Selection of a carbohydrate-binding domain with a helix-loop-helix structure

Biochemistry

Volumn 47, Issue 26, 2008, Pages 6745-6751

  Matsubara, Teruhiko ^a   Iida, Mie ^a   Tsumuraya, Takeshi ^b   Fujii, Ikuo ^b   Sato, Toshinori ^a  

^a KEIO UNIVERSITY   (Japan)

^b Osaka Prefecture University   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOMOLECULES; CARBOHYDRATES; CARBOXYLIC ACIDS; DICHROISM; DISSOCIATION; HEALTH; OPTICAL PROPERTIES; ORGANIC ACIDS; ORGANIC COMPOUNDS; POLYPEPTIDES; SCANNING; SPECTROSCOPIC ANALYSIS; SURFACE PLASMON RESONANCE;

AFFINITY SELECTION; AMERICAN CHEMICAL SOCIETY (ACS); AMINO ACID RESIDUES; ARGININE (ARG); BINDING DOMAIN (BD); BINDING PROTEINS; CHOLERA TOXIN (CT); CIRCULAR DICHROISM (DC); COAT PROTEIN (CP); DISSOCIATION CONSTANTS; GALACTOSE (GLCN); HELICAL STRUCTURES; HELIX PEPTIDE; HELIX STRUCTURES; HIGH AFFINITY; PEPTIDE LIBRARIES; PHAGE CLONES; PHENYLALANINE (PHE); SIALIC ACID (SIA); SPECTROSCOPIC STUDIES; SURFACE-PLASMON RESONANCE SPECTROSCOPY (SPRS); SYNTHETIC PEPTIDES;

AMINES;

CARBOHYDRATE BINDING PROTEIN; CHOLERA TOXIN B SUBUNIT; GANGLIOSIDE; HELIX LOOP HELIX PROTEIN; SIALIC ACID;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; MOLECULAR MODEL; NONHUMAN; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PURIFICATION; SENSITIVITY AND SPECIFICITY; SPECTROSCOPY; SURFACE PLASMON RESONANCE;

AMINO ACID SEQUENCE; BINDING SITES; CIRCULAR DICHROISM; DATABASES, PROTEIN; GANGLIOSIDES; HELIX-LOOP-HELIX MOTIFS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SURFACE PLASMON RESONANCE;

EID: 46049109920     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi8000837     Document Type: Article

References (43)

