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Prediction of Packing of Secondary Structure

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

Abstract

It is believed that a unique tertiary structure of a protein is dictated by its amino acid sequence. The folding process is finished within a limited time, possibly by the testing of reasonable number of candidate conformations and not by searching a myriad of conceivable structures. The role of the side chains of hydrophobic amino acids such as Leu, Ile, Val, and Phe in the nucleation must be very important for a stable tertiary structure to be attained within a limited period of time. On the other hand, the methods proposed so far to simulate the folding process have met with insurmountable difficulties: energies-minimization approaches lead to the multiple-minima problem, and combinatorial approaches sometimes have to handle an enormous number of conformations to be tested.

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References

  • Anderson, C. M., McDonald, R. C., and Steitz, T. A., 1978, Sequencing a protein by x-ray crystallography. I. Interpretation of yeast hexokinase B at 2.5 Ã… resolution by model building, J. Mol. Biol. 123:1–13.

    Article  PubMed  CAS  Google Scholar 

  • Banner, D. W., Bloomer, A. C., Petsko, G. A., Phillips, D. C., Pogson, C. I., Wilson, I. A., Corrao, P. H., Furth, A. J., Milman, J. D., Offord, R. E., Priddle, J. D., and Waley, S. G., 1975, Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 Ã… resolution using amino acid sequence data, Nature (London) 255:609–614.

    Article  CAS  Google Scholar 

  • Bernstein, F. C., Koetzle, T. F., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M., 1977, The protein data bank: A computer-based archival file for macromolecular structures, J. Mol. Biol. 112:535–542.

    Article  PubMed  CAS  Google Scholar 

  • Blake, C. C. F., and Rice, D. W., 1981, Phosphoglycerate kinase, Phil. Trans. R. Soc. Lond. [A] 293:93–104.

    Article  CAS  Google Scholar 

  • Bradshaw, R. A., Cancedda, F., Ericsson, L. H., Neumann, P. A., Piccoli, S. P., Schlesinger, M. J., Schriefer, K., and Walsh, K. A., 1981, Amino acid sequence of Escherichia coli alkaline phosphatase, Proc. Natl. Acad. Sci. U.S.A. 78:3473–3477.

    Article  PubMed  CAS  Google Scholar 

  • Bränden, C.-I., Schneider, G., Lindqvist, Y., Andersson, I., Knight, S., and Lorimer, G., 1987, Structural and evolutionary aspects of the key enzymes in photorespiration: RuBisCO and glycolate oxidase, Cold Spring Harb. Symp. Quant. Biol. 52:491–498.

    PubMed  Google Scholar 

  • Cederlund, E., Lindqvist, Y., Sölerlund, G., Branden, C.-I., and Jörnvall, H., 1988, Primary structure of glycolate oxidase from spinach, Eur. J. Biochem. 173:523–530.

    Article  PubMed  CAS  Google Scholar 

  • Chin, C. C. Q., Brewer, J. M., and Wold, F., 1981, The amino acid sequence of yeast enolase, J. Bioi. Chem. 256:1377–1384.

    CAS  Google Scholar 

  • Chothia, C., 1988, The 14th barrel rolls out, Nature (London) 333:598–599.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J., 1983, Secondary structure assignment for α/ß proteins by a combinatorial approach, Biochemistry 22:4894–4904.

    Article  PubMed  CAS  Google Scholar 

  • Crawford, I. P., Niermann, T., and Kirschner, K., 1987, Prediction of secondary structure by evolutionary comparison: Application to the a subunit of tryptophan synthase, Proteins 2:118–129.

    Article  PubMed  CAS  Google Scholar 

  • Eisenberg, D., Almassy, R. J., Janson, C. A., Chapman, M. S., Suh, S. W., Casio, D., and Smith, W. W., 1987, Some evolutionary relationships of the primary biological catalysts glutamine synthase and RuBisCO, Cold Spring Harb. Symp. Quant. Biol. 52:483–490.

    PubMed  CAS  Google Scholar 

  • Epp, O., Ladenstein, R., and Wendel, A., 1983, The refined structure of the selenoenzyme glutathione peroxidase at 0.2-nm resolution, Eur. J. Biochem. 133:51–59.

    Article  PubMed  CAS  Google Scholar 

  • Farber, G. K., Petsko, G. A., and Ringe, D., 1987, The 3.0 Ã… crystal structure of xylose isomerase from Streptomyces olivochromogenes, Protein Engineering 1:459–466.

    Article  PubMed  CAS  Google Scholar 

  • Garnier, J., Osguthorp, D. J., and Robson, B., 1978, Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins, J. Mol. Biol. 120:97–120.

