The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin

Journal of Molecular Biology

Volumn 282, Issue 1, 1998, Pages 181-194

  Meekhof, Alison E ^a   Hamill, Stefan J ^a   Arcus, Vickery L ^a,b   Clarke, Jane ^a   Freund, Stefan M V ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Backbone dynamics; Boundary selection; Domain; Fibronectin type III; NMR

Indexed keywords

FIBRONECTIN; TENASCIN;

ACCURACY; ARTICLE; CARBOXY TERMINAL SEQUENCE; HUMAN; HYDROGEN BOND; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION;

EID: 0032508555     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2019     Document Type: Article

References (44)

1. Abragam, A. (1961). The Principles of Nuclear Magnetism, Clarendon Press, Oxford.
2. Akke, M., Liu, J., Cavanagh, J., Erickson, H. P. & Palmer, A. G. (1998). Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain. Nature Struct. Biol. 5, 55-59.
3. Baron, M., Norman, D. G. & Campbell, I. D. (1991). Protein modules. Trends Biochem. Sci. 16, 13-17.
4. Beeser, S. A., Goldenberg, D. P. & Oas, T. G. (1997). Enhanced protein flexibility caused by a destabilizing amino acid replacement in BPTI. J. Mol. Biol. 269, 154-164.
5. Bloom, M., Reeves, L. W. & Wells, E. J. (1965). Spin echoes and conformational exchange. J. Chem. Phys. 42, 1615-1624.
6. Bork, P. (1992). Mobile modules and motifs. Curr. Opin. Struct. Biol. 2, 413-421.
7. Bork, P. & Doolittle, R. (1992). Proposed acquisition of an animal protein domain by bacteria. Proc. Natl Acad. Sci. USA, 89, 8990-8994.
8. Brünger, A. T., Huber, R. & Karplus, M. (1987). Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain. Biochemistry, 26, 5153-5162.
9. Carr, P. A., Erickson, H. P. & Palmer, A. G. (1997). Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin. Structure, 5, 949-959.
10. Clarke, J., Hamill, S. J. & Johnson, C. M. (1997). Folding and stability of a fibronectin type III domain of human tenascin. J. Mol. Biol. 270, 771-778.
11. 15N NMR: comparisons with X-ray data on the fab. Proteins: Struct. Funct. Genet. 15, 290-311.
12. Derome, A. E. (1987). Modern NMR Techniques for Chemistry Research, Pergamon Press, Oxford.
13. Erickson, H. P. (1997). A tenascin knockout with a phenotype. Nature Genet. 17, 5-7.
14. 15N NMR relaxation. Biochemistry, 33, 5984-6003.
15. Forman-Kay, J. D., Clore, G. M. & Gronenborn, A. M. (1992). Relationship between electrostatics and redox function in human theoredoxin: characterization of pH titration shifts using two-dimensional homo- and heteronuclear NMR. Biochemistry, 31, 3442-3452.
16. 2O in protein NMR. Application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115, 12593-12594.
17. Hamill, S. J., Meekhof, A. E. & Clarke, J. (1998). Effects of boundary selection on the stability and folding of a fibronectin type III domain from human tenascin. Biochemistry, 37, 8071-8079.
18. 1H exchange. Biochemistry, 36, 2278-2290.
19. Improta, S., Politou, A. S. & Pastore, A. (1993). Immuno-globulin-like modules from titin I-band: extensible components of muscle elasticity. Structure, 4, 323-337.
20. 15N inverse detected heteronuclear NMR spectroscopy: application to staphyloccocal nuclease. Biochemistry, 28, 8972-8979.
21. Kay, L. E., Keifer, P. & Saarinen, T. (1992). Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Am. Chem. Soc. 114, 10663-10665.
22. Koradi, R., Billeter, M. & Wüthrich, K. (1996). MOLMOL: a program for display and analysis of macro-molecular structures. J. Mol. Graphics, 14, 51-55.
23. Kraulis, P. (1991). Molscript - a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
24. Lane, A. N. & Lefévre, J.-F. (1994). Nuclear magnetic resonance measurements of slow conformational dynamics in macromolecules. Methods Enzymol. 239, 596-619.
25. Leahy, D. J., Hendrickson, W. A., Aukhil, I. & Erickson, H. A. (1992a). Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. PDB file (1ten).
26. Leahy, D. J., Hendrickson, W. A., Aukhil, I. & Erickson, H. A. (1992b). Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. Science, 258, 987-991.
27. Leahy, D. J., Aukhil, I. & Erickson, H. A. (1996). 2.0 Å crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region. Cell, 84, 155-164.
28. Lim, W. A., Fox, R. O. & Richards, F. M. (1994). Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein Sem-5. Protein Sci. 3, 1261-1266.
29. Lipari, G. & Szabo, A. (1982a). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559.
30. Lipari, G. & Szabo, A. (1982b). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104, 4559-4570.
31. 15N NMR spectroscopy. Eur. J. Biochem. 219, 887-896.
32. Peng, J. W. & Wagner, G. (1992a). Mapping of spectral density functions using heteronuclear NMR relaxation measurements. J. Magn. Reson. 98, 308-332.
33. Peng, J. W. & Wagner, G. (1992b). Mapping of the spectral densities of N-H bond motions in eglin C using heternuclear relaxation measurements. Biochemistry, 31, 8571-8586.
34. Peng, J. W. & Wagner, G. (1994). Investigation of protein motions via relaxation measurements. Methods Enzymol. 239, 563-596.
35. Pfuhl, M., Improta, S., Politou, A. S. & Pastore, A. (1997). When a module is also a domain: the role of the N terminus in the stability and the dynamics of immunoglobulin domains from titin. J. Mol. Biol. 265, 242-256.
36. Phan, I. Q. H., Boyd, J. & Campbell, I. A. (1996). Dynamic studies of a fibronectin type I module pair at three frequencies: anisotropic modelling and direct determination of conformational exchange. J. Biomol. NMR, 8, 369-378.
37. Piotto, M., Saudek, V. & Sklenár, V. (1992). Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR, 2, 661-665.
38. Politou, A. S., Gautel, M. & Pastore, J. A. (1994). Immunoglobulin-type domains of titin are stabilized by amino-terminal extension. FEBS Letters, 352, 27-31.
39. Ringe, D. & Petsko, G. A. (1986). Study of protein dynamics by X-ray diffraction. Methods Enzymol. 131, 389-433.
40. Ross, A., Czisch, M. & King, G. C. (1997). Systematic errors associated with the CPMG pulse sequence and their effect on motional analysis of biomolecules. J. Magn. Reson. 124, 355-365.
41. Smith, B. O., Downing, A. K., Driscoll, P. C., Dudgeon, T. J. & Campbell, I. A. (1995). The solution structure and backbone dynamics of the fibronectin type I and epidermal growth factor-like pair of modules of tissue-type plasminogen activator. Structure, 3, 823-833.
42. Spitzfaden, C., Grant, R. P., Mardon, H. J. & Campbell, I. A. (1997). Module-module interactions in the cell binding region of fibronectin: stability, flexibility and specificity. J. Mol. Biol. 265, 565-579.
43. 15N NMR relaxation. J. Am. Chem. Soc. 117, 12562-12566.
44. Wyss, D., Dayie, K. T. & Wagner, G. (1997). The counterreceptor binding site of human CD2 exhibits and extended surface patch with multiple conformations fluctuating with millisecond to microsecond motions. Protein Sci. 6, 534-542.