The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p

Nature Structural Biology

Volumn 5, Issue 2, 1998, Pages 140-147

  Lubkowski, Jacek ^a   Hennecke, Frank ^b   Plückthun, Andreas ^b   Wlodawer, Alexander ^a  

^a FCRDC   (United States)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE DNA; GENE 3 PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; BINDING SITE; CRYSTAL STRUCTURE; DIFFRACTION; NONHUMAN; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DNA-BINDING PROTEINS; INOVIRUS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PROTEIN CONFORMATION; SELENOMETHIONINE; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL FUSION PROTEINS;

UNIDENTIFIED BACTERIOPHAGE;

EID: 0031911439     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0298-140     Document Type: Review

References (50)

1. Smith, G.P. Filamentous fusion phage; novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315-1317 (1985).
2. Phizicky, E.M. & Fields, S. Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94-123 (1995).
3. Cortese, R. et al. Selection of biologically active peptides by phage display of random peptide libraries. Curr. Opin. Biotechnol. 7, 616-621 (1996).
4. Dunn, I.S. Phage display of proteins. Curr Opin. Biotechnol 7, 547-553 (1996).
5. Spada, S., Krebber, C. & Plückthun, A. Selectively infective phages (SIP). Biol. Chem. 378, 445-456 (1997).
6. Gray, C.W., Brown, R.S. & Marvin, D .A. Adsorption complex of filamentous fd virus. J. Mol. Biol. 146, 621-627 (1981).
7. Jacobson, A. Role of F pili in the penetration of bacteriophage fl. J. Virol. 10, 835-843 (1972).
8. Sun, T.P. & Webster, R.E. fii, a bacterial locus required for filamentous phage infection and its relation to colicin-tolerant tolA and tolB. J. Bacteriol. 165, 107-115 (1986).
9. Sun, T.P. & Webster, R.E. Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli J. Bacteriol. 169, 2667-2674 (1987).
10. Riechmann, L. & Holliger, P. The C-terminal domain of TolA is the coreceptor for filamentous phage infection of E. coli. Cell 90, 351-360 (1997).
11. Nelson, F.K., Friedman, S.M. & Smith, G.P. Filamentous phage DNA cloning vectors: a noninfective mutant with a nonpolar deletion in gene III. Virology 108, 338-350 (1981).
12. Crissman, J.W. & Smith, G.P, Gene-Ill protein of filamentous phages; evidence for a carboxyl-terminal domain with a role in morphogenesis. Virology 132, 445-455 (1984).
13. Endemann, H., Gailus, V. & Rasched, I. Interchangeability of the adsorption proteins of bacteriophages Ff and IKe, J. Virol. 67, 3332-3337 (1993).
14. Hutchinson, E.G. & Thornton, J.M PROMOTIF - a program to identify and analyze structural motifs in proteins Protein Sci. 5, 212-220 (1996).
15. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138 (1993).
16. Cabrai, J.H, et al. Crystal structure of a PDZ domain. Nature 382, 649-652 (1996).
17. Faber, H.R. et al. 1.8 Å crystal structure of the C-terminal domain of rabbit serum haemopexin. Structure 3, 551-559 (1995).
18. Viguera, A.R., Blanco, F.J. & Serrano, L. The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247, 670-681 (1995).
19. Holliger, P. & Riechmann, L. A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage Fd. Structure 5, 265-275 (1997).
20. Koradi, R., Billeter, M. & Wüthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-5, 29-32 (1996).
21. Baldwin, E.T. et al. Crystal structure of interleukin-8: symbiosis of NMR and crystallography. Proc. Natl, Acad. Sci. USA 88, 502-506 (1991).
22. Lubkowski, J. etal. The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions. Nature Struct. Biol. 4, 64-69 (1997).
23. Stengele, l., Bross, P., Garces, X., Giray, J. & Rasched, l. Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites. J. Mol. Biol. 212, 143-149 (1990).
24. Krebber, C. et al. Selectively-infective phage (SIP); a mechanistic dissection of a novel in vivo selection for protein-ligand interactions. J. Mol. Biol. 268, 607-618 (1997).
