T., Inayama, S., Hayashida, H., Miyata, T., and Numa, S., 1985, Primary structure of the α-subunit of Torpedo californica (Na + + K + )ATPase deduced from cDNA sequence, Nature 316: 733–736.PubMedCrossRefGoogle Scholar
  284. Kelly, L., and Holladay, L. A., 1987, Comparison of scales of amino acid side chain properties by conservation during evolution of four proteins, Protein Eng. 1:137–140.PubMedCrossRefGoogle Scholar
  285. Kim, P. S., and Baldwin, R. L., 1982, Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding, Annu. Rev. Biochem. 51:459–489.PubMedCrossRefGoogle Scholar
  286. Klapper, I., Hagstrom, R., Fine, R., Sharp, K., and Honig, B., 1986, Focussing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino acid modification, Proteins 1:47–59.PubMedCrossRefGoogle Scholar
  287. Kleffel, B., Garavito, R. M., Baumeister, W., and Rosenbusch, J. P., 1985, Secondary structure of a channel-forming protein: Porin from E. coli outer membrane, EMBO J. 4:1589–1592.PubMedGoogle Scholar
  288. Klein, P., 1986, Prediction of protein structural class by discriminant analysis, Biochim. Biophys. Acta 874: 205–215.PubMedCrossRefGoogle Scholar
  289. Klein, P., and DeLisi, C., 1986, Prediction of protein structural class from amino acid sequence, Biopolymers 25:1659–1672.PubMedCrossRefGoogle Scholar
  290. Klein, P., Kanehisa, M., and DeLisi, C., 1984, Prediction of protein function from sequence properties. Discriminant analysis of a data base, Biochim. Biophys. Acta 787:221–226.PubMedCrossRefGoogle Scholar
  291. Klein, P., Kanehisa, M., and DeLisi, C., 1985, The detection of membrane-spanning proteins, Biochim. Biophys. Acta 815:468–476.PubMedCrossRefGoogle Scholar
  292. Klein, P., Jacquez, J. A., and DeLisi, C., 1986, Prediction of protein function by discriminant analysis, Math. Biosci. 81:177–189.CrossRefGoogle Scholar
  293. Kneale, G. G., and Bishop, M. J., 1985, Nucleic acid and protein sequence databases, Cabios Rev. 1:11–17.Google Scholar
  294. Kolaskar, A. S., Ramabrahmam, V., and Soman, K. V., 1980, Reversal of polypeptide chain in globular proteins, Int. J. Peptide Protein Res. 16:1–11.CrossRefGoogle Scholar
  295. Kolb, E., Hudson, P. J., and Harris, J. I.,1980, Phosphofructokinase: Complete amino acid sequence of the enzyme from Bacillus stearothermophilus, Eur. J. Biochem. 108:587–597.PubMedCrossRefGoogle Scholar
  296. Kopito, R. R., and Lodish, H. F., 1985, Primary structure and transmembrane orientation of the murine anion exchange protein, Nature 316:234–238.PubMedCrossRefGoogle Scholar
  297. Kopito, R. R., Andersson, M., and Lodish, H. F., 1987, Structure and organization of the murine band 3 gene, J. Biol. Chem. 262:8035–8040.PubMedGoogle Scholar
  298. Kosower, E. M., 1982, in: International Symposium on Structure and Dynamics of Nucleic Acids and Protein, pp. 52–53.Google Scholar
  299. Kosower, E. M., 1983a, Partial tertiary structure assignment for the acetylcholine receptor on the basis of the hydrophobicity of amino acid sequences and channel location using single group rotation theory, Biochem. Biophys. Res. Commun. 111:1022–1024.PubMedCrossRefGoogle Scholar
  300. Kosower, E. M., 1983b, Partial tertiary structure assignments of the ß1-,-γ-, and δ subunits of the acetylcholine receptor on the basis of the hydrophobicity of amino acid sequences and channel location using single group theory, FEBS Lett. 155:245–247.PubMedCrossRefGoogle Scholar
  301. Kosower, E. M., 1987, A structural and dynamic model for the nicotinic acetylcholine receptor, Eur. J. Biochem. 168:431–449.PubMedCrossRefGoogle Scholar
  302. Kotelchuck, D., and Scheraga, H. A., 1968, The influence of short-range interactions on protein conformation. I. Side-chain-backbone interactions with a single peptide unit, Proc. Natl. Acad. Sci. U.S.A. 61:1163–1170.PubMedCrossRefGoogle Scholar
  303. Kotelchuck, D., and Scheraga, H. A., 1969, The influence of short-range interactions on protein conformation II. A model for predicting the α-helical regions of proteins, Proc. Natl. Acad. Sci. U.S.A. 62:14–21.PubMedCrossRefGoogle Scholar
  304. Krchnak, V., Mach, O., and Maly, A., 1987, Computer prediction of potential immunogenic determinants from protein amino acid sequence, Anal. Biochem. 165:200–207.PubMedCrossRefGoogle Scholar
  305. Krebs, K. E., and Phillips, M. C., 1984, The contribution of α-helices to the surface activities of proteins, FEBS Lett. 175:263–266.PubMedCrossRefGoogle Scholar
  306. Kubo, T., Fukuda, K., Mikami, A., Maeda, A., Takahashi, H., Mishina, M., Hoga, T., Haga, K., Ichiyama, A., Kangawa, K., Kojima, M., Matsuo, H., Hirose, T., and Numa, S., 1986, Cloning, sequencing and expression of complementary DNA encoding the muscarinic acetylcholine receptor, Nature 323:411–416.PubMedCrossRefGoogle Scholar
  307. Kubota, Y., Takahashi, S., Nishikawa, K., and Ooi, T., 1981, Homology in protein sequences expressed by correlation coefficients, J. Theor. Biol. 91:347–361.PubMedCrossRefGoogle Scholar
  308. 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
  309. Kuntz, I. D., 1972, Protein folding, J. Am. Chem. Soc. 94:4009–4012.PubMedCrossRefGoogle Scholar
  310. Kuntz, I. D., 1975, An approach to the tertiary structure of globular proteins, J. Am. Chem. Soc. 97:4362–4366.PubMedCrossRefGoogle Scholar
  311. Kuntz, I. D., and Crippen, G. M., 1979, Protein densities, Int. J. Peptide Protein Res. 13:223–228.CrossRefGoogle Scholar
  312. Kuntz, I. D., Crippen, G. M., Kollman, P. A., and Kimelman, D., 1976, Calculation of protein tertiary structure, J. Mol. Biol. 106:983–994.PubMedCrossRefGoogle Scholar
  313. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., and Ferrin, T. E., 1982, A geometric approach to macromolecule-ligand interactions, J. Mol. Biol. 161:269–288.PubMedCrossRefGoogle Scholar
  314. 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
  315. Lathrop, R. H., Webster, T. A., and Smith, T. F., 1987, ARIADNE: Pattern-directed inference and hierarchical abstraction in protein structure recognition, Commun. ACM 30:909–921.CrossRefGoogle Scholar
  316. Laursen, R. A., Samiullah, M., and Lees, M. B., 1984, The structure of bovine brain myelin proteolipid and its organization in myelin, Proc. Natl. Acad. Sci. U.S.A. 81:2912–2916.PubMedCrossRefGoogle Scholar
  317. Lee, B., and Richards, F. M., 1971, An interpretation of protein structures: Estimation of static accessibility, J. Mol. Biol. 55:379–400.PubMedCrossRefGoogle Scholar
  318. Lee, C. A., and Saier, M. H., Jr., 1983, Mannitol-specific enzyme II of the bacterial phosphotransferase system, J. Biol. Chem. 258:10761–10767.PubMedGoogle Scholar
  319. Lenstra, J. A., 1977, Evolution of secondary structure prediction of proteins, Biochim. Biophys. Acta 491:333–398.PubMedGoogle Scholar
  320. Lenstra, J. A., Hofsteenge, J., and Beintema, J. J., 1977, Invariant features of the structure of pancreatic ribonuclease. A test of different predictive models, J. Mol. Biol. 109:185–193.PubMedCrossRefGoogle Scholar
  321. Lesk, A. M., and Chothia, C., 1980, How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins, J. Mol. Biol. 136:225–270.PubMedCrossRefGoogle Scholar
  322. Lesk, A. M., and Rose, G. D., 1981, Folding units in globular proteins. Proc. Natl. Acad. Sci. U.S.A. 78: 4304–4308.PubMedCrossRefGoogle Scholar
  323. Lesk, A., Levitt, M., and Chothia, C., 1986, Alignment of the amino acids sequences of distantly related proteins using variable gap penalties, Protein Eng. 1:77–78.PubMedCrossRefGoogle Scholar
  324. Leszczynski, J., and Rose, G. D., 1986, Loops in globular proteins: A novel category of secondary structure, Science 234:849–855.PubMedCrossRefGoogle Scholar
  325. Leung, D. W., Spenser, S. A., Cachianes, G., Hammonds, R. G., Collins, C., Henzel, W. J., Barnard, R., Waters, M. J., and Wood, W. I., 1987, Growth hormone receptor and serum binding protein: Purification, cloning and expression, Nature 330:537–543.PubMedCrossRefGoogle Scholar
  326. Levin, J. M., Robson, B., and Garnier, J., 1986, An algorithm for secondary structure determination in proteins based on sequence similarity, FEBS Lett. 205:303–308.PubMedCrossRefGoogle Scholar
  327. Levinthal, C., 1968, Are there pathways for protein folding? J. Chem. Phys. 65:44–45.Google Scholar
  328. Levitt, M., 1974, On the nature of the binding of hexa-N-acetylglucosamine substrate to lysozyme, in: Peptides, Polypeptides, and Proteins (E. R. Blout, F. A. Bovey, M. Goodman, and N. Lotan, eds.), John Wiley & Sons, New York, pp. 99–113.Google Scholar
  329. Levitt, M., 1976, A simplified representation of protein conformations for rapid simulation of protein folding, J. Mol. Biol. 104:59–107.PubMedCrossRefGoogle Scholar
  330. Levitt, M., 1978, Conformational preferences of amino acids in globular proteins, Biochemistry, 17:4277–4285.PubMedCrossRefGoogle Scholar
  331. Levitt, M., 1983, Protein folding by restrained energy minimization and molecular dynamics, J. Mol. Biol. 170: 723–764.PubMedCrossRefGoogle Scholar
  332. Levitt, M., and Chothia, C., 1976, Structural patterns in globular proteins, Nature 261:552–558.PubMedCrossRefGoogle Scholar
  333. Levitt, M., and Greer, J., 1977, Automatic identification of secondary structure in globular proteins, J. Mol. Biol. 114:181–293.PubMedCrossRefGoogle Scholar
  334. Levitt M., and Lifson, S., 1969, Refinement of protein conformations using a macromolecular energy minimization procedure, J. Mol. Biol. 46:269–279.PubMedCrossRefGoogle Scholar
  335. Levitt, M., and Warshel, A., 1975, Computer simulation of protein folding, Nature 253:694–698.PubMedCrossRefGoogle Scholar
  336. Lewis, P. N., and Bradbury, E. M., 1974, Effect of electrostatic interactions on the prediction of helices in proteins, Biochim. Biophys. Acta 336:153–164.Google Scholar
  337. Lewis, P. N., and Scheraga, H. A., 1971, Predictions of structural homologies in cytochrome c proteins, Arch. Biochem. Biophys. 144:576–583.PubMedCrossRefGoogle Scholar
  338. Lewis, P. N., Go, N., Go, M., Kotelchuck, D., and Scheraga, H. A., 1970, Helix probability profiles of denatured proteins and their correlation with native structures, Proc. Natl. Acad. Sci. U.S.A. 65: 810–815.PubMedCrossRefGoogle Scholar
  339. Lewis, P. N., Momany, F. A., and Scheraga, H. A., 1971, Folding of polypeptide chains in proteins: A proposed mechanism for folding, Proc. Natl. Acad. Sci. U.S.A. 68:2293–2297.PubMedCrossRefGoogle Scholar
  340. Lewis, P. N., Momany, F. A., and Scheraga, H. A., 1973a, Chain reversals in proteins, Biochim. Biophys. Acta 303:211–229.PubMedGoogle Scholar
  341. Lewis, P. N., Momany, F. A., and Scheraga, H. A., 1973b, Energy parameters in polypeptides. VI. Conformational energy analysis of the N-acetyl-N’-methyl amides of the twenty naturally occurring amino acids, Israel J. Chem. 11:121–152.Google Scholar
  342. Lifson, S., and Roig, A., 1961, On the theory of helix-coil transitions in polypeptides, J. Chem. Phys. 34: 1963–1974.CrossRefGoogle Scholar
  343. Lifson, S., and Sander, C., 1979, Antiparallel and parallel ß-strands differ in amino acid residue preferences, Nature 282: 109–111.PubMedCrossRefGoogle Scholar
  344. Lifson, S., and Sander, C., 1980a, Specific recognition in the tertiary structure of ß-sheets in proteins, J. Mol. Biol. 139:627–639.PubMedCrossRefGoogle Scholar
  345. Lifson, S., and Sander, C., 1980b, Composition, cooperativity and recognition in proteins, in: Protein Folding (R. Jaenicke, ed.), Elsevier/North-Holland Biomedical Press, Amsterdam, pp. 289–316.Google Scholar
  346. Lifson, S., and Warshel, A., 1968, Consistent force field calculations, vibrational spectra, and enthaipies of cycloalkane and n-alkane molecules, J. Chem. Phys. 49:5116–5129.CrossRefGoogle Scholar
  347. Liljas, A., and Rossman, M. G., 1974, X-ray studies of protein interactions, Annu. Rev. Biochem. 43:475–507.CrossRefGoogle Scholar
  348. Lim, V. I., 1974a, Structural principles of the globular organization of protein chains: A stereochemical theory of globular protein secondary structure, J. Mol. Biol. 88:857–872.PubMedCrossRefGoogle Scholar
  349. Lim, V. I., 1974b, Algorithms for prediction of α-helices and ß-structural regions in globular proteins, J. Mol. Biol. 88:873–894.PubMedCrossRefGoogle Scholar
  350. Lipman, D. J., and Pearson, W. R., 1985, Rapid and sensitive protein similarity searches, Science 227:1435–1441.PubMedCrossRefGoogle Scholar
  351. Lisium, 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.Google Scholar
  352. London, E., and Khorana, H. G., 1982, Denaturation and renaturation of bacteriorhodopsin in detergents and lipid-detergent mixtures, J. Biol. Chem. 257:7003–7011.PubMedGoogle Scholar
  353. Long, M. M., Urry, D. W., and Stoeckenius, W., 1977, Circular dichroism of biological membranes: Purple membrane of Halobacterium halobium, Biochem. Biophys. Res. Commun. 75:725–731.PubMedCrossRefGoogle Scholar
  354. Lopez, J. A., Chung, D. W., Fujikawa, K., Hagen, F. S., Papayannopoulou, T., and Roth, G. J., 1987, Cloning of the α chain of human platlet glycoprotein 1b: A transmembrane protein with homology to leucine-rich α2-glycoprotein, Proc. Natl. Acad. Sci. U.S.A. 84:5615–5619.PubMedCrossRefGoogle Scholar
  355. Loucheux-Lefebvre, M.-H., 1978, Predicted ß-turns in peptide and glycopeptide antifreezes, Biochem. Biophys. Res. Commun. 81:1352–1356.PubMedCrossRefGoogle Scholar
  356. Loucheux-Lefebvre, M.-H., Aubert, J.-P., and Jolles, P., 1978, Prediction of the conformation of the cow and sheep k-caseins, Biophys. J. 23:323–336.PubMedCrossRefGoogle Scholar
  357. Low, B. W., Lovell, F. M., and Rudko, A. D., 1968, Prediction of α-helical regions in proteins of known sequence, Proc. Natl. Acad. Sci. U.S.A. 60:1519–1526.PubMedCrossRefGoogle Scholar
  358. Maclennan, D. H., Brandl, C. J., Korczak, B., and Green, N. M., 1985, Amino acid sequences of a Ca+ + Mg +-dependent ATPase from rabbit muscle sarcoplasmic reticulum, deduced from its complementary DNA sequence, Nature 316:696–700.PubMedCrossRefGoogle Scholar
  359. Maizel, J. V., Jr., and Lenk, R. P., 1981, Enhanced graphic matrix analysis of nucleic acid and protein sequence, Proc. Natl. Acad. Sci. U.S.A. 78:7665–7669.PubMedCrossRefGoogle Scholar
  360. Manavalan, P., and Ponnuswamy, P. K., 1977, A study of the preferred environment of amino acid residues in globular proteins, Arch. Biochem. Biophys. 184:476–487.PubMedCrossRefGoogle Scholar
  361. Manavalan, P., and Ponnuswamy, P. K., 1978, Hydrophobic character of amino acid residues in globular proteins, Nature 275:673–674.PubMedCrossRefGoogle Scholar
  362. Mao, D., and Wallace, B. A., 1984, Differential light scattering and absorption flattening optical effects are minimal in circular dichroism spectra of small unilamellar vesicles, Biochemistry 23:2667–2673.PubMedCrossRefGoogle Scholar