1. Varki, A. (1993) Biological roles of oligosaccharides: All of the theories are correct. Glycobiology 3, 97-130.
2. Kannagi, R., and Hakomori, S. (2001) A guide to monoclonal antibodies directed to glycotopes. Adv. Exp. Med. Biol. 491, 587-630.
3. Qiu, J. X., Kai, M., Padlan, E. A., and Marcus, D. M. (1999) Structure-function studies of an anti-asialo GM1 antibody obtained from a phage display library. J. Neuroimmunol. 97, 172-181.
4. Bradbury, A. R., and Marks, J. D. (2004) Antibodies from phage antibody libraries. J. Immunol. Methods 290, 29-49.
5. x from a phage display library. J. Immunol. 157, 732-738.
6. x. Proc. Natl. Acad. Sci. U.S.A. 96, 6953-6958.
7. Wang, L., Radic, M. Z., Siegel, D., Chang, T., Bracy, J., and Galili, U. (1997) Cloning of anti-Gal Fabs from combinatorial phage display libraries: Structural analysis and comparison of Fab expression in pComb3H and pComb8 phage. Mol. Immunol. 34, 609-618.
8. Ravn, P., Danielczyk, A., Jensen, K. B., Kristensen, P., Christensen, P. A., Larsen, M., Karsten, U., and Goletz, S. (2004) Multivalent scFv display of phagemid repertoires for the selection of carbohydrate-specific antibodies and its application to the Thomsen-Friedenreich antigen. J. Mol. Biol. 343, 985-996.
9. Rojas, G., Talavera, A., Munoz, Y., Rengifo, E., Krengel, U., Angstrom, J., Gavilondo, J., and Moreno, E. (2004) Light-chain shuffling results in successful phage display selection of functional prokaryotic-expressed antibody fragments to N-glycolyl GM3 ganglioside. J. Immunol. Methods 293, 71-83.
10. Yamamoto, K., Maruyama, I. N., and Osawa, T. (2000) Cyborg lectins: Novel leguminous lectins with unique specificities. J. Biochem. 127, 137-142.
11. Yim, M., Ono, T., and Irimura, T. (2001) Mutated plant lectin library useful to identify different cells. Proc. Natl. Acad. Sci. U.S.A. 98, 2222-2225.
12. Yamada, S., Suzuki, Y., Suzuki, T., Le, M. Q., Nidom, C. A., Sakai-Tagawa, Y., Muramoto, Y., Ito, M., Kiso, M., Horimoto, T., Shinya, K., Sawada, T., Usui, T., Murata, T., Lin, Y., Hay, A., Haire, L. F., Stevens, D. J., Russell, R. J., Gamblin, S. J., Skehel, J. J., and Kawaoka, Y. (2006) Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors. Nature 444, 378-382.
13. Stevens, J., Blixt, O., Tumpey, T. M., Taubenberger, J. K., Paulson, J. C., and Wilson, I. A. (2006) Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science 312, 404-410.
14. DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., and Lombardi, A. (1999) De novo design and structural characterization of proteins and metalloproteins. Annu. Rev. Biochem. 68, 779-819.
15. Baltzer, L., and Nilsson, J. (2001) Emerging principles of de novo catalyst design. Curr. Opin. Biotechnol. 12, 355-360.
16. Bolon, D. N., Voigt, C. A., and Mayo, S. L. (2002) De novo design of biocatalysts. Curr. Opin. Chem. Biol. 6, 125-129.
17. Gibas, C., and Subramaniam, S. (1997) Knowledge-based design of a soluble bacteriorhodopsin. Protein Eng. 10, 1175-1190.
18. Hosse, R. J., Rothe, A., and Power, B. E. (2006) A new generation of protein display scaffolds for molecular recognition. Protein Sci. 15, 14-27.
19. Uchiyama, F., Tanaka, Y., Minari, Y., and Tokui, N. (2005) Designing scaffolds of peptides for phage display libraries. J. Biosci. Bioeng. 99, 448-456.
20. Rosinski, J. A., and Atchley, W. R. (1999) Molecular evolution of helix-turn-helix proteins. J. Mol. Evol. 49, 301-309.
21. Merritt, E. A., Sarfaty, S., van den Akker, F., L'Hoir, C., Martial, J. A., and Hol, W. G. (1994) Crystal structure of cholera toxin B-pentamer bound to receptor GM1 pentasaccharide. Protein Sci. 3, 166-175.
22. Kuziemko, G. M., Stroh, M., and Stevens, R. C. (1996) Cholera toxin binding affinity and specificity for gangliosides determined by surface plasmon resonance. Biochemistry 35, 6375-6784.
23. Harder, T., Scheiffele, P., Verkade, P., and Simons, K. (1998) Lipid domain structure of the plasma membrane revealed by patching of membrane components. J. Cell Biol. 141, 929-942.
24. Yanagisawa, K. (2007) Role of gangliosides in Alzheimer's disease. Biochim. Biophys. Acta 1768, 1943-1951.
25. Matsubara, T., Ishikawa, D., Taki, T., Okahata, Y., and Sato, T. (1999) Selection of ganglioside GM1-binding peptides by using a phage library. FEBS Lett. 456, 253-256.
26. Matsubara, T., Iijima, K., Nakamura, M., Taki, T., Okahata, Y., and Sato, T. (2007) Specific Binding of GM1-Binding Peptides to High-Density GM1 in Lipid Membranes. Langmuir 23, 708-714.
27. Fujitani, N., Shimizu, H., Matsubara, T., Ohta, T., Komata, Y., Miura, N., Sato, T., and Nishimura, S. (2007) Structural transition of a 15 amino acid residue peptide induced by GM1. Carbohydr. Res. 342, 1895-1903.
28. Gram, H., Marconi, L. A., Barbas, C. F., III, Collet, T. A., Lerner, R. A., and Kang, A. S. (1992) In vitro selection and affinity maturation of antibodies from a naive combinatorial immunoglobulin library. Proc. Natl. Acad. Sci. U.S.A. 89, 3576-3580.
29. Greenfield, N., and Fasman, G. D. (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8, 4108-4116.
30. Suzuki, N., and Fujii, I. (1999) Optimization of the loop length for folding of a helix loop helix peptide. Tetrahedron Lett. 40, 6013-6017.
31. Fujii, I., Takaoka, Y., Suzuki, K., and Tanaka, T. (2001) A conformationally purified α-helical peptide library. Tetrahedron Lett. 42, 3323-3325.
32. Rockendorf, N., Bade, S., Hirst, T. R., Gorris, H. H., and Frey, A. (2007) Synthesis of a fluorescent ganglioside G(M1) derivative and screening of a synthetic peptide library for G(M1) binding sequence motifs. Bioconjugate Chem. 18, 573-578.
33. Weis, W. I., and Drickamer, K. (1996) Structural basis of lectin-carbohydrate recognition. Annu. Rev. Biochem. 65, 441-473.
34. Hyun, S., Kim, J., Kwon, M., and Yu, J. (2007) Selection and syntheses of tentacle type peptides as 'artificial' lectins against various cell-surface carbohydrates. Bioorg. Med. Chem. 15, 511-517.
35. Yang, J. T., Wu, C.-S. C., and Martinez, H. M. (1986) Calculation of protein conformation from circular dichroism. Methods Enzymol. 130, 208-269.
36. Vila, J. A., Ripoll, D. R., and Scheraga, H. A. (2000) Physical reasons for the unusual α helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl. Acad. Sci. U.S.A. 97, 13075-13079.
37. Gronow, S., and Brade, H. (2001) Lipopolysaccharide biosynthesis: Which steps do bacteria need to survive? J. Endotoxin Res. 7, 3-23.
38. Rudiger, H., and Gabius, H. J. (2001) Plant lectins: Occurrence, biochemistry, functions and applications. Glycoconjugate J. 18, 589-613.
39. Love, K. R., and Seeberger, P. H. (2002) Carbohydrate arrays as tools for glycomics. Angew. Chem., Int. Ed. 41, 3583-3586.
40. Hirabayashi, J., and Kasai, K. (2002) Separation technologies for glycomics. J. Chromatogr., B 771, 67-87.
41. Feizi, T., Fazio, F., Chai, W., and Wong, C. H. (2003) Carbohydrate microarrays: A new set of technologies at the frontiers of glycomics. Curr. Opin. Struct. Biol. 13, 637-645.
42. Matsubara, T., and Sato, T. (2007) Identification of oligosaccharide- recognition molecules by phage-display technology. Trends Glycosci. Glycotechnol. 19, 121-132.
43. Lis, H., and Sharon, N. (1998) Lectins: Carbohydrate-specific proteins that mediate cellular recognition. Chem. Rev. 98, 637-674.