25. Peters, B.P.H., Peters, R.M., Schoenmakers, J.G.G. & Konings, R.N.H. Nucleotide sequence and genetic organizaton of the genome of the N-specific filamentous bacteriophage IKe. Comparison with the genome of the F-specific filamentous phages M13, fd and fl. J. Mol. Biol. 181, 27-39 (1985).
26. Frost, L.S., Ippen-lhler, K. & Skurray, R.A. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev. 58, 162-210 (1994).
27. Marvin, D.A. & Folkhard, W. Structure of F-pili: reassessment of the symmetry. J. Mol. Biol. 191, 299-300 (1986).
28. Glucksman, M.J., Bhattacharjee, S. & Makowski, L. Three-dimensional structure of a cloning vector. X-ray diffraction studies of filamentous bacteriophage M13 at 7 Å resolution. J. Mol. Biol. 226, 455-470 (1992).
29. Lin, T.C., Webster, R.E. & Konigsberg, W. Isolation and characterization of the C and D proteins coded by gene IX and gene VI in the filamentous bacteriophage fl and fd. J. Biol. Chem. 255, 10331-10337 (1980).
30. Grant, R.A., Lin, T.C., Webster, R.E. & Konigsberg, W. Structure of filamentous bacteriophage: isolation, characterization, and localization of the minor coat proteins and orientation of the DNA. Prog. Clin. Biol. Res. 64: 413-428 (1981).
31. Tzagoloff, H. & Pratt, D. The initial steps in infection with coliphage M13. Virology 24, 372-380 (1964).
32. Goldsmith, M.E. & Konigsberg, W.H. Adsorption protein of the bacteriophage fd: isolation, molecular properties, and location in the virus. Biochemistry 16, 2686-2694 (1977).
33. Beck, E. & Zink, B. Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd. Gene 16, 35-58 (1981).
34. Freund, C., Ross, A., Guth, B., Pluckthun, A. & Holak, T.A. Characterization of the linker peptide of the single-chain Fv fragment of an antibody by NMR spectroscopy. FEBS Lett. 320, 97-100 (1993).
35. Studier, F.W. & Moffatt, B.A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189, 113-130 (1986).
36. Qoronfleh, M.W. et al. Production of selenomethionine-labeled recombinant human neutrophil collagenase in Escherichid coli. J. Biotechnol. 39, 119-128 (1995).
37. Pluckthun, A., et al. Producing antibodies in Escherichia coli: from PCR to fermentation. In Antibody engineering: a practical approach (eds McCafferty, J. & Hoogenboom, H.R., Chriswell, DJ.) 203-252 (IRL Press, Oxford; 1996).
38. Hendrickson, W.A., Horton, J.R. & LeMaster, D.M, Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three dimensional structure, EMBO J. 9. 1665-1672 (1990).
39. Matthews, B.W. Solvent content of protein crystals. J. Mol. Biol. 33, 491-497 (1968).
40. Qtwinowski, Z. An oscillation data processing suite for macromolecular crystallography (Vale University, New Haven, Connecticut, USA; 1992).
41. Jones, T.A. & Kjeldgaard, M. O -the manual (Uppsala University, Uppsala, 1994).
42. Brünger, A. X-plor version 3,1: a system for X-ray crystallography and NMR (Yale University Press, New Haven, Connecticut, USA; 1992).
43. Furey, W. SE Swaminathaa S. PHASES - A program package for the processing and analysis of diffraction data for macromolecules. Acta Crystallogr, 18, 73 (1990).
44. Sheldrick, G,M. Patterson superposition and ab initio phasing. Meth. Enz. 276, 628-641 (1997).
45. Wang, B.C. Resolution of phase ambiguity in macromolecular crystallography. Meth. Enz. 115, 90-112 (1985).
46. CCP4:SERC Collaborative computing project no. 4 (Warrington, UK; 1979).
47. Lundblad, R.L & Noyes, CM. Chemical modification of tryptophan. In Chemical reagents for protein modification (eds. Lundblad, R.L. & Noyes, CM,) 47-71 (CRC Press, Boca Raton, Florida; 1984).
48. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950 (1991).
49. Carson, M. RIBBONS 4.0. J. Appl Crystallogr. 24, 958-961 (1991).
50. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: A program to check the stereothemical quality of protein structures. J. Appl. Crystaltogr. 26, 283-291 (1993).