  363. Masu, Y., Nakayama, K., Tamaki, H., Harada, Y., Kuno, M., and Nakanishi, S., 1987, cDNA cloning of bovine substance-K receptor through oocyte expression system, Nature 329:836–838.PubMedCrossRefGoogle Scholar
  364. Matthew, J. B., 1985, Electrostatic effects in proteins, Annu. Rev. Biophys. Biophys. Chem. 14:387–417.PubMedCrossRefGoogle Scholar
  365. Matthew, J. B., and Gurd, F. R. N., 1986a, Calculation of electrostatic interactions in proteins, Methods Enzymol. 130:413–436.PubMedCrossRefGoogle Scholar
  366. Matthew, J. B., and Gurd, F. R. N., 1986b, Stabilization and destabilization of protein structure by charge interactions, Methods Enzymol. 130:437–453.PubMedCrossRefGoogle Scholar
  367. Matthews, B. W., 1975, Comparison of the predicted and observed secondary structure of T4 phage lysozyme, Biochim. Biophys. Acta 405:442–451.PubMedGoogle Scholar
  368. Matthews, F. S., Argos, P., and Levine, M., 1971, The structure of cytochrome bs at 2.0 Å resolution, Cold Spring Harbor Symp. Quant. Biol. 36:387.Google Scholar
  369. Maxfield, F. R., and Scheraga, H. A., 1975, The effect of neighboring charges on the helix forming ability of charged amino acids in proteins, Macromolecules 8:491–493.PubMedCrossRefGoogle Scholar
  370. Maxfield, F. R., and Scheraga, H. A., 1976, Status of empirical methods for the prediction of protein backbone topography, Biochemistry 15:5138–5153.PubMedCrossRefGoogle Scholar
  371. Maxfield, F. R., and Scheraga, H. A., 1979, Improvements in the prediction of protein backbone topography by reduction of statistical errors, Biochemistry 18:697–704.PubMedCrossRefGoogle Scholar
  372. McCammon, J. A., Gelin, B. R., and Karplus, M., 1977, Dynamics of folded proteins. Nature 267:585–590.PubMedCrossRefGoogle Scholar
  373. McCarthy, M. P., Earnest, J. P., Young, E. F., Choe, S., and Stroud, R. M., 1986, The molecular neurobiology of the acetylcholine receptor, 1986, Annu. Rev. Neurosci. 9:383–413.PubMedCrossRefGoogle Scholar
  374. McCubbin, W. D., Oikawa, K., and Kay, C. M., 1971, Circular dichroism studies on concanavalin A, Biochem. Biophys. Res. Commun. 43:666–674.PubMedCrossRefGoogle Scholar
  375. McGregor, M. J., Islam, S. A., and Sternberg, M. J. E., 1987, Analysis of the relationship between side-chain conformation and secondary structure in globulary proteins, J. Mol. Biol. 198:295–310.PubMedCrossRefGoogle Scholar
  376. McLachlan, A. D., 1971, Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome C551, J. Mol. Biol. 61:409–424.PubMedCrossRefGoogle Scholar
  377. McLachlan, A. D., 1977, Quantum chemistry and protein folding: The art of the possible, Int. J. Quant. Chem. 13(Suppl. 1):371–385.Google Scholar
  378. McLachlan, A. D., and Karn, J., 1983, Periodic features in the amino acid sequence of nemotode myosin rod, J. Mol. Biol. 164:605–626.PubMedCrossRefGoogle Scholar
  379. McLachlan, A. D., and Stewart, M., 1976, The 14-fold periodicity in α-tropomyosin and the interaction with actin, J. Mol. Biol. 103:271–298.PubMedCrossRefGoogle Scholar
  380. McLachlan, A. D., Bloomer, A. C., and Butler, P. J. G., 1980, Structural repeats and evolution of tobacco mosaic virus coat protein and RNA, J. Mol. Biol. 136:203–224.PubMedCrossRefGoogle Scholar
  381. Meirovitch, S., Rackovsky, S., and Scheraga, H. A., 1980, Empirical studies of hydrophobicity. 1. Effect of protein size on the hydrophobic behavior of amino acids, Macromolecules 13:1398–1405.CrossRefGoogle Scholar
  382. Menick, D. R., Carrasco, N., Antes, L., Patel, L., and Kaback, H. R., 1986, Lac permease of Escherichia coli: Arginine-302 as a component of the postulated proton relay, Biochemistry 26:6638–6644.CrossRefGoogle Scholar
  383. Mercier, J.-C., and Chobert, J. M., 1976, Comparative study of the amino acid sequences of the caseino-macropeptides from seven species, FEBS Lett. 72:208–214.PubMedCrossRefGoogle Scholar
  384. Mercier, J.-C., Uro, J., Ribadeau-Daumas, B., and Grosclaude, F., 1972, Structure primaire du caséino-macropeptide de la caséine kß, bovine, Eur. J. Biochem. 27:535–547.PubMedCrossRefGoogle Scholar
  385. Miles, E. W., Yutani, K., and Ogarsahara, K., 1982, Guanidine hydrochloride-induced unfolding of the α-subunit of tryptophan synthetase and of the two α-proteolytic fragments. Evidence for stepwise unfolding of the two α domains, Biochemistry 21:2586–2592.PubMedCrossRefGoogle Scholar
  386. Milner-White, E. J., 1988, Recurring loop motif in proteins that occurs in right-handed and left-handed forms. Its relationship with alpha-helices and beta-bulge loops, J. Mol. Biol. 199:503–511.PubMedCrossRefGoogle Scholar
  387. Milner-White, E. J., and Poet, R., 1986, Four classes of ß-hairpins in proteins, Biochem. J. 240:289–292.PubMedGoogle Scholar
  388. Milner-White, E. J., and Poet, R., 1987, Loops, bulges, turns and hairpins in proteins, Trends Biochem. Sci. 12: 189–192.CrossRefGoogle Scholar
  389. Modrow, S., and Wolf, H., 1986, Characterization of two related Epstein-Barr virus-encoded membrane proteins that are differentially expressed in Burkitt lymphoma and in vitro-transformed cell lines, Proc. Natl. Acad. Sci. U.S.A. 83:5703–5707.PubMedCrossRefGoogle Scholar
  390. Mohana-Rao, J. K., and Argos, P., 1986, A conformational preference parameter to predict helices in integral membrane proteins, Biochim. Biophys. Acta 869:197–214.PubMedCrossRefGoogle Scholar
  391. Mohana-Rao, J. K., Hargrave, P. A., and Argos, P., 1983, Will the seven-helix bundle be a common structure for integral membrane proteins? FEBS Lett. 156:165–169.CrossRefGoogle Scholar
  392. Momany, F. A., MacGuire, R. F., Burgess, A. W., and Scheraga, H. A., 1975, Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interaction, and intrinsic torsion potentials for the naturally occurring amino acids, J. Phys. Chem. 79: 2361–2381.CrossRefGoogle Scholar
  393. Mononen, I., and Karjalainen, E., 1984, Structural comparisons of protein sequences around potential N-glycosylation sites, Biochim. Biophys. Acta 788:364–367.CrossRefGoogle Scholar
  394. Moore, W. M., Holladay, L. A., Puett, D., and Brody, R. N., 1974, On the conformation of the acetylcholine receptor protein from Torpedo nobiliana. FEBS Lett. 45:145–149.PubMedCrossRefGoogle Scholar
  395. Moran, E. C., Chou, P. Y., and Fasman, G. D., 1977, Conformational transitions of glucagon in solution: The α ⇄ ß transition, Biochem. Biophys. Res. Commun. 77:1300–1306.PubMedCrossRefGoogle Scholar
  396. Morgan, D. O., Edman. J. c., Standring, D. N., Fried, V. A., Smith, M. C., Roth, R. A., and Rutter, W. J., 1987, Insulin-like growth factor II receptor as a multifunctional binding protein, Nature 329: 301–307.PubMedCrossRefGoogle Scholar
  397. Morgan, R. S., and McAdon, J. H., 1980, Predictor for sulfur-aromatic interactions in globular proteins, Int. J. Peptide Protein Res. 15:177–180.CrossRefGoogle Scholar
  398. Moser, R., Thomas, R. M., and Gutte, B., 1983, An artificial crystalline DDT-binding polypeptide, FEBS Lett. 157:247–251.CrossRefGoogle Scholar
  399. Moser, R., Frey, S., Münger, K., Hehlgans, T., Klausen, S., Langen, H., Winnacker, E.-L., Mertz, R., and Gutte, B., 1987, Expression of the synthetic gene of an artificial DDT-binding polypeptide of E. coli. Protein Eng. 1:339–343.Google Scholar
  400. Moult, J., and James, M. N. G., 1987, An algorithm for determining the conformation of polypeptide segments in proteins by systematic search, Proteins 1:146–163.CrossRefGoogle Scholar
  401. Mueckler. M., Caruso, C., Baldwin, S. A., Panico, M., Blench, I., Morris, H. R., Ailard, W. J., Lienhard, G. E., and Lodish, H. F., 1985, Sequence and structure of a human glucose transporter, Science 299:941–945.CrossRefGoogle Scholar
  402. Murakami, M., 1985, Mutation affecting the 12th and 61st amino acids of p21 protein result in decreased probability of ß3-tum occurrence around the mutation positions: A prediction, J. Theor. Biol. 114: 193–198.PubMedCrossRefGoogle Scholar
  403. Murakami, M., 1987, Critical amino acids of p21 protein are located within ß-turns: Further evaluation, J. Theor. Biol. 128:339–347.PubMedCrossRefGoogle Scholar
  404. Murata, M., Richardson, J. S., and Sussman, J., 1985, Simultaneous comparison of three protein sequences, Proc. Natl. Acad. Sci. U.S.A. 82:3073–3077.PubMedCrossRefGoogle Scholar
  405. Murphy, J., Zhang. W.-J., Macaulay, W., Fasman. G., and Merrifield, R. B., 1988, The relation of predicted structure to observed conformation and activity of glucagon analogs containing replacements at positions 19,22 and 23, J. Biol. Chem. 262:17304–17312.Google Scholar
  406. Murzin, A. G., and Finkelstein, A. V., 1983, Polyhedra describing the packing of helices in a protein globule, Biofisika 28:905–911.Google Scholar
  407. Mutter, M., 1985, The construction of new proteins and enzymes. A prospect for the future, Angew. Chem. [Engl.] 24:639–653.CrossRefGoogle Scholar
  408. Nabedryk, E., Bardin, A. M., and Breton, J., 1985, Further characterization of protein secondary structures in purple membrane by circular dichroism and polarized infrared spectroscopies, Biophys. J. 48:873–876.PubMedCrossRefGoogle Scholar
  409. Nagano, K., 1973, Logical analysis of the mechanism of protein folding. I. Prediction of helices, loops and ß-structures from primary structure, J. Mol. Biol. 75:401–420.PubMedCrossRefGoogle Scholar
  410. Nagano, K., 1974, Logical analysis of the mechanism of protein folding. II. The nucleation process, J. Mol. Biol. 84:337–372.PubMedCrossRefGoogle Scholar
  411. Nagano, K., 1977, Triplet information in helix prediction applied to the analysis of super-secondary structures, J. Mol. Biol. 109:251–274.PubMedCrossRefGoogle Scholar
  412. Nagarajan, M., and Rao, V. S. R., 1977, Conformational analysis of glycoproteins. Part I. Conformation of the protein segment at the site of peptide-sugar linkage, Current Sci. 46:395–400.Google Scholar
  413. Nakashima, H., Nishikawa, K., and Ooi, T., 1986, The folding type of a protein is relevant to the amino acid composition, J. Biochem. (Tokyo) 99:153–162.Google Scholar
  414. Narayana, S. V. L., and Argos, P., 1984, Residue contacts in protein structures and implications for protein folding, Int. J. Peptide Protein Res. 24:25–39.CrossRefGoogle Scholar
  415. Needleman, S. B., and Blair, T. T., 1969, Homology of Pseudomonas cytochrome c-551 with eukaryotic c-cytochromes, Proc. Natl. Acad. Sci. U.S.A. 63:1227–1233.PubMedCrossRefGoogle Scholar
  416. Needleman, S. B., and Wunsch, C. D., 1970, A general method applicable to the search for similarities in the amino acid sequences of two proteins, J. Mol. Biol. 48:443–453.PubMedCrossRefGoogle Scholar
  417. Nemethy, G., 1974, Conformational energy calculations and the folding of proteins, PAABS Rev. 3:51–61.Google Scholar
  418. Nemethy, G., and Scheraga, H. A., 1977, Protein folding, Q. Rev. Biophys. 3:239–352.CrossRefGoogle Scholar
  419. Nemethy, G., and Scheraga, H. A., 1980, Stereochemical requirements for the existence of hydrogen bonds in ß-bends, Biochem. Biophys. Res. Commun. 95:320–327.PubMedCrossRefGoogle Scholar
  420. Neuberger, A., and Marshall, R. D., 1968, Aspects of the structure of glycoproteins, in: Carbohydrates and Their Roles (H. W. Schultze, R. F. Cain, and R. W. Molstad, eds.), AVI, Westport, CT, p. 115.Google Scholar
  421. Nishikawa, K., 1983, Assessment of secondary structure prediction of proteins: Comparisons of computerized Chou-Fasman method with others, Biochim. Biophys. Acta 748:285–299.PubMedCrossRefGoogle Scholar
  422. Nishikawa, K., and Ooi, T., 1986, Amino acid sequence homology applied to the prediction of protein secondary structure, and joint prediction with existing methods, Biochim. Biophys. Acta 871:45–54.PubMedCrossRefGoogle Scholar
  423. Nishikawa, K., Momany, F. A., and Scheraga, H. A., 1974, Low energy structure of two dipeptides and their relationship to bend conformation, Macromolecules 7:797–806.PubMedCrossRefGoogle Scholar
  424. 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 c-DNA sequence, Nature 299:793–797.PubMedCrossRefGoogle Scholar
  425. Noda, M., Takahashi, H., Tanabe, T., Toyosato, M., Kikyotani, S., Furutani, Y., Hirose, T., Takashima, G., Inayama, S., Miyata, T., and Numa, S., 1983, Structural homology of Torpedo californica receptor subunits, Nature 302:528–532.PubMedCrossRefGoogle Scholar
  426. Noda, M., Shimizu, S., Tanabe, T., Takai, T., Kayano, T., Ikeda, T., Takahashi, H., Nakayama, H., Kanaoka, Y., Minamino, N., Kangawa, K., Matsuo, H., Raftery, M. A., Hirose, T., Inayama, S., Hayashida, H., Miyata, T., and Numa, S., 1984, Primary structure of Electrophorus electricus sodium channel deduced from c-DNA sequence, Nature 312:121–127.PubMedCrossRefGoogle Scholar
  427. Noda, M., Ikeda, T., Kayano, T., Suzuki, H., Takeshima, I.-H., Kurasaki, M., Takahashi, T., and Numa, S., 1986, Existence of distinct sodium channel messenger RNAs in rat brain, Nature 320:188–192.PubMedCrossRefGoogle Scholar
  428. Novotny, J., and Auffray, C., 1984, A program for prediction of protein secondary structure from nucleotide sequence data: Application to histocompatability antigens, Nucleic Acids Res. 12:243–255.PubMedCrossRefGoogle Scholar
  429. Novotny, J., and Haber, E., 1985, Structural invariants of antigen binding: Comparison of immunoglobulin V2-VH and V2-V2 domain dimers, Proc. Natl. Acad. Sci. U.S.A. 82:4592–4596.PubMedCrossRefGoogle Scholar
  430. Novotny, J., Bruccoleri, R. E., and Newell, J., 1984, Twisted hyperboloid (strophoid) as a model of ß-barrels in proteins, J. Mol. Biol. 177:567–573.PubMedCrossRefGoogle Scholar
  431. Nozaki, Y., and Tanford, C., 1971, The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions, J. Biol. Chem. 246:2211–2217.PubMedGoogle Scholar
  432. Nussbaum, S., Beaudette, N. V., Fasman, G. D., Potts, J. T., Jr., and Rosenblatt, M., 1985, Design of analogues of parathyroid hormone: A conformational approach, J. Protein Chem. 4:391–406.CrossRefGoogle Scholar
  433. Otvös, L., Jr., Hollosi, M., Perczel, A., Dietzschold, B., and Fasman, G. D., 1988, Phosphorylation loops in synthetic peptides of the human neurofilament protein middle-sized subunit, J. Protein Chem. 7:365–376.PubMedCrossRefGoogle Scholar
  434. Ovchinnikov, Yu. A., 1982, Rhodopsin and bacteriorhodopsin: Structure-function relationships, FEBS Lett. 148:179–191.PubMedCrossRefGoogle Scholar
  435. Ovchinnikov, Yu., A., Abdulaev, N. G., Feigina, M. Y., Kiselev, A. V., and Lobanov, N. A., 1979, The structural basis of the functioning of bacteriorhodopsin: An overview, FEBS Lett. 100:219–224.PubMedCrossRefGoogle Scholar
