Mapping domain structures in silks from insects and spiders related to protein assembly

Journal of Molecular Biology

Volumn 335, Issue 1, 2004, Pages 27-40

  Bini, Elisabetta ^a   Knight, David P ^b   Kaplan, David L ^a  

^a Tufts University   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Protein folding; Self assembly; Silk; Silkworm; Spider

Indexed keywords

PROTEIN; WATER;

AMINO TERMINAL SEQUENCE; CARBOXY TERMINAL SEQUENCE; GENETIC ENGINEERING; HYDROPHILICITY; HYDROPHOBICITY; INSECT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW; SEQUENCE ANALYSIS; SILK; SPIDER; STRUCTURE ANALYSIS;

ARANEAE; BOMBYX MORI; HEXAPODA;

EID: 0345118157     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.10.043     Document Type: Review

References (61)

1. Gosline J.M., Guerette P.A., Ortlepp C.S., Savage K.N. The mechanical design of spider silks: from fibroin sequence to mechanical function. J. Expt. Biol. 202:1999;3295-3303.
2. Cunniff P.M., Fossey S.A., Auerbach M.A., Song J.W., Kaplan D.L., Adams W.W., et al. Mechanical and thermal properties of dragline silk from the spider Nephila clavipes. Polym. Advan. Technol. 5:1994;401-4103.
3. Arcidiacono S., Mello C., Kaplan D., Cheley S., Bayley H. Purification and characterization of recombinant spider silk expressed in Escherichia coli. Appl. Microbiol. Biotechnol. 49:1998;31-38.
4. Prince J.T., McGrath K.P., DiGirolamo C.M., Kaplan D.L. Construction, cloning, and expression of synthetic genes encoding spider dragline silk. Biochemistry. 34:1995;10879-10885.
5. Lewis R.V., Hinman M., Kothakota S., Fournier M.J. Expression and purification of a spider silk protein: a new strategy for producing repetitive proteins. Protein Expr. Purif. 7:1996;400-406.
6. Fahnestock S.R., Irwin S.L. Synthetic spider dragline silk proteins and their production in Escherichia coli. Appl. Microbiol. Biotechnol. 47:1997;23-32.
7. Fukushima Y. Genetically engineered syntheses of tandem repetitive polypeptides consisting of glycine-rich sequence of spider dragline silk. Biopolymers. 45:1998;269-279.
8. Winkler S., Szela S., Avtges P., Valluzzi R., Kirschner D.A., Kaplan D. Designing recombinant spider silk proteins to control assembly. Int. J. Biol. Macromol. 24:1999;265-270.
9. Winkler S., Kaplan D.L. Silk produced by engineered bacteria. Encyclopedia of Materials: Science and Technology. 2001;Elsevier, Amsterdam. pp. 8615-8618.
10. Candelas G.C., Arroyo G., Carrasco C., Dompenciel R. Spider silkglands contain a tissue-specific alanine tRNA that accumulates in vitro in response to the stimulus for silk protein synthesis. Dev. Biol. 140:1990;215-220.
11. Knight D.P., Vollrath F. Biological liquid crystal elastomers. Phil. Trans. Roy. Soc. Ser. B. 357:2002;155-163.
12. Zhou C.Z., Confalonieri F., Jacquet M., Perasso R., Li Z.G., Janin J. Silk fibroin: structural implications of a remarkable amino acid sequence. Proteins: Struct. Funct. Genet. 44:2001;119-122.
13. Craig C.L., Riekel C. Comparative architecture of silks, fibrous proteins and their coding genes in insects and spiders. Comp. Biochem. Physiol. B. 133:2002;493-507.
14. Kenney J.M., Knight D., Wise M.J., Vollrath F. Amyloidogenic nature of spider silk. Eur. J. Biochem. 269:2002;4159-4163.
15. Fahnestock S.R., Bedzyk L.A. Production of synthetic spider dragline silk protein in Pichia pastoris. Appl. Microbiol. Biotechnol. 47:1997;33-39.
16. Szela S., Avtges P., Valluzzi R., Winkler S., Wilson D., Kirschner D., Kaplan D.L. Reduction-oxidation control of beta-sheet assembly in genetically engineered silk. Biomacromolecules. 1:2000;534-542.