    Article  PubMed  CAS  Google Scholar 

  • Goldman, A., Ollis, D. L., and Steitz, T. A., 1987, Crystal structure of muconate lactonizing enzyme at 3 Ã… resolution, J. Mol. Biol. 194:143–153.

    Article  PubMed  CAS  Google Scholar 

  • Hellinga, H. W., and Evans, P. R., 1985, Nucleotide sequence and high-level expression of the major Escherichia coli phosphofructokinase, Eur. J. Biochem. 149:363–373.

    Article  PubMed  CAS  Google Scholar 

  • Janin, J., and Chothia, C., 1980, Packing of α-helices onto ß-pleated sheets and the anatomy of α/ß proteins, J. Mol. Biol. 143:95–128.

    Article  PubMed  CAS  Google Scholar 

  • Lebioda, L., and Stec, B., 1988, Crystal structure of enolase indicates that enolase and pyruvate kinase evolved from a common ancestor, Nature (London) 333:683–686.

    Article  CAS  Google Scholar 

  • Lederer, F., Cortial, S., Becam, A.-M., Haumont, P.-Y., and Perez, L., 1985, Complete amino acid sequence of flavocytochrome b 2 from baker’s yeast, Eur. J. Biochem. 152:419–428.

    Article  PubMed  CAS  Google Scholar 

  • Lifson, S., and Sander, C., 1979, Antiparallel and parallel ß-strands differ in amino acid residue preferences, Nature (London) 282: 109–111.

    Article  CAS  Google Scholar 

  • Lim, L. W., Shamala, N., Mathews, F. S., Steenkamp, D. J., Hamlin, R., and Xuong, N.-h., 1986, Three-dimensional structure of the iron-sulfur flavoprotein trimethylamine dehydrogenase at 2.4 Ã… resolution, J. Biol. Chem. 261:15140–15146.

    PubMed  CAS  Google Scholar 

  • Matthews, B. W., and Remington, S. J., 1974, The three dimensional structure of the lysozyme from bacteriophage T4, Proc. Natl. Acad. Sci. U.S.A. 71:4178–4182.

    Article  PubMed  CAS  Google Scholar 

  • McLachlan, A. D., and Stewart, M., 1975, Tropomyosin coiled-coil interactions: Evidence for an unstaggered structure, J. Mol. Biol. 98:293–304.

    Article  PubMed  CAS  Google Scholar 

  • Motherwell, S., 1978, PLUTO78, Cambridge Crystallographic Database User’s Manual, pp. 56–66, Cambridge, Crystallographic Data Centre, Cambridge, England.

    Google Scholar 

  • Muirhead, H., Clayden, D. A., Barford, D., Lorimer, C. G., Fothergill-Gilmore, L. A., Schiltz, E., and Schmitt, W., 1986, The structure of cat muscle pyruvate kinase, EMBO J. 5:475–481.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Nagano, K., 1974, Logical analysis of the mechanism of protein folding. II. The nucleation process, J. Mol. Biol. 84:337–372.

    Article  PubMed  CAS  Google Scholar 

  • Nagano, K., 1977a, Logical analysis of the mechanism of protein folding. IV. Super-secondary structures, J. Mol. Biol. 109:235–250.

    Article  PubMed  CAS  Google Scholar 

  • Nagano, K., 1977b, Triplet information in helix prediction applied to the analysis of super-secondary structures, J. Mol. Biol. 109:251–274.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Nagano, K., and Hasegawa, K., 1975, Logical analysis of the mechanism of protein folding. III. Prediction of the strong long-range interactions, J. Mol. Biol. 94:257–281.

    Article  PubMed  CAS  Google Scholar 

  • Nagano, K., and Ponnuswamy, P. K., 1984, Prediction of packing of secondary structure, Adv. Biophys. 18: 115–148.

    Article  PubMed  CAS  Google Scholar 

  • Nargang, F., McIntosh, L., and Somerville, C., 1984, Nucleotide sequence of the ribulosebisphosphate carbox-ylase gene from Rhodospirillum rubrum, Mol. Gen. Genet. 193:220–224.

    Article  CAS  Google Scholar 

  • Poulos, T. L., Finzel, B. C., Gunsalus, I. C., Wagner, G. C., and Kraut, J., 1985, The 2.6-Ã… crystal structure of Pseudomonas putida cytochrome P-450, J. Biol. Chem. 260:16122–16130.

    PubMed  CAS  Google Scholar 

  • Priestle, J. P., Grütter, M. G., White, J. L., Vincent, M. G., Kania, M., Wilson, E., Jardetzky, T. S., Kirschner, K., and Jansonius, J. N., 1987, Three-dimensional structure of the bifunctional enzyme N-(5′phosphoribosyl) anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 84:5690–5694.