  436. Ovchinnikov, Yu., A., Abdulaev, N. G., Vasilov, R. G., Vturina, I. Yu., Kuryatov, A. B., and Kiselev, A. V., 1985, The antigenic structure and topography of bacteriorhodopsin in purple membranes as determined by interaction with monoclonal antibodies, FEBS Lett. 179:343–350.CrossRefGoogle Scholar
  437. Ovchinnikov, Yu., A., Modyanov, N. N., Brovde, N. E., Petrukhin, K. E., Grishin, A. V., Arzamazova, N. M., Aldanova, N. A., Monastyrskaya, G. S., and Sverdlov, E. D., 1986, Pig kidney, Na+ + K+ ATPase, FEBS Lett. 201:237–245.PubMedCrossRefGoogle Scholar
  438. Padlan, E. A., 1977, Structural implications of sequence variability in immunoglobulins, Proc. Natl. Acad. Sci. U.S.A. 74:2551–2555.PubMedCrossRefGoogle Scholar
  439. Palau, J., Argos, P., and Puigdomenech, P., 1982, Protein secondary structure studies on the limits of prediction accuracy, Int. J. Peptide Protein Res. 19:394–401.CrossRefGoogle Scholar
  440. Pallai, P. V., Mabilla, M., Goodman, M., Vale, W., and Rivier, J., 1983, Structural homology of corticotropin-releasing factor, sauvagine and urotensin I: Circular dichroism and prediction studies, Proc. Natl. Acad. Sci. U.S.A. 80:6770–6774.PubMedCrossRefGoogle Scholar
  441. Parrilla, A., Domenech, A., and Querol, E., 1986, A PASCAL microcomputer program for prediction of protein secondary structure and hydropathic segments, Cabios 2:211–215.PubMedGoogle Scholar
  442. Pashley, R. M., McGuiggan, P. M., Ninham, B. W, and Evans, D. F., 1985, Attractive forces between uncharged hydrophobic surfaces: Direct measurements in aqueous solution, Science 229:1088–1089.PubMedCrossRefGoogle Scholar
  443. Patten, P., Yokota, T., Rothbard, J., Chien, Y.-H., Arai, K.-I., and Davis, M. M., 1984, Structure, expression and divergence of T-cell receptor ß-chain variable regions, Nature 312:40–46.PubMedCrossRefGoogle Scholar
  444. Pattus, F., Heitz, F., Martinez, C., Provencher, S. W., and Lazdunski, C. L., 1985, Secondary structure of the pore-forming colicin A and its C-terminal fragment. Experimental fact and structure prediction, Eur. J. Biochem. 152:681–689.PubMedCrossRefGoogle Scholar
  445. Paul, C., and Rosenbusch, J. P., 1985, Folding patterns of porin and bacteriorhodopsin, EMBO J. 4:1593–1597.PubMedGoogle Scholar
  446. Paul, C. H., 1982, Building models of globular proteins. Molecules from their amino acid sequences. I. Theory, J. Mol. Biol. 155:53–62.PubMedCrossRefGoogle Scholar
  447. Pauling, L., and Corey, R. B., 1951, Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets, Proc. Natl. Acad. Sci. U.S.A. 37:729–740.PubMedCrossRefGoogle Scholar
  448. Peralta, E. G., Winslow, J. W., Peterson, G. L., Smith, D. H., Ashkenazi, A., Ramachandran, J., Schimerlik, M. I., and Capon, D. J., 1987, Primary structure and biochemical properties of an M2 muscarinic receptor, Science 236:600–605.PubMedCrossRefGoogle Scholar
  449. Periti, P. F., Quagliarotti, G., and Liquori, A. M., 1967, Recognition of α-helical segments in proteins of known primary structure, J. Mol. Biol. 24:313–322.PubMedCrossRefGoogle Scholar
  450. Perutz, M. F., 1980, Electrostatic effects in proteins, Science 201:1187–1191.CrossRefGoogle Scholar
  451. Perutz, M. F., Gronenborn, A. M., Clore, G. M., Fogg, J. H., and Shih, D. T.-B, 1985, The pKa values of two histidine residues in human haemoglobin, the Bohr effect, and the dipole moments of α-helices, J. Mol. Biol. 183:491–498.PubMedCrossRefGoogle Scholar
  452. Phillips, D. C., 1970, in: British Biochemistry, Past and Present (T. W. Goodwin, ed.), Academic Press, London, pp. 11–28.Google Scholar
  453. Pincus, M. R., and Klausner, R. D., 1982, Predictions of the three-dimensional structure of the leader sequence of pre-K-light chain, a hexadecapeptide, Proc. Natl. Acad. Sci. U.S.A. 79:3413–3417.PubMedCrossRefGoogle Scholar
  454. Pohlman, R., Nagel, G., Schmidt, B., Stein, M., Lorkowski, G., Krentler, C., Cully, J., Meyer, H. E., Grzeschik, K.-H., Mersmann, G., Hasilik, A., and von Figura, K., 1987, Cloning of a c-DNA encoding the human cation-dependent mannose-6-phosphate receptor, Proc. Nat. Acad. Sci. U.S.A. 84:5575–5579.CrossRefGoogle Scholar
  455. Ponder, J. W., and Richards, F. M., 1987, Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes, J. Mol. Biol. 193:775–791.PubMedCrossRefGoogle Scholar
  456. Pongor, S., and Szaley, A. A., 1985, Prediction of homology and divergence in the secondary structure of polypeptides, Proc. Natl. Acad. Sci. U.S.A. 82:366–370.PubMedCrossRefGoogle Scholar
  457. Ponnuswamy, P. K., Worme, P. K., and Scheraga, H. A., 1973, Role of medium-range interactions in proteins, Proc. Natl. Acad. Sci. U.S.A. 70:830–833.PubMedCrossRefGoogle Scholar
  458. Ponnuswamy, P. K., Prabhakran, M., and Manavalan, P., 1981, Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins, Biochim. Biophys. Acta 623:301–316.Google Scholar
  459. Popot, J.-L., Gerchman, S.-E., and Engelman, D. M., 1987, Refolding of bacteriorhodopsin in lipid bilayers. A thermodynamically controlled two-stage process, J. Mol. Biol. 198:655–676.PubMedCrossRefGoogle Scholar
  460. Post, C. B., Brooks, B. R., Karplus, M., Dobson, C. M., Artymiuk, P. C., Cheetham, J. C., and Phillips, D. C., 1986, Molecular dynamics. Simulations of native and substrate bound lysozyme. A study of the average structures and atomic fluctuations, J. Mol. Biol. 190:455–479.PubMedCrossRefGoogle Scholar
  461. Potts, J. T., Jr., Kronenberg, H. M., and Rosenblatt, M., 1982, Parathyroid hormone: Chemistry, biosynthesis, and mode of action, Adv. Protein Chem. 35:322–396.Google Scholar
  462. Prothero, J. W., 1966, Correlation between the distribution of amino acids and alpha helices, Biophys. J. 6: 367–370.PubMedCrossRefGoogle Scholar
  463. Prothero, J. W., 1968, A model of alpha-helical distribution in proteins, Biophys. J. 8:1236–1255.PubMedCrossRefGoogle Scholar
  464. Ptitsyn, O. B., 1969, Statistical analyses of the distribution of amino acid residues among helical and nonhelical regions in globular proteins, J. Mol. Biol. 42:501–510.PubMedCrossRefGoogle Scholar
  465. Ptitsyn, O. B., 1981, Protein folding: General physical model, FEBS Lett. 131:197–202.CrossRefGoogle Scholar
  466. Ptitsyn, O. B., 1985, Physical principles of protein structure and protein folding, J. Biosci. 8:1–13.CrossRefGoogle Scholar
  467. Ptitsyn, O. B., and Finkelstein, A. V., 1970a, Connection between the secondary and primary structures of globular proteins, Biofisika 15:757–768.Google Scholar
  468. Ptitsyn, O. B., and Finkelstein, A. V., 1970b, Prediction of helical portions of globular proteins according to their primary structure, Dokl. Akad. Nauk. SSSR 195:221–224.PubMedGoogle Scholar
  469. Ptitsyn, O. B., and Finkelstein, A. V., 1979, Coiling and topology of the parallel ß-structure, Biofisika 24:27–30.Google Scholar
  470. Ptitsyn, O. B., and Finkelstein, A. V., 1983, Theory of protein secondary structure and algorithm of its prediction, Biopolymers 22:15–25.PubMedCrossRefGoogle Scholar
  471. Ptitsyn, O. B., and Rashin, A. A., 1975, A model of myoglobin self-organization, Biophys. Chem. 3:1–20.PubMedCrossRefGoogle Scholar
  472. Ptitsyn, O. B., Finkelstein, A. V., and Falk, P., 1979, Principal folding pathway and topology of all ß-proteins, FEBS Lett. 101:1–5.PubMedCrossRefGoogle Scholar
  473. Pullman, B., and Pullman, A., 1974, Molecular orbital calculations on the conformation of amino acid residues of proteins, Adv. Protein Chem. 28:347–526.PubMedCrossRefGoogle Scholar
  474. Pumphrey, R. S. H., 1986a, Computer models of the human immunoglobulins. I. Shape and segmental flexibility, Immunol. Today 7:174–178.CrossRefGoogle Scholar
  475. Pumphrey, R. S. H., 1986b, Computer models of the human immunoglobulins. II. Binding sites and molecular interactions, Immunol. Today 7:206–211.CrossRefGoogle Scholar
  476. Quiocho, F. A., Sack, J. S., and Vyas, N. K., 1987, Stabilization of charges on isolated ionic groups sequestered in proteins by polarized peptide units, Nature 329:561–564.PubMedCrossRefGoogle Scholar
  477. Rackovsky, S., and Goldstein, D. A., 1987, Differential geometry and protein conformation. V. Medium-range conformational influence of the individual amino acids, Biopolymers 26: 1163–1187.PubMedCrossRefGoogle Scholar
  478. Ralph, W. W., Webster, T., and Smith, T. F., 1987, A modified Chou and Fasman protein structure algorithm, Cabios 3:211–216.PubMedGoogle Scholar
  479. Ramachandran, G. N., Ramakrishnan, C., and Sasisekharan, V., 1963, Stereochemistry of polypeptide chain configurations, J. Mol. Biol. 7:95–99.PubMedCrossRefGoogle Scholar
  480. Rao, S. T., and Rossman, M. G., 1973, Comparison of super-secondary structures in proteins, J. Mol. Biol. 76: 241–250.PubMedCrossRefGoogle Scholar
  481. Rao, J. K. M., Hargrave, P. A., and Argos, P., 1983, Will the seven-helix bundle be a common structure for integral membrane proteins? FEBS Lett. 156:165–169.CrossRefGoogle Scholar
  482. Rashin, A. A., 1981, Location of domains in globular proteins, Nature 291:85–86.PubMedCrossRefGoogle Scholar
  483. Rashin, A. A., and Honig, B., 1984, On the environment of ionizable groups in globular proteins, J. Mol. Biol. 173:515–521.PubMedCrossRefGoogle Scholar
  484. Rawlings, N., Ashman, K., and Wittman-Leibold, B., 1983, Computerized version of the Chou and Fasman protein secondary structure predictive method, Int. J. Peptide Protein Res. 22:515–524.CrossRefGoogle Scholar
  485. Remington, S. J., and Matthews, B. W., 1978, A general method to assess similarity of protein structures, with applications to T4 bacteriophage lysozyme, Proc. Natl. Acad. Sci. U.S.A. 75:2180–2184.PubMedCrossRefGoogle Scholar
  486. Remington, S. J., Anderson, W. F., Owen, J., Ten Eyck, L. F., Grainger, C. T., and Matthews, B. W., 1978, Structure of the lysozyme from bacteriophage T4: An electron density map at 2.4 Å resolution, J. Mol. Biol. 118:81–98.PubMedCrossRefGoogle Scholar
  487. Renugopalakrishnan, V., Strawich, E. S., Horowitz, P. M., and Glimcher, M. J., 1986, Studies on the secondary structures of amelogenin from bovine tooth enamel, Biochemistry 25:4879–4887.PubMedCrossRefGoogle Scholar
  488. Ricard, J. M., Perez, J. J., Pons, M., and Giralt, E., 1983, Conformational basis of N-glycosylation of proteins: Conformational analysis of Ac-Asn-Ala-Thr-NH2, Int. J. Bioi. Macromol. 5:279–282.CrossRefGoogle Scholar
  489. Richards, F. M., 1974, The interpretation of protein structures: Total volume, group volume distributions and packing density, J. Mol. Biol. 82:1–14.PubMedCrossRefGoogle Scholar
  490. Richards, F. M., 1977, Areas, volumes, packing, and protein structure, Annu. Rev. Biophys. Bioeng. 6:151–176.PubMedCrossRefGoogle Scholar
  491. Richardson, J. S., 1976, Handedness of crossover connections in ß sheets. Proc. Natl. Acad. Sci. U.S.A. 73: 2619–2623.PubMedCrossRefGoogle Scholar
  492. Richardson, J. S., 1977, ß-Sheet topology and the relatedness of proteins, Nature 268:495–500.PubMedCrossRefGoogle Scholar
  493. Richardson, J. S., 1981, The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34: 167–339.PubMedCrossRefGoogle Scholar
  494. Richmond, T. J., 1984, Solvent accessible surface area and excluded volume in proteins, J. Mol. Biol. 178:63–89.PubMedCrossRefGoogle Scholar
  495. Richmond, T. J., and Richards, F. M., 1978, Packing of α-helices: Geometrical constraints and contact areas, J. Mol. Biol. 119:775–791.CrossRefGoogle Scholar
  496. Robson, B., 1974, Analysis of the code relating sequence to conformation in globular proteins: Theory and application of expected information, Biochem. J. 141:853–867.PubMedGoogle Scholar
  497. Robson, B., and Garnier, J., 1986, Introduction to Proteins and Protein Engineering, Elsevier, Amsterdam.Google Scholar
  498. Robson, B., and Osguthorpe, D. J., 1979, Refined models for computer simulations of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor, J. Mol. Biol. 132:19–51.PubMedCrossRefGoogle Scholar
  499. Robson, B., and Pain, R. H., 1971, Analyses of the code relating sequence to conformation in proteins: Possible implications for the mechanism of formation of helical regions, J. Mol. Biol. 58:237–259.PubMedCrossRefGoogle Scholar
  500. Robson, B., and Pain, R. H., 1972, Directional information transfer in protein helices, Nature (New Biol.) 238: 107–108.Google Scholar
  501. Robson, B., and Pain, R. H., 1974a, Analysis of the code relating sequence to conformation in globular proteins: Development of a stereochemical alphabet on the basis of intra-residue information, Biochem. J. 141:869–882.PubMedGoogle Scholar
  502. Robson, B., and Pain, R. H., 1974b, Analysis of the code relating sequence to conformation in globular proteins: An informational analysis of the role of the residue in determining the conformation of its neighbours in the primary sequence, Biochem. J. 141:869–882.PubMedGoogle Scholar
  503. Robson, B., and Pain, R. H., 1974c, Analysis of the code relating sequence to conformation in globular proteins: The distribution of residue pairs in turns and kinks in the backbone chain, Biochem. J. 141:899–904.PubMedGoogle Scholar
  504. Robson, B., and Platt, E., 1986, Refined models for computer calculations in protein engineering. Calibration and testing of atomic potential functions compatible with more efficient calculations, J. Mol. Biol. 188: 259–281.PubMedCrossRefGoogle Scholar
  505. Robson, B., and Suzuki, E., 1976, Conformational properties of amino acid residues in globular proteins, J. Mol. Biol. 107:327–356.PubMedCrossRefGoogle Scholar
  506. Robson, B., Platt, E., Fishleigh, R. V., Marsden, A., and Millard, P., 1987, Expert system for protein engineering: Its application in the study or chloroamphenicol acetyltransferase and avian pancreatic polypeptide, J. Mol. Graphics 5:8–17.CrossRefGoogle Scholar
  507. Rogers, N. K., 1986, The modelling of electrostatic interactions in the function of globular proteins, Prog. Biophys. Mol. Biol. 48:37–66.PubMedCrossRefGoogle Scholar
  508. Rogers, N. K., and Sternberg, M. J. E., 1984, Electrostatic interactions in globular proteins. Different dielectric models applied to the packing of α-helices, J. Mol. Biol. 174:527–542.PubMedCrossRefGoogle Scholar
  509. Rose, G. D., 1978, Prediction of chain turns in globular proteins on a hydrophobic basis, Nature 272:586–590.PubMedCrossRefGoogle Scholar
  510. Rose, G. D., 1979, Hierarchic organization of domains in globular proteins, J. Mol. Biol. 134:447–470.PubMedCrossRefGoogle Scholar
  511. Rose, G. D., and Roy, S., 1980, Hydrophobic basis of packing in globular proteins, Proc. Natl. Acad. Sci. U.S.A. 77:4643–4647.PubMedCrossRefGoogle Scholar
  512. Rose, G. D., and Seltzer, J. P., 1977, A new algorithm for finding the peptide chain turns in a globular proteins, J. Mol. Biol. 113:153–164.PubMedCrossRefGoogle Scholar