17. Asakura T., Nitta K., Yang M., Yao J., Nakazawa Y., Kaplan D.L. Synthesis and characterization of chimeric silkworm silk. Biomacromolecules. 4:2003;815-820.
18. Vollrath F., Knight D.P. Liquid crystalline spinning of spider silk. Nature. 410:2001;541-548.
19. Kerkam K., Viney C., Kaplan D., Lombardi S. Liquid crystallinity of natural silk secretions. Nature. 349:1991;596-598.
20. De Gennes P.G. The Physics of Liquid Crystals. 1st edit. 1974;Clarendon Press, Oxford.
21. Feng D., Knight D.P. The effect of pH on fibrillogenesis of collagen in the egg capsule of the dogfish, Scyliorhinus canicula. Tissue Cell. 26:1994;649-659.
22. Braun F.N., Viney C. Fluctuation-entanglement mechanism for director anchoring at nematic polymer surfaces. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 63:2001;031708/1-031708/4.
23. Jin H.-J., Kaplan D.L. Mechanism of silk processing in insects and spiders. Nature. 424:2003;1057-1061.
24. Jin H.-J., Park J., Valluzzi R., Cebe P., Kaplan D.L. Biomaterial films of Bombyx mori silk with poly(ethylene oxide). Biomacromolecules. 2003;. in the press.
25. Datta A., Ghosh A.K., Kundu S.C. Differential expression of the fibroin gene in developmental stages of silkworm, Antheraea mylitta (Saturniidae). Comp. Biochem. Physiol. B. 129:2001;197-204.
26. Sezutsu H., Yukuhiro K. Dynamic rearrangement within the Antheraea pernyi silk fibroin gene is associated with four types of repetitive units. J. Mol. Evol. 51:2000;329-338.
27. Zurovec M., Sehnal F. Unique molecular architecture of silk fibroin in the waxmoth, Galleria mellonella. J. Biol. Chem. 277:2002;22639-22647.
28. Zhou C.-Z., Confalonieri F., Medina N., Zivanovic Y., Esnault C., Yang T., et al. Fine organization of Bombyx mori fibroin heavy chain gene. Nucl. Acids Res. 28:2000;2413-2419.
29. Kusuda J., Tazima Y., Onimaru K., Ninaki O., Suzuki Y. The sequence around the 5′ end of the fibroin gene from the wild silkworm, Bombyx mandarina, and comparison with that of the domesticated species, B. mori. Mol. Gen. Genet. 203:1986;359-364.
30. Zurovec M., Vaskova M., Kodrik D., Sehnal F., Kumaran A.K. Light-chain fibroin of Galleria mellonella L. Mol. Gen. Genet. 247:1995;1-6.
31. Kikuchi Y., Mori K., Suzuki S., Yamaguchi K., Mizuno S. Structure of the Bombyx mori fibroin light-chain-encoding gene: upstream sequence elements common to the light and heavy chain. Gene. 110:1992;151-158.
32. Xu M., Lewis R.V. Structure of a protein superfiber: spider dragline silk. Proc. Natl Acad. Sci. USA. 87:1990;7120-7124.
33. Beckwitt R., Arcidiacono S. Sequence conservation in the C-terminal region of spider silk proteins (Spidroin) from Nephila clavipes (Tetragnathidae) and Araneus bicentenarius (Araneidae). J. Biol. Chem. 269:1994;6661-6663.
34. Gatesy J., Hayashi C., Motriuk D., Woods J., Lewis R. Extreme diversity, conservation, and convergence of spider silk fibroin sequences. Science. 291:2001;2603-2605.
35. Guerette P.A., Ginzinger D.G., Weber B.H., Gosline J.M. Silk properties determined by gland-specific expression of a spider fibroin gene family. Science. 272:1996;112-115.
36. Ren H.-L., Liu Z.-S., Pan F.-G., Zhao J., Li Y.-S. Construction of Araneus ventricosus major ampullate gland cDNA library and screening spider silk gene. Shengwu Jishu. 12:2002;1-3.
37. Colgin M.A., Lewis R.V. Spider minor ampullate silk proteins contain new repetitive sequences and highly conserved non-silk-like "spacer regions" Protein Sci. 7:1998;667-672.