    Article  PubMed  CAS  Google Scholar 

  • Schneider, G., Lindqvist, Y., Bränden, C.-I., and Lorimer, G., 1986, Three-dimensional structure of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum at 2.9 Ã… resolution, EMBO J. 5:3409–3415.

    PubMed  CAS  Google Scholar 

  • Sowadski, J. M., Handschumacher, M. D., Murthy, H. M. K., Foster, B. A., and Wyckoff, H. W., 1985, Refined structure of alkaline phosphatase from Escherichia coli at 2.8 Ã… resolution, J. Mol. Biol. 186:417–433.

    Article  PubMed  CAS  Google Scholar 

  • Stachelek, C., Stachelek, J., Swan, J., Botstein, D., and Konigsberg, W., 1986, Identification, cloning and sequence determination of the genes specifying hexokinase A and B from yeast, Nucleic Acids Res. 14: 945–962.

    Article  PubMed  CAS  Google Scholar 

  • Stone, D., and Smillie, L. B., 1978, The amino acid sequence of rabbit skeletal α-tropomyosin. The NH2-terminal half and complete sequence, J. Biol. Chem. 253:1137–1148.

    PubMed  CAS  Google Scholar 

  • Stuart, D. I., Levine, M., Muirhead, H., and Stammers, D. K., 1979, Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6 Ã…, J. Mol. Biol. 134:109–142.

    Article  PubMed  CAS  Google Scholar 

  • Sygusch, J., Beaudry, D., and Allaire, M., 1987, Molecular architecture of rabbit skeletal muscle aldolase at 2.7 Ã… resolution, Proc. Natl. Acad. Sci. U.S.A. 84:7846–7850.

    Article  PubMed  CAS  Google Scholar 

  • Tanaka, I., Appelt, K., Dijk, J., White, S. W., and Wilson, K. S., 1984, 3-Ã… resolution structure of a protein with histone-like properties in prokaryotes, Nature (London) 310:376–381.

    Article  CAS  Google Scholar 

  • Taylor, W. R., and Thornton, J. M., 1983, Prediction of supersecondary structure in proteins, Nature (London) 301:540–542.

    Article  CAS  Google Scholar 

  • Taylor, W. R., and Thornton, J. M., 1984, Recognition of super-secondary structure in proteins, J. Mol. Biol. 173:487–514.

    Article  PubMed  CAS  Google Scholar 

  • Tolan, D. R., Amsden, A. B., Putney, S. D., Urdea, M. S., and Penhoet, E. E., 1984, The complete nucleotide sequence for rabbit muscle aldolase A messenger RNA, J. Biol. Chem. 259:1127–1131.

    PubMed  CAS  Google Scholar 

  • Vlahos, C. J., and Dekker, E. E., 1988, The complete amino acid sequence and identification of the active-site arginine peptide of Escherichia coli 2-keto-4-hydroxyglutarate aldolase, J. Biol. Chem. 263: 11683–11691.

    PubMed  CAS  Google Scholar 

  • Weijer, W. J., Hofsteenge, J., Beintema, J. J., Wierenga, R. K., and Drenth, J., 1983, p-Hydroxybenzoate hydroxylase from Pseudomonas fluorescens. 2. Fitting of the amino-acid sequence to the tertiary structure, Eur. J. Biochem. 133: 109–118.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Winter, G., Koch, G. L. E., Hartley, B. S., and Barker, D. G., 1983, The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus, Eur. J. Biochem. 132:383–387.

    Article  PubMed  CAS  Google Scholar 

  • Xia, Z.-x., Shamala, N., Bethge, P. H., Lim, L. W., Bellamy, H. D., Xuong, N.-h., Lederer, F., and Mathews, F. S., 1987, Three-dimensional structure of flavocytochrome b 2 from baker’s yeast at 3.0-Ã… resolution, Proc. Natl. Acad. Sci. U.S.A. 84:2629–2633.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Faculty of Pharmaceutical Sciences, University of Tokyo, Tokyo, 113, Japan

    Kozo Nagano

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  1. Kozo Nagano
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Editors and Affiliations

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

    Gerald D. Fasman

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© 1989 Plenum Press, New York

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Nagano, K. (1989). Prediction of Packing of Secondary Structure. In: Fasman, G.D. (eds) Prediction of Protein Structure and the Principles of Protein Conformation. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-1571-1_11

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  • DOI: https://doi.org/10.1007/978-1-4613-1571-1_11

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4612-8860-2

  • Online ISBN: 978-1-4613-1571-1

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