  513. Rose, G. D., and Wetlaufer, D. B., 1977, The number of turns in globular proteins, Nature 268:769–770.PubMedCrossRefGoogle Scholar
  514. Rose, G. D., Young, W. B., and Gierasch, L. M., 1983, Interior turns in globular proteins, Nature 304:655–657.CrossRefGoogle Scholar
  515. Rose, G. D., Gierasch, L. M., and Smith, J. A., 1985, Turns in peptides and proteins, Adv. Protein Chem. 37: 1–109.PubMedCrossRefGoogle Scholar
  516. Rosenblatt, M., Habener, J. F., Tyler, F. A., Shepard, G. L., and Potts, J. T., Jr., 1979, Chemical synthesis of the precursor-specific region of preproparathyroid hormone, J. Biol. Chem. 254:1414–1421.PubMedGoogle Scholar
  517. Rosenblatt, M., Beaudette, N. V., and Fasman, G. D., 1980, Conformational studies of the synthetic precursor-specific regions of pre-parathyroid hormone, Proc. Natl. Acad. Sci. U.S.A. 77:3983–3987.PubMedCrossRefGoogle Scholar
  518. Rosenblatt, M., Majzoub, J. A., Beaudette, N. V., Kronenberg, H. M., Potts, J. T., Fasman, G. D., and Habener, J. F., 1981, Chemically synthesized precursor-specific fragment of preproparathyroid hormone: Conformational and biological properties, in: Peptides 1980. Proceedings of the Sixteenth European Peptide Symposium (K. Brunfeldt, ed.), Scriptor, Copenhagen, pp. 572–577.Google Scholar
  519. Rossman, M. G., and Argos, P., 1981, Protein folding, Annu. Rev. Biochem. 50:497–533.CrossRefGoogle Scholar
  520. Rossman, M. G., and Liljas, A., 1974, Recognition of structural domains in globular proteins, J. Mol. Biol. 85: 177–181.PubMedCrossRefGoogle Scholar
  521. Rottier, P. J. M., Welling, G. W., Welling-Wester, S., Niesters, G. M., Lenstra, J. A., and van der Zeijst, B. A. M., 1986, Predicted membrane topology of the coronavirus E1, Biochemistry 25:1335–1339.PubMedCrossRefGoogle Scholar
  522. Sack, G. H., Jr., 1983, Molecular cloning of human genes for serum amyloid A, Gene 22: 19–29.CrossRefGoogle Scholar
  523. Salemme, F. R., 1981, Conformational and geometrical properties of ß-sheets in proteins: III. Isotropically stressed configurations, J. Mol. Biol. 146:143–156.PubMedCrossRefGoogle Scholar
  524. Salemme, F. R., 1983, Structural properties of protein ß-sheets, Prog. Biophys. Mol. Biol. 42:95–133.PubMedCrossRefGoogle Scholar
  525. Salemme, F. R., and Weatherford, D. W., 1981a, Conformational and geometrical properties of ß-sheets in proteins: I. Parallel ß-sheets, J. Mol. Biol. 146:101–117.PubMedCrossRefGoogle Scholar
  526. Salemme, F. R., and Weatherford, D. W., 1981b, Conformation and geometrical properties of ß-sheets in proteins: II. Antiparallel and mixed ß-sheets, J. Mol. Biol. 146:119–141.PubMedCrossRefGoogle Scholar
  527. Sander, C., and Schulz, G. E., 1979, Degeneracy of the information contained in amino acid sequences: Evidence for overlaid genes, J. Mol. Evol. 13:245–252.PubMedCrossRefGoogle Scholar
  528. Saraste, M., and Walker, J. E., 1982, Internal sequence repeats and the path of polypeptide in mitochondrial ADP/ATP translocase, FEBS Lett. 144:250–254.PubMedCrossRefGoogle Scholar
  529. Sawyer, L., and James, M. N. G., 1982, Carboxyl-carboxylate interactions in proteins, Nature 295:79–80.PubMedCrossRefGoogle Scholar
  530. Sayre, R., Anderson, B., and Bogorad, L., 1986, The topology of a membrane protein: The orientation of the 32 kd Qb-binding chloroplast thylakoid membrane protein, Cell 47:601–608.PubMedCrossRefGoogle Scholar
  531. Scheraga, H. A., 1960, Structural studies of ribonuclease III. A model for the secondary and tertiary structure, J. Am. Chem. Soc. 82:3847–3852.CrossRefGoogle Scholar
  532. Scheraga, H. A., 1968, Calculations of conformations of polypeptides, Adv. Phys. Org. Chem. 6:103–184.CrossRefGoogle Scholar
  533. Scheraga, H. A., 1971, Theoretical and experimental studies of conformations of polypeptides, Chem. Rev. 71: 195–217.PubMedCrossRefGoogle Scholar
  534. Scheraga, H. A., 1985, Calculations of the three-dimensional structures of proteins, Ann. N.Y. Acad. Sci. 439: 170–194.PubMedCrossRefGoogle Scholar
  535. 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.PubMedCrossRefGoogle Scholar
  536. Schiffer, M., Wu, T. T., and Kabat, E. A., 1986, Subgroups of variable regions genes of ß-chains of T-cell receptors for antigen, Proc. Natl. Acad. Sci. U.S.A. 83:4461–4463.PubMedCrossRefGoogle Scholar
  537. 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 Bamard, E. A., 1987, Sequence and functional expression of the GABAA receptor shows a ligand-gated receptor super-family, Nature 328: 221–227.PubMedCrossRefGoogle Scholar
  538. Schulz, G. E., 1977, Structural rules for globular proteins, Angew. Chem. [Engl.] 16:23–32.CrossRefGoogle Scholar
  539. Schulz, G. E., 1980, Gene duplication in glutathione reductase, J. Mol. Biol. 138:335–347.PubMedCrossRefGoogle Scholar
  540. Schulz, G. E., and Schirmer, R. H., 1974, Topological comparison of adenyl kinase with other proteins, Nature 250:142–144.PubMedCrossRefGoogle Scholar
  541. Schulz, G. E., and Schirmer, R. H., 1979, Principles of Protein Structure, Springer-Verlag, New York.Google Scholar
  542. Schulz, G. E., Barry, C. D., Friedman, J., Chou, P. Y., Fasman, G. D., Finkelstein, A. V., Lim, V. I., Ptitsyn, O. B., Kabat, E. A., Wu., T. T., Levitt, M., Robson, B., and Nagano, K., 1974a, Comparison of predicted and experimentally determined secondary structure of adenylate kinase, Nature 250: 140–142.PubMedCrossRefGoogle Scholar
  543. Schulz, G. E., Elzinga, M., Marx, F., and Schirmer, R. H., 1974b, Three-dimensional structure of adenyl kinase, Nature 250:120–123.PubMedCrossRefGoogle Scholar
  544. Segrest, J. P., and Feldman, R. J., 1977, Amphipathic helices and plasma lipoproteins. A computer study, Biopolymers 16:2053–2065.PubMedCrossRefGoogle Scholar
  545. Sellers, P., 1974, On the theory and computation of evolutionary distances, J. Appl. Math. 26:787–793.Google Scholar
  546. Sellers, P., 1979, Pattern recognition in genetic sequences, Proc. Natl. Acad. Sci. U.S.A. 76:3041.PubMedCrossRefGoogle Scholar
  547. Senior, A. E., 1983, Secondary and tertiary structure of membrane proteins involved in proton translocation, Biochim. Biophys. Acta 726:81–95.PubMedGoogle Scholar
  548. Serrano, R., Kiedland-Brandt, M. C., and Fink, G. R., 1986, Yeast plasma membrane ATPase is essential for growth and has homology with (Na+ + K+), K+-and Ca2+-ATPases, Nature 319:689–693.PubMedCrossRefGoogle Scholar
  549. Sheridan, R. P., Dixon, J. S., Venkataraghavan, R., Kuntz, I. D., and Scott, K. P., 1985, Amino acid composition and hydrophobicity patterns of protein domains correlate with their structure, Biopolymers 24: 1995–2023.PubMedCrossRefGoogle Scholar
  550. Sheridan, R. P., and Allen, L. C., 1980, The electrostatic potential of the alpha helix (electrostatic potential/α-helix/secondary structure/helix dipole), Biophys. Chem. 11:133–136.PubMedCrossRefGoogle Scholar
  551. Sheridan, R. P., Levy, R. M., and Salemme, F. R., 1982, α-Helix dipole model and electrostatic stabilization of 4-α-helical proteins, Proc. Natl. Acad. Sci. U.S.A. 79:4545–4549.PubMedCrossRefGoogle Scholar
  552. Shin, H.-C., and McFarlane, E. F., 1987, The secondary structure of myelin P2 protein derived by secondary structure prediction methods, circular dichroism, and 400-MHz 1H-NMR spectroscopy: Implications for tertiary structure, Biochim. Biophys. Acta 913: 155–162.PubMedCrossRefGoogle Scholar
  553. Shinohara, T., Dietzschold, B., Craft, C. M., Wistow, G., Early, J. J., Donoso, L. A., Horowitz, J., and Tao, R., 1987, Primary and secondary structure of bovine retinal S antigen (48 kDa protein), Proc. Natl. Acad. Sci. U.S.A. 84:6975–6979.PubMedCrossRefGoogle Scholar
  554. Shipman, L. L., and Christoffersen, R. E., 1973, Ab initio calculations on large molecules using molecular fragments. Model peptide studies, J. Am. Chem. Soc. 95:1408–1416.PubMedCrossRefGoogle Scholar
  555. Shoemaker, K. R., Kim, P. S., York, E. J., Stewart, J. M., and Baldwin, R. L., 1987, Tests of the helix dipole model for stabilization of α-helices, Nature 326:563–567.PubMedCrossRefGoogle Scholar
  556. Shor, N. Z., 1977, Cut-off method with space extension in convex programming problems, Cybernetics 12:94–96.Google Scholar
  557. Shotton, D. M., and Watson, H. C., 1970, Three-dimensional structure of tosyl-elastase, Nature 235:811–816.CrossRefGoogle Scholar
  558. Shull, G., Schwartz, A., and Lingrel, J. B., 1985, Amino-acid sequence of the catalytic subunit of the (Na + + K+) ATPase deduced from a complementary DNA, Nature 316:691–695.PubMedCrossRefGoogle Scholar
  559. Sibanda, B. L., and Thornton, J. M., 1985, ß-Hairpin families in globular proteins, Nature 316:170–174.PubMedCrossRefGoogle Scholar
  560. Simon, I., Nemethy, G., and Scheraga, H. A., 1978, Conformational energy calculations of the effects of sequence variation on the conformations of two tetrapeptides, Macromolecules 11:797–804.CrossRefGoogle Scholar
  561. Singh, J., and Thornton, J. M., 1985, The interaction between phenylalanine rings in proteins, FEBS Lett. 191: 1–6.CrossRefGoogle Scholar
  562. Sippl, M. J., 1982, On the problem of comparing protein structures. Development and application of a new method for the assessment of structural similarities of pòlypeptide conformations, J. Mol. Biol. 156:359–388.PubMedCrossRefGoogle Scholar
  563. Small, D., Chou, P. Y., and Fasman, G. D., 1977, Occurrence of phosphorylated residues in predicted ß-turns: Implications for ß-turns participation in control mechanisms, Biochem. Biophys. Res. Commun. 79:341–346.PubMedCrossRefGoogle Scholar
  564. Smith, T. F., and Waterman, M. S., 1981, Identification of common molecular subsequences, J. Mol. Biol. 147:195–197.PubMedCrossRefGoogle Scholar
  565. Smythies, J. R., 1980, An hypothesis concerning the molecular structure of the nicotinic acetylcholine receptor, Med. Hypothesis 6:943–950.CrossRefGoogle Scholar
  566. Sneath, P. H. A., 1966, Relations between chemical structure and biological activity in peptides, J. Theor. Biol. 12: 157–195.PubMedCrossRefGoogle Scholar
  567. Snell, C. R., and Smyth, D. G., 1975, Proinsulin: A proposed three-dimensional structure, J. Biol. Chem. 250: 6291–6295.PubMedGoogle Scholar
  568. Srere, P. A., and Brooks, G. C., 1969, The circular dichroism of glucagon solutions, Arch. Biochem. Biophys. 129:708–710.PubMedCrossRefGoogle Scholar
  569. Staden, R., 1982, An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences, Nucleic Acids Res. 10:2951–2961.PubMedCrossRefGoogle Scholar
  570. Steitz, T. A., Goldman, A., and Engelman, D. M., 1982, Quantitative application of the helical hairpin hypothesis to membrane proteins, Biophys. J. 37:124–125.PubMedCrossRefGoogle Scholar
  571. Stephan, M. M., and Jacobson, G. R., 1986, Membrane disposition of the Escherichia coli mannitol permease: Identification of membrane-bound and cytoplasmic domains, Biochemistry 25:8230–8234.PubMedCrossRefGoogle Scholar
  572. Sternberg, M. J. E., 1983, The analysis and prediction of protein structure, in: Computing in Biological Sciences (M. Geisow and A. Barret, eds.), Elsevier, Amsterdam, pp. 143–177.Google Scholar
  573. Sternberg, M. J. E., and Cohen, F. E., 1982, Prediction of the secondary and tertiary structures of interferon from four homologous amino acid sequences, Int. J. Biol. Macromol. 4:137–144.CrossRefGoogle Scholar
  574. Sternberg, M. J. E., and Taylor, W. R., 1984, Modelling the ATP-binding site of oncogene products, the epidermal growth factor receptor and related proteins, FEBS Lett. 175:387–392.PubMedCrossRefGoogle Scholar
  575. Sternberg, M. J. E., and Thornton, J. M., 1976, On the conformation of proteins: The handedness of the ß-strand-α-helix-ß-strand unit, J. Mol. Biol. 105:367–382.PubMedCrossRefGoogle Scholar
  576. Sternberg, M. J. E., and Thornton, J. M., 1977a, On the conformation of proteins: The handedness of the connection between parallel ß-strands, J. Mol. Biol. 110:269–283.PubMedCrossRefGoogle Scholar
  577. Sternberg, M. J. E., and Thornton, J. M., 1977b, On the conformation of proteins: An analysis of ß-pleated sheets, J. Mol. Biol. 110:285–296.PubMedCrossRefGoogle Scholar
  578. Sternberg, M. J. E., and Thornton, J. M., 1977c, On the conformation of proteins: Hydrophobic ordering of strands in ß-pleated sheets, J. Mol. BioL. 115: 1–17.PubMedCrossRefGoogle Scholar
  579. Sternberg, M. J. E., and Thornton, J. M., 1978, Prediction of protein structure from amino acid sequence, Nature 271:15–20.PubMedCrossRefGoogle Scholar
  580. Sternberg, M. J. E., Cohen, F. E., Taylor, W. R., and Feldman, R. J., 1981, Analysis and prediction of structural motifs in the glycolytic enzymes, Phil. Trans. R. Soc. Land. [Biol.] 293:177–189.CrossRefGoogle Scholar
  581. Sternberg, M. J. E., Cohen, F. E., and Taylor, W. R., 1982, A combinatorial approach to the prediction of the tertiary fold of globular proteins, Biochem. J. 10:299–301.Google Scholar
  582. Sternberg, M. J. E., Hayes, F. R. F., Russell, A. J., Thomas, P. G., and Ferscht, A. R., 1987, Prediction of electrostatic effects of engineering of protein charges, Nature 330:86–88.PubMedCrossRefGoogle Scholar
  583. Stroud, R. M., and Finer-Moore, J., 1985, Acetylcholine receptor structure, function and evolution, Annu. Rev. Cell. Biol. 1:317–351.PubMedCrossRefGoogle Scholar
  584. Stuber, K., Deutscher, J., Sobek, H. M., Hengstenberg, W., and Beyreuther, K., 1985, Amino acid sequence of the amphiphilic phosphocarrier protein factor IIIlac of the lactose-specific phosphotransferase system of Staphylococcus aureus, Biochemistry 24:1164–1168.PubMedCrossRefGoogle Scholar
  585. Stuber, M., 1982, Doctoral Thesis, University of Cologne, Cologne, Germany.Google Scholar
  586. Sundaralingam, M., Sekharudu, Y. C., Yathindra, N., and Ravichandran, V., 1987, Ion pairs in alpha-helices, Proteins: Structure, Function and Genetics 2:64–71.CrossRefGoogle Scholar
  587. Sweet, R. M., 1986, Evolutionary similarity among peptide segments is a basis for prediction of protein folding, Biopolymers 25:1565–1577.PubMedCrossRefGoogle Scholar
  588. Sweet, R. M., and Eisenberg, D., 1983, Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure, J. Mol. Biol. 171:479–488.PubMedCrossRefGoogle Scholar
  589. Tanabe, T., Takeshima, H., Mikami, A., Flockerzi, V., Takahashi, H., Kangawa, K., Kojima, M., Matsuo, H., Hirose, T., and Numa, S., 1987, Primary structure of the receptor for calcium channel blockers from skeletal muscle, Nature 328:313–318.PubMedCrossRefGoogle Scholar
  590. Tanaka, S., and Scheraga, H. A., 1976a, Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins, Macromolecules 9: 142–159.PubMedCrossRefGoogle Scholar
