Structural studies of the streptavidin binding loop

Protein Science

Volumn 6, Issue 6, 1997, Pages 1157-1166

  Freitag, Stefanie ^a   Trong, Isolde L E ^a   Klumb, Lisa ^a   Stayton, Patrick S ^a   Stenkamp, Ronald E ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Biotin; Flexible loop; Molecular recognition; Protein ligand interactions; Streptavidin

Indexed keywords

BIOTIN; LIGAND; PROTEIN SUBUNIT; STREPTAVIDIN;

ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STABILITY;

EID: 0342601407     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060604     Document Type: Article

References (42)

1. Bayer EA, Wilchek M. 1990. Avidin-biotin technology. Methods Enzymol 184. Forthcoming.
2. Brünger AT. 1992a. X-PLOR, A system for crystallography and NMR, v. 3.1. New Haven, Connecticut: Yale University Press.
3. Brünger AT. 1992b. Free R-value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472-475.
4. Chaiet L, Wolf FJ. 1964. The properties of streptavidin, a biotin binding protein produced by streptomyces. Arch Biochem Biophys 106:1-5.
5. Chilkoti A, Stayton PS. 1995. Molecular origins of the slow streptavidin-biotin dissociation kinetics. J Am Chem Soc 117:10622-10628.
6. Chilkoti A, Tan PH, Stayton PS. 1995. Site-directed mutagenesis studies of the high-affinity streptavidin-biotin complex: Contributions of the tryptophan residues 79, 108 and 120. Proc Natl Acad Sci USA 92:1754-1758.
7. Devlin JJ, Panganiban LC, Devlin DE. 1990. Random peptide libraries: A source of specific protein binding molecules. Science 249:404-406.
8. Engh RA, Huber R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A47:392-400.
9. Giebel LB, Cass RT, Milligan DL, Young DC, Arze R, Johnson CR. 1995. Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities. Biochemistry 34:15430-15435.
10. Green NM. 1975. Avidin. Adv Protein Chem 29:85-143.
11. Hemming SA, Bochkarev A, Darst SA, Kornberg RD, Ala P, Yang DSC, Edwards AM. 1995. The mechanism of protein crystal growth from lipid layers. J Mol Biol 246:308-316.
12. Hendrickson WA, Pähler A, Smith JL, Satow Y, Merrit EA, Phizackerley RP. 1989. Crystal structure of core streptavidin determined from multiwave-length anomalous diffraction of synchrotron radiation. Proc Natl Acad Sci USA 86:2190-2194.
13. Higashi T. 1990. PROCESS: A program for indexing and processing R-AXIS II imaging plate data. Tokyo: Rigaku Corp.
14. Howard AJ, Gilliland GL, Finzel BC, Poulos TL, Ohlendorf DH, Salemme FR. 1987. The use of an imaging proportional counter in macromolecular crystallography. J Appl Crystallogr 20:383-387.
15. Hutchinson EG, Thornton JM. 1996. PROMOTIF - A program to identify and analyze structural motifs in proteins. Protein Sci 5:212-220.
16. Jones ML, Kurzban GP. 1995. Noncooperativity of biotin binding to tetrameric streptavidin. Biochemistry 34:11750-11756.
17. Katz BA. 1995. Binding to protein targets of peptidic leads discovered by phage display: Crystal structures of streptavidin bound linear and cyclic peptide ligands containing the HPQ sequence. Biochemistry 34:15421-15429.
18. Katz BA, Stroud RM, Collins N, Liu B, Arze R. 1995a. Topochemistry for preparing ligands that dimerize receptors. Chem Biol 2:591-600.
19. Katz BA, Cass RT, Liu B, Arze R, Collins N. 1995b. Topochemical catalysis achieved by structure-based ligand design. J Biol Chem 270:31210-31218.
20. Katz BA. 1996. Preparation of a protein-dimerizing ligand by topochemistry and structure-based design. J Am Chem Soc 118:2535-2536.
21. Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
22. Kurzban GP, Bayer EA, Wilchek M, Horowitz PM. 1991. The quaternary structure of streptavidin in urea. J Biol Chem 266:14470-14477.
23. Lam KS, Salmon SE, Hersh EM, Hruby VJ, Kazmurski WM, Knapp RJ. 1991. A new type of synthetic peptide library for identifying ligand binding activity. Nature 354:82-84.
24. Laskowski RA, Mac-Arthur MW, Moss DS, Thomton JM. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291.
25. Livnah O, Bayer EA, Wilchek M, Sussman JL. 1993. Three-dimensional structures of avidin and the avidin-biotin complex. Proc Natl Acad Sci USA 90:5076-5080.
26. McRee DE. 1992. A visual protein crystallographic software system for X11/XView. J Mol Graph 10:44-46.
27. Moews PC, Kretsinger RH. 1975. Refinement of the structure of carp muscle calcium-binding parvalbumin by model building and difference fourier analysis. J Mol Biol 91:201-228.
28. Morag E, Bayer EA, Wilchek M. 1996. Reversibility of biotin-binding by selective modification of tyrosine in avidin. Biochem J 316:193-199.
29. Pahler A, Hendrickson WA, Gawinowicz Kolks MA, Argaraña CA, Cantor CR. 1987. Characterization and crystallization of core streptavidin. J Biol Chem 262:13933-13937.
30. Parkin S, Moezzi B, Hope H. 1995. XABS2: An empirical absorption correction program. J Appl Crystallogr 25:53-56.
31. Pugliese L, Coda A, Malcovati M, Bolognesi M. 1993. Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 Å resolution. J Mol Biol 231:698-710.
32. Rossmann MG. 1972. The molecular replacement method. New York: Gordon and Breach.
33. Sano T, Cantor CR. 1990. Cooperative biotin binding by streplavidin. J Biol Chem 265:3369-3373.
34. Schmidt TGN, Koepke J, Frank R, Skerra A. 1996. Molecular interactions between the strep-tag affinity peptide and its cognate target, streptavidin. J Mol Biol 255:753-766.
35. Sheldrick GM. 1996. SHELXL-96, program for structure refinement, β-test version. Göttingen: University of Göttingen.
36. Vriend G, Sander C. 1993. Quality control of protein models: Directional atomic contact analysis. J Appl Crystallogr 26:47-60.
37. Weber PC, Cox MJ, Salemme FR, Ohlendorf DH. 1987. Crystallographic data for streptomyces avidinii streptavidin. J Biol Chem 262:12728-12729.
38. Weber PC, Ohlendorf DH, Wendoloski JJ, Salemme FR. 1989. Structural origins of high-affinity biotin binding to streptavidin. Science 243:85-88.
39. Weber PC, Pantoliano MW, Thompson LD. 1992a. Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin. Biochemistry 31:9350-9354.
40. Weber PC, Wendoloski JJ, Pantoliano MW, Salemme FR. 1992b. Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin. J Am Chem Soc 114:3197-3200.
41. Weber PC, Pantoliano MW, Simons DM, Salemme FR. 1994. Structure-based design of synthetic azobenzene ligands for streptavidin. J Am Chem Soc 116:2717-2724.
42. Weber PC, Pantoliano MW, Salemme FR. 1995. Crystallographic and thermodynamic comparison of structurally diverse molecules binding to streptavidin. Acta Crystallogr D51:590-596.