38. Hayashi C.Y., Lewis R.V. Molecular architecture and evolution of a modular spider silk protein gene. Science. 287:2000;1477-1479.
39. Hayashi C.Y., Lewis R.V. Evidence from flagelliform silk cDNA for the structural basis of elasticity and modular nature of spider silks. J. Mol. Biol. 275:1998;773-784.
40. Donald A.M., Windle A.H. Liquid Crystalline Polymers. 1992;Cambridge University Press, Cambridge.
41. Myers E.W., Miller W. Approximate matching of regular expressions. Bull. Math Biol. 51:1989;5-37.
42. Rost B., Sander C., Schneider R. PHD - an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10:1994;53-60.
43. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1997;1-6.
44. Tanaka K., Inoue S., Mizuno S. Hydrophobic interaction of P25, containing Asn-linked oligosaccharide chains, with the H-L complex of silk fibroin produced by Bombyx mori. Insect Biochem. Mol. Biol. 29:1999;269-276.
45. Zurovec M., Kodrik D., Yang C., Sehnal F., Scheller K. The P25 component of Galleria silk. Mol. Gen. Genet. 257:1998;264-270.
46. Tanaka K., Mizuno S. Homologues of fibroin L-chain and P25 of Bombyx mori are present in Dendrolimus spectabilis and Papilio xuthus but not detectable in Antheraea yamamai. Insect Biochem. Mol. Biol. 31:2001;665-677.
47. Jackson C., O'Brien J.P. Molecular weight distribution of Nephila clavipes dragline silk. Macromolecules. 28:1995;5975-5977.
48. Michal C.A., Simmons A.H., Chew B.G., Zax D.B., Jelinski L.W. Presence of phosphorus in Nephila clavipes dragline silk. Biophys. J. 70:1996;489-493.
49. Winkler S., Wilson D., Kaplan D.L. Controlling β-sheet assembly in genetically engineered silk by enzymatic phosphorylation/dephosphorylation. Biochemistry. 39:2000;12739-12746.
50. Inoue S., Tanaka K., Arisaka F., Kimura S., Ohtomo K., Mizuno S. Silk fibroin of Bombyx mori is secreted, assembling a high molecular mass elementary unit consisting of H-chain, L-chain, and P25, with a 6:6:1 molar ratio. J. Biol. Chem. 275:2000;40517-40528.
51. Weiskopf A., Senecal K., Vouros P., Kaplan D., Mello C.M. The carbohydrate composition of spider silk: Nephila clavipes dragline. Glycobiology. 6:1996;1703.
52. Maurer-Stroh S., Eisenhaber B., Eisenhaber F. N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J. Mol. Biol. 317:2002;541-557.
53. Mita K., Ichimura S., James T.C. Highly repetitive structure and its organization of the silk fibroin gene. J. Mol. Evol. 38:1994;583-592.
54. Hayashi C.Y., Lewis R.V. Spider flagelliform silk: lessons in protein design, gene structure, and molecular evolution. Bioessays. 23:2001;750-756.
55. + channel-Fab complex at 2.0 angstrom resolution. Nature. 414:2001;43-48.
56. Tsuda H., Kobayashi M., Tanaka T., Inoue S., Magoshi Y., Magoshi J. Different behaviour of elution profile of silk fibroin on existence of calcium and potassium ion. Abstr. Pap. Am. Chem. Soc. 223:2002;067-POLY.
57. Wong Po Foo C., Kaplan D. Genetic engineering of fibrous proteins: spider dragline silk and collagen. Adv. Drug Deliv. Rev. 54:2002;1131.
58. Hijirida D.H., Do K.G., Michal C., Wong S., Zax D., Jelinski L. C-13 NMR of Nephila clavipes major ampullate silk gland. Biophys. J. 71:1996;3442-3447.
59. Oroudjev E., Hansma H.G. Segmented nanofibers of spider dragline silk: atomic force microscopy and single-molecule force spectroscopy. Proc. Natl Acad. Sci.USA. 99:2002;6460-6465.
60. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
61. Blom N., Gammeltoft S., Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294:1999;1351-1362.