  591. Tanaka, S., and Scheraga, H. A., 1976b, Statistical mechanical treatment of protein conformation. II. A three-state model for specific-sequence copolymers of amino acids, Macromolecules 9:159–167.PubMedCrossRefGoogle Scholar
  592. Tanaka, S., and Scheraga, H. A., 1976c, Statistical mechanical treatment of protein conformation. III. Prediction of protein conformation based on a three-state model, Macromolecules 9:168–182.PubMedCrossRefGoogle Scholar
  593. Tanaka, S., and Scheraga, H. A., 1976d, Statistical mechanical treatment of protein conformation. IV. A four-state model for specific-sequence copolymers of amino acids, Macromolecules 9:812–833.PubMedCrossRefGoogle Scholar
  594. Tanford, C., 1962, Contributions of hydrophobic interactions to the stability of the globular conformation of proteins, J. Am. Chem. Soc. 84:4240–4247.CrossRefGoogle Scholar
  595. Tanford, C., 1980, The Hydrophobic Effect, 2nd ed., John Wiley & Sons, New York.Google Scholar
  596. Taylor, W. R., 1984, An algorithm to compare secondary structure predictions, J. Mol. Biol. 173:512–514.PubMedCrossRefGoogle Scholar
  597. Taylor, W. R., 1986a, Identification of protein sequence homology by consensus template alignment, J. Mol. Biol. 188:233–258.PubMedCrossRefGoogle Scholar
  598. Taylor, W. R., 1986b, The classification of amino acid conservation, J. Theor. Biol. 119:205–218.PubMedCrossRefGoogle Scholar
  599. Taylor, W. R., and Geisow, M. J., 1987, Predicted structure for the calcium-dependent membrane-binding proteins, p35, p36, p32, Protein Eng. 1:183–187.PubMedCrossRefGoogle Scholar
  600. Taylor, W. R., and Thornton, J. M., 1983, Prediction of super-secondary structure in proteins, Nature 301: 540–542.PubMedCrossRefGoogle Scholar
  601. Taylor, W. R., and Thornton, J. M., 1984, Recognition of super-secondary structures in proteins, J. Mol. Biol. 173:487–514.PubMedCrossRefGoogle Scholar
  602. Thornton, J. M., and Chakauya, B. L., 1982, Conformation of the terminal regions in proteins, Nature 298: 296–297.PubMedCrossRefGoogle Scholar
  603. Thornton, J. M., and Sibanda, B. L., 1983, Amino and carboxyl-terminal regions in globular proteins, J. Mol. Biol. 167:443–460.PubMedCrossRefGoogle Scholar
  604. Tillinghast, J. P., Behlke, M. A., and Loh, D. Y., 1986, Structure and diversity of the human T-cell receptor ß-chain variable region genes, Science 233:879–883.PubMedCrossRefGoogle Scholar
  605. Titani, K., Hermodson, M. A., Ericsson, C. H., Walsh, K. A., and Neurath, H., 1982, Amino acid sequence of thermolysin, Nature [New Biol.] 238:35–37.Google Scholar
  606. Titani, K., Takio, K., Handa, M., and Ruggeri, Z. M., 1987, Amino acid sequences of the von Willebrand factor-binding domain of platelet membrane glycoprotein Ib, Proc. Natl. Acad. Sci. U.S.A. 84: 5610–5614.PubMedCrossRefGoogle Scholar
  607. Toda, 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 cDNA sequence, Nature 299:793–797.CrossRefGoogle Scholar
  608. Toh, H., Hayashida, H., and Miyata, T., 1983, Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus, Nature 305:827–829.PubMedCrossRefGoogle Scholar
  609. Toitskii, G. V., and Zav’yalov, V. P., 1972, Calculation of the conformations of proteins with the aid of a modified nonagram. Establishment of the interrelationship between the primary and secondary structures of the polypeptide chain, J. Mol. Biol. 6:645–647.Google Scholar
  610. Trewhella, H., Anderson, S., Fox, R., Gogol, R., Khan, S., Engelman, D., and Zaccai, G., 1983, Assignment of segments of the bacteriorhodopsin sequence to positions in the structural map, Biophys. J. 42:233–241.PubMedCrossRefGoogle Scholar
  611. Trewhella, J., Gogol, E., Zaccai, G., and Engelman, D. M., 1984, Neutron diffraction studies of bacteriorhodopsin structure, in: Neutrons in Biology (B. P. Schoenborn, ed.), Plenum Press, New York, pp. 227–246.Google Scholar
  612. Ullrich, A., Bell, J. R., Chen, E. Y., Herrera, R., Petruzzelli, L. M., Dull, T. J., Gray, A., Coussens, L., Liao, Y.-C., Tsubokawa, M., Mason, A., Seeburg, P. H., Grunfeld, C., Rosen, O. M., and Ramachandran, J., 1985, Human insulin receptor and its relationship to the tyrosine kinase family of oncogenes, Nature 313:756–761.PubMedCrossRefGoogle Scholar
  613. Van Belle, D., Couplet, I., Prevost, M., and Wodak, S., 1987, Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles, J. Mol. Biol. 198:721–735.PubMedCrossRefGoogle Scholar
  614. van Duijnen, P. T., Thole, B. T., and Hol, W. G. J., 1979, On the role of the active site helix in papain. An ab initio molecular orbital study, Biophys. Chem. 9:273–280.PubMedCrossRefGoogle Scholar
  615. Varghese, J. N., Laver, W. G., and Colman, P. M., 1983, Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9Å resolution, Nature 303:35–40.PubMedCrossRefGoogle Scholar
  616. Venkatachalan, C. M., 1968, Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units, Biopolymers 6:1425–1436.CrossRefGoogle Scholar
  617. Vickery, L. E., 1987, Interactive analysis of protein structure using a microcomputer spread sheet, Trends Biochem. Sci. 12:37–39.CrossRefGoogle Scholar
  618. Visser, L., and Blout, E. R., 1971, Elastase. II. Optical properties and the effects of sodium dodecyl sulfate, Biochemistry 10:743–752.PubMedCrossRefGoogle Scholar
  619. Vogel, H., and Jähnig, F., 1986, Models for the structure of outer-membrane proteins of Escherichia coli derived from Raman spectroscopy and prediction methods, J. Mol. Biol. 190:191–199.PubMedCrossRefGoogle Scholar
  620. Vogel, H., Wright, I. K., and Jähnig, F., 1985, The structure of the lactase permease derived from Raman spectroscopy and prediction methods, EMBO J. 4:3625–3631.PubMedGoogle Scholar
  621. Vogel, S., Freist, W., and Hoppe, J., 1986, Assignment of conserved amino acid residues to the ATP site in the protein kinase domain of the receptor for epidermal growth factor, Eur. J. Biochem. 154:529–532.PubMedCrossRefGoogle Scholar
  622. Vonderviszt, F., and Simon, I., 1986, A possible way for prediction of domain boundaries in globular proteins from amino acid sequence, Biochem. Biophys. Res. Commun. 139:11–17.PubMedCrossRefGoogle Scholar
  623. Vonderviszt, F., Matrai, G., and Simon, I., 1986, Characteristic sequential residue environment of amino acids in proteins, Int. J. Peptide Protein Res. 27:483–492.CrossRefGoogle Scholar
  624. von Heijne, G., 1981a, On the hydrophobic nature of signal sequences, Eur. J. Biochem. 116:419–422.CrossRefGoogle Scholar
  625. von Heijne, G., 1981b, Membrane proteins. The amino acid composition of membrane-penetrating segments, Eur. J. Biochem. 120:275–278.CrossRefGoogle Scholar
  626. von Heijne, G., and Blomberg, C., 1977, The ß-structure: Inter-strand correlations, J. Mol. Biol. 117:821–824.CrossRefGoogle Scholar
  627. von Heijne, G., and Blomberg, C., 1978, Some global ß-sheet characteristics, Biopolymers 7:2033–2037.CrossRefGoogle Scholar
  628. von Heijne, G., and Blomberg, C., 1979, Trans-membrane translocation of proteins. The direct transfer model, Eur. J. Biochem. 97:175–181.CrossRefGoogle Scholar
  629. Wada, A., 1976, The α-helix as an electric macro-dipole, Adv. Biophysics 9:1–63.Google Scholar
  630. Wada, A., and Nakamura, H., 1981, Nature of the charge distribution in proteins, Nature 293:757–758.PubMedCrossRefGoogle Scholar
  631. Walker, J. E., Crane, A. F., and Schmitt, H., 1979, The topology of the purple membrane, Nature 278:653–654.PubMedCrossRefGoogle Scholar
  632. Walker, J. E., Saraste, M., Runswick, M. J, and Gay, N. J., 1982, Distantly related sequences in the α-and ß-subunits of ATP synthase, myosin, kinases, and other A TP-requiring enzymes and a common nucleotide binding fold, EMBO J. 1:945–951.PubMedGoogle Scholar
  633. Walker, J. E., Saraste, M., and Gay, N. J., 1984, The unc operon. Nucleotide sequence, regulation and structure of ATP-synthase, Biochim. Biophys. Acta 768:164–200.PubMedGoogle Scholar
  634. Wallace, B. A., Cascio, M., and Mielke, D. L., 1986, Evaluation of methods for the prediction of membrane protein secondary structure, Proc. Natl. Acad. Sci. U.S.A. 83:9423–9427.PubMedCrossRefGoogle Scholar
  635. Warshel, A., and Russell, S. T., 1984, Calculations of electrostatic interactions in biological systems and in solution, Quart. Rev. Biophys. 17:283–422.CrossRefGoogle Scholar
  636. Warwicker, J., and Watson, H. C., 1982, Calculation of the electric potential in the active site cleft due to α-helix dipoles, J. Mol. Biol. 157:671–679.PubMedCrossRefGoogle Scholar
  637. Waterman, M. S., Smith, T. F., and Beyer, W. A., 1976, Some biological sequence metrics, Adv. Math. 20: 367–387.CrossRefGoogle Scholar
  638. Weatherford, D. W., and Salemme, F. R., 1979, Conformations of twisted parallel ß-sheets and the origin of chirality in protein structures, Proc. Nat. Acad. Sci. U.S.A. 76:19–23.CrossRefGoogle Scholar
  639. Weber, P. C., and Salemme, F. R., 1980, Structural and functional diversity in 4-α-helical proteins, Nature 287:82–84.PubMedCrossRefGoogle Scholar
  640. Webster, T. A., Lathrop, R. H., and Smith, T. F., 1987, Prediction of a common structural domain in amino acid-tRNA synthetases through use of a new pattern-directed inference system, Biochemistry 26:6950–6957.PubMedCrossRefGoogle Scholar
  641. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., and Weiner, P., 1984, A new force field for molecular mechanical simulation of nucleic acids and proteins, J. Am. Chem. Soc. 106:765–784.CrossRefGoogle Scholar
  642. Wertz, D. H., and Scheraga, H. A., 1978, Influence of water on protein structure. An analysis of the preferences of amino acids residues for the inside or outside and for specific conformations in a protein molecule, Macromolecules 11:9–15.PubMedCrossRefGoogle Scholar
  643. Wetlaufer, D. B., 1973, Nucleation, rapid folding, and globular intrachain regions in proteins, Proc. Natl. Acad. Sci. U.S.A. 70:697–701.PubMedCrossRefGoogle Scholar
  644. Wetlaufer, D. B., 1981, Folding of protein fragments, Adv. Protein Chem. 34:61–92.PubMedCrossRefGoogle Scholar
  645. Wetlaufer, D. B., and Ristow, S., 1973, Acquisition of three-dimensional structure of proteins, Annu. Rev. Biochem. 42:135–158.PubMedCrossRefGoogle Scholar
  646. Wickner, W., 1979, The assembly of proteins into biological membranes: The membrane trigger hypothesis, Annu. Rev. Biochem. 48:23–45.PubMedCrossRefGoogle Scholar
  647. Wierenga, R. K., Terpstra, P., and Hol, W. G. J., 1986, Prediction of the occurrence of the ADP-binding ßαß-fold in proteins, using an amino acid sequence fingerprint, J. Mol. Biol. 187:101–107.PubMedCrossRefGoogle Scholar
  648. Wilbur, W. J., and Lipman, D. J., 1983, Rapid similarity searches of nucleic acids and protein data banks, Proc. Natl. Acad. Sci. U.S.A. 80:726–730.PubMedCrossRefGoogle Scholar
  649. Williams, R. W., Chang, A., Juretic, D., and Loughran, S., 1987, Secondary structure predictions and medium-range interactions, Biochim. Biophys. Acta 916:200–204.PubMedCrossRefGoogle Scholar
  650. Wilmot, C. M., and Thornton, J. M., 1988, Analysis and prediction of the different types of ß-tum in proteins, J. Mol. Biol. 203:221–232.PubMedCrossRefGoogle Scholar
  651. Wilson, I. A., Haft, D. H., Getzoff, E. D., Tainer, J. A., Lerner, R. A., and Brenner, S., 1985, Identical short peptide sequences in unrelated proteins can have different conformations: A testing ground for theories of immune recognition, Proc. Natl. Acad. Sci. U.S.A. 82:5255–5259.PubMedCrossRefGoogle Scholar
  652. Wodak, S. J., and Janin, J., 1980, Analytical approximation to the accessible surface area of proteins, Proc. Natl. Acad. Sci. U.S.A. 77:1736–1740.PubMedCrossRefGoogle Scholar
  653. Wodak, S. J., and Janin, J., 1981, Location of structural domains in proteins, Biochemistry 20:6544–6552.PubMedCrossRefGoogle Scholar
  654. Wolfenden, R., 1983, Waterlogged molecules, Science 222:1087–1093.PubMedCrossRefGoogle Scholar
  655. Wolfenden, R., Anderson, L., Cullis, P. M., and Southgate, C. C. B., 1981, Affinities of amino acid side chains for solvent water, Biochemistry 20:849–855.PubMedCrossRefGoogle Scholar
  656. Wolfenden, R. Y., Cullis, P. M., and Southgate, C. C. F., 1979, Water, protein folding, and the genetic code, Science 206:575–577.PubMedCrossRefGoogle Scholar
  657. Wu, C.-S. C., Hachimori, A., and Yang, J. T., 1982, Lipid induced ordered conformation of some peptide hormones and bioactive oligopeptides: Predominance of helix over ß-form, Biochemistry 21:4556–4562.PubMedCrossRefGoogle Scholar
  658. Wu, T. T., and Kabat, E. A., 1970, An analysis of the sequences of the variable regions of Bence Jones proteins and Myeloma light chains and their implications for antibody complementarity, J. Expt. Med. 132:211–250.CrossRefGoogle Scholar
  659. Yatsunami, K., and Khorana, H. G., 1985, GTPase of bovine rod outer segments: The amino acid sequence of the α-subunit as derived from the c-DNA sequence, Proc. Natl. Acad. Sci. U.S.A. 82:4316–4320.PubMedCrossRefGoogle Scholar
  660. Yockey, H. P., 1977, A prescription which predicts functionally equivalent residues at given sites in protein sequences, J. Theor. Biol. 67:337–343.PubMedCrossRefGoogle Scholar
  661. Youvan, D. C., Bylina, E. J., Albert, M., Begusch, H., and Hearest, J., 1984, Nucleotide and deduced polypeptide sequence of the photosynthetic reaction center, B870 antenna, and flanking polypeptides from R. capsulata, Cell 37:949–957.PubMedCrossRefGoogle Scholar
  662. Yuschok, T. J., and Rose, G. D., 1983, Hierarchic organization of globular proteins. A control study, Int. J. Peptide Prot. Res. 21:479–484.CrossRefGoogle Scholar
  663. Zehfus, M. H., Seltzer, J. P., and Rose, G. D., 1985, Fast approximation for accessible surface area and molecular volume of protein segments, Biopolymers 24:2511–2519.PubMedCrossRefGoogle Scholar
  664. Zimm, B. H., and Bragg, J. K., 1959, Theory of the phase transition between the helix and random chain in polypeptide chains, J. Chem. Phys. 31:526–535.CrossRefGoogle Scholar
  665. Zimmerman, J. M., Eliezer, N., and Simha, R., 1968, The characterization of amino acid sequences in proteins by statistical methods, J. Theor. Biol. 21: 170–201.PubMedCrossRefGoogle Scholar
  666. Zimmerman, S. S., and Scheraga, H. A., 1977, Local interactions in bends of protein, Proc. Natl. Acad. Sci. U.S.A. 74:4126–4129.PubMedCrossRefGoogle Scholar
  667. Zimmerman, S. S., Pottle, M. S., Nemethy, G., and Scheraga, H. A., 1977, Conformational analysis of the 20 naturaliy occurring amino acid residues using ECEPP, Macromolecules 10:1–9.PubMedCrossRefGoogle Scholar
  668. Zvelebil, M. J., Barton, G. J., Taylor, W. R., and Sternberg, M. J. E., 1987, Prediction of protein secondary structure and active sites using alignment of homologous sequence, J. Mol. Biol. 195:957–961.PubMedCrossRefGoogle Scholar

Appendix 1: List of Reviews on Protein Folding and Prediction of Secondary and Tertiary Structure

  1. Argos, P., and Mohana Rao, J. K., 1986, Prediction of protein structure, Methods Enzymol. 130:185–207.PubMedCrossRefGoogle Scholar
  2. Bajaj, M., and Blundell, T., 1984, Evolution and the tertiary structure of proteins, Annu. Rev. Biophys. Biophys. Chem. 13:453–492.Google Scholar
  3. Blake, C. C. F., and Johnson, L. N., 1984, Protein structure, Trends Biochem. Sci. 9:147–151.CrossRefGoogle Scholar
  4. Blundell, T., and Sternberg, M. J. E., 1985, Computer-aided design in protein engineering, Trends Biotechnol. 3:228–235.CrossRefGoogle Scholar
  5. Blundell, T. L., Sibanda, B. L., Sternberg, M. J. E., and Thornton, J. M., 1987, Knowledge-based prediction of protein structures and the design of novel molecules, Nature 326:347–352.PubMedCrossRefGoogle Scholar
  6. Cantor, C. R., and Schimmel, P. R., 1980, Biophysical Chemistry, Volume I, W. H. Freeman, San Francisco.Google Scholar
  7. Chothia, C., 1984, Principles that determine the structure of proteins, Annu. Rev. Biochem. 53:537–572.PubMedCrossRefGoogle Scholar
  8. Chou, P. Y., and Fasman, G. D., 1977, Secondary structural prediction of proteins from their amino acid sequence, Trends Biochem. Sci. 2:128–132.CrossRefGoogle Scholar
  9. Chou, P. Y., and Fasman, G. D., 1978a, Empirical predictions of protein conformation, Annu. Rev. Biochem. 47:251–276.PubMedCrossRefGoogle Scholar
  10. Chou, P. Y., and Fasman, G. D., 1978b, Prediction of the secondary structure of proteins from their amino acid sequence, Adv. Enzymol. 47:45–108.PubMedGoogle Scholar
  11. Creighton, T. E., 1983, Proteins, W. H. Freeman, New York.Google Scholar
  12. Doolittle, R. F., 1986, Of URFS and ORFS. A Primer on How to Analyse Derived Amino Acid Sequences, University Science Books, Mill Hill, CA.Google Scholar
  13. Edsall, J. T., and McKenzie, H. A., 1983, Water and proteins II. The location and dynamics of water in protein systems and its relation to their stability and properties, Adv. Biophys. 16:53–183.PubMedCrossRefGoogle Scholar
  14. Eisenberg, D., 1984, Three-dimensional structure of membrane and surface proteins, Annu. Rev. Biochem. 53: 595–623.PubMedCrossRefGoogle Scholar
  15. Engelman, D. M., Steitz, T. A., and Goldman, A., 1986, Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins, Annu. Rev. Biophys. Biophys. Chem. 15:321–353.PubMedCrossRefGoogle Scholar
  16. Fasman, G. D., 1980, Prediction of protein conformation from the primary structure, Ann. N.Y. Acad. Sci. 348: 147–159.CrossRefGoogle Scholar
  17. Fasman, G. D., 1985, A critique of the utility of the prediction of protein secondary structure, J. Biosci. 8:15–23.CrossRefGoogle Scholar
  18. Fasman, G. D., 1987, The road from poly-α-amino acids to the prediction of protein conformation, Biopolymers 26:S59–S79.PubMedCrossRefGoogle Scholar
  19. Fletterick, R., and Zoller, M., eds., 1986, Computer graphics and molecular modeling, in: Current Communications in Molecular Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.Google Scholar
  20. Ghelis, C., and Yon, J., 1982, Protein Folding. Academic Press, New York.Google Scholar
  21. Go, N., 1983, Theoretical studies of protein folding, Annu. Rev. Biophys. Biophys. Chem. 12:183–210.Google Scholar
  22. Hohne, E., and Kretschmer, R. G., 1985, Description of secondary structure in proteins, Stud. Biophys. 108: 165–186.Google Scholar
  23. Honig, B. H., Hubbell, W. L., and Flewling, R. F., 1986, Electrostatic interactions in membranes and proteins, Annu. Rev. Biophys. Biophys. Chem. 15:163–193.PubMedCrossRefGoogle Scholar
  24. Jaenicke, R., ed., 1984, Protein Folding. Elsevier/North-Holland Biomedical Press, Amsterdam.Google Scholar
  25. Jaenicke, R., 1987, Folding and association of proteins, Prog. Biophys. Mol. Biol. 49:117–237.PubMedCrossRefGoogle Scholar
  26. Janin, J., and Wodak, S. J., 1983, Structural domains in proteins and their role in the dynamics of protein function, Prog. Biophys. Mol. Biol. 42:21–78.PubMedCrossRefGoogle Scholar
  27. Jungck, J. R., Friedman, R. M., 1984, Mathematical tools for molecular genetics data: An annotated bibliography, Bull. Math. Biol. 46:699–744.Google Scholar
  28. Kauzmann, W., 1959, Some factors in the interpretation of protein denaturation, Adv. Protein Chem. 14:1–63.PubMedCrossRefGoogle Scholar
  29. Kneale, G. G., and Bishop, M. J., 1985, Nucleic acid and protein sequence databases, Cabios 1:11–17.PubMedGoogle Scholar
  30. Kollman, P., 1987, Molecular modeling, Annu. Rev. Phys. Chem. 38:303–316.CrossRefGoogle Scholar
  31. Lesk, A. M., and Hardman, K. D., 1985, Computer-generated pictures of proteins, Methods Enzymol. 115: 381–390.PubMedCrossRefGoogle Scholar
  32. Levitt, M., 1982, Protein conformation, dynamics, and folding by computer simulation. Annu. Rev. Biophys. Bioeng. 11:251–271.PubMedCrossRefGoogle Scholar
  33. Matthew, J. B., and Gurd, F. R. N., 1986a, Stabilization and destabilization of protein structure by charge interactions, Methods Enzymol. 130:437–453.PubMedCrossRefGoogle Scholar
  34. Matthew, J. B., and Gurd, F. R. N., 1986b, Calculation of electrostatic interactions in proteins, Methods Enzymol. 130:413–436.PubMedCrossRefGoogle Scholar
  35. Matthews, J. B., 1985, Electrostatic effects in proteins, Annu. Rev. Biophys. Biophys. Chem. 14:387–417.CrossRefGoogle Scholar
  36. Nagano, K. and Ponnuswamy, P. K., 1984, Prediction of packing of secondary structure, Adv. Biophys. 18: 115–148.PubMedCrossRefGoogle Scholar
  37. Nemethy, G., and Scheraga, H. A., 1977, Protein folding, Q. Rev. Biophys. 10:239–352.PubMedCrossRefGoogle Scholar
  38. Ptitsyn, O. B., and Finkelstein, A. V., 1980, Similarities of protein topologies: Evolutionary divergence, functional convergence or principles of folding, Q. Rev. Biophys. 13:339–386.PubMedCrossRefGoogle Scholar
  39. Richards, F. M., 1977, Areas, volumes, packing, and protein structure, Adv. Biophys. Bioeng. 6:151–176.CrossRefGoogle Scholar
  40. Richards, J. S., 1985, Schematic drawings of protein structures, Methods Enzymol. 115:359–380.CrossRefGoogle Scholar
  41. Richardson, J., 1981, The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34:167–339.PubMedCrossRefGoogle Scholar
  42. Richardson, J. S., 1985, Describing patterns of protein tertiary structure, Methods Enzymol. 115:341–358.PubMedCrossRefGoogle Scholar
  43. Robson, B., 1982, The prediction of molecular conformation, Biochem. J. 10:297–298.Google Scholar
  44. Robson, R., and Garnier, J., 1986, Introduction to Proteins and Protein Engineering, Elsevier, Amsterdam.Google Scholar
  45. Rose, G. D., Gierasch, L. M., and Smith, J. A., 1985, Turns in peptides and proteins, Adv. Protein Chem. 37: 1–109.PubMedCrossRefGoogle Scholar
  46. Rossman, M. G., and Argos, P., 1981, Protein folding, Annu. Rev. Biochem. 53:497–533.CrossRefGoogle Scholar
  47. Salemme, F. R., 1983, Structural properties of protein ß-sheets, Prog. Biophys. Mol. Biol. 42:95–133.PubMedCrossRefGoogle Scholar
  48. Scheraga, H. A., 1985, Calculations of the three-dimensional structure of proteins, Ann. N.Y. Acad. Sci. 439: 170–194.PubMedCrossRefGoogle Scholar
  49. Schulz, G. E., 1977, Structural rules for globular proteins, Angew. Chem. [Engl.] 16:23–32.CrossRefGoogle Scholar
  50. Schulz, G. E., and Schirmer, R. H., 1979, Principles of Protein Structure, Springer-Verlag, Berlin.Google Scholar
  51. Sternberg, M. J. E., 1983, The analysis and prediction of protein structure, in: Computing in Biological Sciences (M. S. Geisow and A. N. Barrett, eds.), Elsevier Biomedical Press, Amsterdam, pp. 143–177.Google Scholar
  52. Sternberg, M. J. E., 1986, Prediction of protein structure from amino acid sequence, Anticancer Drug Design 1: 169–178.Google Scholar
  53. Sternberg, M. J. E., and Thornton, J. M., 1978, Prediction of protein structure from amino acid sequence, Nature 271:15–20.PubMedCrossRefGoogle Scholar
  54. Taylor, W. R., 1987, Protein structure prediction in: Nucleic Acid and Protein Sequence Analysis (M. J. Bishop and G. J. Rawlings, eds.), IRL Press: Oxford.Google Scholar
  55. von Heijne, G., 1987, Sequence Analysis in Molecular Biology, Academic Press, New York.Google Scholar
  56. Warshel, A., and Russell, S. T., 1984, Calculations of electrostatic interactions in biological systems and in solutions, Q. Rev. Biophys. 17:283–422.PubMedCrossRefGoogle Scholar
  57. Wetlaufer, D. B., 1981, Folding of protein fragments, Adv. Protein Chem. 34:335–347.Google Scholar
  58. Wetlaufer, D. B., ed., 1984, The Protein Folding Problem, AAAS, Washington.Google Scholar
  59. Wetlaufer. D. B., and Ristow, S., 1973, Acquisition of three-dimensional structure of proteins, Annu. Rev. Biochem. 42:135–158.PubMedCrossRefGoogle Scholar

Appendix 2: Programs Available through This Publication for Protein Secondary Structure Prediction

  1. 1.
    Chou-Fasman-Prevelige derived from the original Chou-Fasman algorithm [C-F-P]: a. Chou, P. Y., and Fasman, G. D., 1974, Prediction of protein conformation, Biochemistry 13:222-245. b. Chou, P. Y., and Fasman, G. D., 1978, Prediction of the secondary structure of proteins from their amino acid sequence, Adv. Enzymol. 47:45-148. c. Chou, P. Y., and Fasman, G. D., 1979, Prediction of ß-turns, Biophys. J. 26:367-384. d. Chou, P. Y., Fasman, G. D., and Prevelige, P., Chapters 9 and 12, this volume. Written in C for IBM-PC-XT.Google Scholar
  2. 2.
    Deléage, F., Tinland, B., and Roux, B., 1987, A computerized version of the Chou and Fasman method for predicting the secondary structure of proteins, Anal. Biochem. 163:292–297. [D-T-R] Some of the qualitative rules in the original rules have been converted to numeric scales to obtain unambiguous predictions. Written for an Apple IIe (l28k) microcomputer.PubMedCrossRefGoogle Scholar
  3. 3.
    Eisenberg, D., Wesson, M., and Wilcox, W., Chapter 16, this volume. [E] Written in FORTRAN to be used on a Vax computer.Google Scholar
  4. 4.
    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. [F-M-S] Finer-Moore, J., Bazan, F., Rubin, J., and Stroud, R. M., 1989, Identification of membrane proteins and soluble protein secondary structural elements, domain structure, and packing arrangements by Fourier-transform amphipathic analysis, Chapter 19, this volume. Written in FORTRAN for use on a VAX computer on a VMS operating system.PubMedCrossRefGoogle Scholar
  5. 5.
    Garnier, J., Osguthorpe, D. G., 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. [G-O-R] and updated: Gibrat, J.-F., Garnier, J., and Robson, B., 1987, Further developments of protein secondary structure prediction using information theory, new parameters, and consideration of residue pairs, J. Mol. Biol. 198:425-443. Garnier, J., and Robson, B., 1989, The G-O-R method for predicting secondary structure in proteins, Chapter 10, this volume. Written in FORTRAN for use on a Micro VAX II computer. Another program is available to be run on a microcomputer (e.g., IBM pC).PubMedCrossRefGoogle Scholar
  6. 6.
    Vogel, H., Wright, J. K., and Jähnig, F., 1985, The structure of the lactose permease derived from raman spectroscopy and prediction methods, EMBO J. 4:3625–3631. [1] Vogel, H., and Jähnig, F., 1986, Models for the structure of outer-membrane proteins of Escherichia coli derived from raman spectroscopy and prediction methods, J. Mol. Biol. 190:191-199. Jähnig, F., 1989, Structure prediction for membrane proteins, Chapter 18, this volume. Written in FORTRAN for use on an IBM PC/AT computer.PubMedGoogle Scholar
  7. 7.
    Klein, P., 1986, Prediction of protein structural class by discriminant analysis. Biochim. Biophys. Acta 874:205–215. [K] Program STRCLS, written for VAX/VMS in FORTRAN.PubMedCrossRefGoogle Scholar
  8. 8.
    Klein, P., Kanehisa, M., and Delisi, C., 1985, The detection and classification of membrane-spanning regions, Biochim. Biophys. Acta 815:468–476. [K-K-D] Written in FORTRAN.PubMedCrossRefGoogle Scholar
  9. 9.
    Kyte, J., and Doolittle, R. F., 1982, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157: 105–132. * [K-D] Program SOAP, written in language C for use in the software system Unix Vax with a C compiler (K-D: Program 8). Will send other programs on 1600 bpi tape. Doolittle Programs: Protein sequence alignment and phylogenetic tree construction. D.-Feng and R. F. Doolittle, 1987, Progressive sequence alignment as a prerequisite to correct phyogenetic trees, J. Mol. Evol. 23:351. Seven programs: format.c-for DNA or protein Score.c-for nearest relationships prealign.c dfalign.c blen.c mulpub.c dfplot.c (The .c indicates that the programs are written in C language. All these programs are in their uncompiled form. Instructions are given to compile the C programs.)PubMedCrossRefGoogle Scholar
  10. 10.
    Lim, V. I., 1974, Algorithms for prediction of α-helical and ß-structural regions in globular proteins, J. Mol. Biol. 88:873–894. Programs written by: Johannes A. Lenstra, Vakgroep Infectieziekten en Immunologie, Facultair Recombinant DNA Laboratorium Fakulteit Der Diergeneeskunde, Rijksuniversiteit Te, Utrecht, Yalelaan 1, Postbus 80-165, 3508 TD Utrecht, The Netherlands, and Kabsch, W. and Sander, C., Biophysics Department, Max Planck Institute of Medical Research, D-6900 Heidelberg, Federal Republic of Germany.PubMedCrossRefGoogle Scholar
  11. 11.
    Nagano, K., 1973, Logical analysis of the mechanism of protein folding. I. Prediction of helices, loops and ß-structures from primary structure, J. Mol. Biol. 75:401–420. [N] Nagano, K., 1974, Logical analysis of the mechanism of protein folding. II. The nucleation process, J. Mol. Biol. 84:337-372. Nagano, K., 1977a, Logical analysis of the mechanism of protein folding. IV. Super-secondary structure, J. Mol. Biol. 109:235-250. Nagano, K., 1977b, Triplet information in helix prediction applied to the analysis of super-secondary structures, J. Mol. Biol. 109:251-274. Nagano, K., 1980, Logical analysis of the mechanism of protein folding. V. Packing game simulation of α/ß proteins, J. Mol. Biol. 138:797-832. Nagano, K., and Ponnuswamy, P. K., 1984, Prediction of packing of secondary structure, Adv. Biophys. 18:115-148. Nagano, K., 1989, Prediction of packing of secondary structure, Chapter 11, this volume. Written in FORTRAN for use with an HITAC M-682H/680 computer system; compatible with the IBM 370 series computer.PubMedCrossRefGoogle Scholar
  12. 12.
    Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H., 1985, Hydrophobicity of amino acids in globular proteins, Science 229:834–838. [R-D] Dworkin, J. E., and Rose, G. D., 1987, Hydrophobicity profiles revisited, in Methods in Protein Sequence Analysis (K. A. Walsh, ed.), Humana Press, Clinton, New Jersey, pp. 573-586. Rose, G. D., and Dworkin, J. E., 1989, The hydrophobicity profile, Chapter 15, this volume. Written in FORTRAN for use on a VAX or MICROVAX computer on a VMS operating system.PubMedCrossRefGoogle Scholar

Appendix 3. Commercially Available Programs

  1. 1.
    Chou, P. Y., and Fasman, G. D., 1978, Adv. Enzymol. 47:45–148; 1978, Annu. Rev. Biochem. 47:251-276.Google Scholar
  2. 2.
    Garnier, J., Osguthorpe, D. J., and Robson, B., 1978, J. Mol. Biol. 120:97–120.Google Scholar
  3. 1.
    Kyte, J., and Doolittle, R. F., 1982, J. Mol. Biol. 157:105–132.Google Scholar
  4. 2.
    Hopp, T. P., and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828.Google Scholar
  5. 3.
    Rose, G., 1978, Nature 272:586–590.Google Scholar
  6. 2.
    MSEQ: A Microcomputer-Based Approach to the Analysis, Display and Prediction of Protein Structure. Black, S. D., and Gloriso, J. C., 1986, Bio Techniques 4:448–460.Google Scholar
  7. Chou, P. Y., and Fasman., G. D., 1978, Secondary structure prediction, Annu. Rev. Biochem. 47:251–276.PubMedCrossRefGoogle Scholar
  8. 1.
    Argos, P., and Palau, J., 1982, Int. J. Peptide Prot. Res. 19:380–393.Google Scholar
  9. 2.
    von Heijne, G., 1981, Eur. J. Biochem. 116:419–422.Google Scholar
  10. 3.
    Hopp, T. P., and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824–3828.Google Scholar
  11. 4.
    Kyte, J., and Doolittle, R. F., 1982, J. Mol. Bio. 157:105–132.Google Scholar
  12. Eisenberg, D., Weiss, R. M., and Terwilliger, T. C., 1982, Nature 299:371–374; Proc. Natl. Acad. Sci. U.S.A. 81:140-144.Google Scholar
  13. Gribskov, M., Burgess, R. R., and Devereux, J., 1986, PEPPLOT: A protein secondary structure analysis program for the UWGCG sequence analysis software package.Google Scholar
  14. 1.
    Chou, P. Y., and Fasman, G. D., 1978, Secondary structure prediction, Adv. Enzymol. 47:45–147.PubMedGoogle Scholar
  15. 2.
    Garnier, J., Osguthorpe, D. J., and Robson, B., 1978, Secondary structure prediction, J. Mol. Biol. 120:97–120.PubMedCrossRefGoogle Scholar
  16. 3.
    Kyte, J., and Doolittle, R. F., 1982, Hydropathy profile, J. Mol. Biol. 157:105–132.PubMedCrossRefGoogle Scholar
  17. 4.
    Eisenberg, D., Sweet, R. M., and Terwilliger, T. C., 1984, Hydrophobic moment, Proc. Natl. Acad. Sci. U.S.A. 81:140–144.PubMedCrossRefGoogle Scholar

Appendix 4: Relevant Programs Described in the Literature

  1. Arnold, J., Eckerrode, U. K., Lemke, J., Phillips, G. J., and Schaeffer, S. W., 1986, A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11, Nucleic Acids Res. 14:239–254.PubMedCrossRefGoogle Scholar
  2. Klein, P., and DeLisi, C., 1986, Prediction of protein structural class from the amino acid sequence, Biopolymers 25:1659–1672.PubMedCrossRefGoogle Scholar
  3. Mount, D. W., 1986, Improved programs for DNA and protein sequence analysis on the IBM personal computer and other standard computer systems, Nucleic Acids Res. 14:443–454.PubMedCrossRefGoogle Scholar
  4. Nakashima, H., Nishikawa, K., and Ooi, T., 1986, The folding type of a protein is relevant to the amino acid composition, J. Biochem. (Tokyo) 99:153–162.Google Scholar
  5. Nishikawa, K., and Ooi, T., 1986, Amino acids sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methods, Biochim. Biophys. Acta 871:45–54.PubMedCrossRefGoogle Scholar
  6. Novotny, J., and Auffray, C., 1984, A program for prediction of protein secondary structure from nucleotide sequence data: Application to histocompatibility antigens, Nucleic Acids Res. 12:243–253. (Editor’s note: A combination of Chou, P. Y., and Fasman, G. D., 1978, Adv. Enzymol. 47:45-148 and Rose, G. D., and Roy, S., 1980, Proc. Natl. Acad. Sci. U.S.A. 77:4643-4647)PubMedCrossRefGoogle Scholar
  7. Peltola, H., Soderlund, H., and Ukkonen, E., 1986, Algorithms for the search of amino acid patterns in nucleic acid sequences, Nucleic Acids Res. 14:99–107.PubMedCrossRefGoogle Scholar
  8. Reisner, A. H., and Bucholtz, C. A., 1986, The MTX package of computer programs for the comparison of sequences of nucleotides and amino acid residues, Nucleic Acids Res. 14:233–238.PubMedCrossRefGoogle Scholar
  9. Staden, R., 1986, The current status and portability of our sequence handling software, Nucleic Acids Res. 14: 217–231.PubMedCrossRefGoogle Scholar
  10. Taylor, P., 1986, A computer program for translating DNA sequences in protein, Nucleic Acids Res. 14:437–441.PubMedCrossRefGoogle Scholar
  11. Trifonov, E. D., and Brendel, V., 1986, GNOMIC. A Dictionary of Genetic Codes, Balaban Publishers, Philadelphia.Google Scholar
  12. van der Berg, J. A., and Osinga, M., 1986, A peptide to DNA conversion program, Nucleic Acids Res. 14:137–140.PubMedCrossRefGoogle Scholar

Review Articles

  1. Moore, J., Engelberg, A., and Bairoch, A., 1988, Using PC/GENE for proteins and nucleic acid analysis, Biotechniques 6:566–572.PubMedGoogle Scholar
  2. Roe, B. A., 1988, Computer programs for molecular biology: An overview of DNA sequencing and protein analysis packages, Biotechniques 6:560–565.PubMedGoogle Scholar

Appendix 6. National Resource Data Bases

  1. Smith, D. H., Brutlag, D., Friedland, P., and Kedes, L. H., 1986, Nucleic Acids Res. 14:17–20.Google Scholar
  2. Kirstofferson, D., 1987, Nature 325:555–556.Google Scholar
  3. Hamm, G. H., and Cameroa, G. N., 1986, The EMBL Data Library, Nucleic Acids Res. 14:5–9.PubMedCrossRefGoogle Scholar
  4. Bilofsky, H. S., Burks, C., Fickett, J. W., Goad, W. B., Lewitter, F. I., Rindone, W., Swindell, C. D., and Tung, C.-S., 1986, The GenBank genetic sequence databank, Nucleic Acids Res. 14:1–4.PubMedCrossRefGoogle Scholar
  5. Smith, T. F., Grushin, K., Tolman, S., and Faulkner, D., 1986, Nucleic Acids Res. 14:25–29.Google Scholar
  6. LOCAL: Dynamic programming maximum local subsequence alignment algorithm, 1981, J. Mol. Biol. 147:195–197.Google Scholar
  7. PRSTRC: A modified Chou and Fasman protein structure algorithm, Ralph, W. W., Webster, T., and Smith, T. F., 1987, Cabios 3:211–216.Google Scholar
  8. ARIADNE: A pattern-directed inference and hierarchical abstraction in protein structure recognition, Lathrop, R. H., Webster, T. A., and Smith, T. F., 1987, Commun. ACM 30:909–921.Google Scholar
  9. RZMAP: A branch and bound algorithm to reconstruct restriction maps from double digest lengths, 1983, Gene 22:19–29.Google Scholar
  10. 1.
    “Fristensky Package”: Brian Fristensky’s Cornell DNA sequence analysis programs.Google Scholar
  11. 2.
    “Mount Package”: The Genetics PC-Software Center of the University of Arizona sequence analysis tools (developed by D. W. Mount, B. Conrad, and E. Myers).Google Scholar
  12. 3.
    “Lipman/Pearson Package”: David Lipman and William Pearson’s rapid biosequence similarity analysis code. Science 227: 1435–1441.Google Scholar
  13. 4.
    “Shalloway Package”: David Shalloway’s restriction/functional site data base management program (IBM-compatible executable code only).Google Scholar
  14. 5.
    “Zucker Package”: Michael Zucker’s RNA secondary structure software.Google Scholar
  15. 6.
    “Caltech Package”: Alan Goldin’s series of routines to analyze DNA or protein sequence data.Google Scholar
  16. George, D. G., Barker, W. C., and Hunt, L. T., 1986, The protein identification resource, Nucleic Acids Res. 14:11–15.PubMedCrossRefGoogle Scholar
  17. Levitt, M., 1976, J. Mol. Biol. 104:59–109.Google Scholar
  18. Bernstein, F. C., Koeyzle, T. F., Williams, G. J. B., Meyer, J. E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tatsumi, M., 1977, The Protein Data Bank: A computer-based archival file for macromolecular structures, J. Mol. Biol. 112:525–542.CrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1989

Authors and Affiliations

  • Gerald D. Fasman
    • 1
  1. 1.Graduate Department of BiochemistryBrandeis UniversityWalthamUSA

Personalised recommendations