2.0 Å crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region

Cell

Volumn 84, Issue 1, 1996, Pages 155-164

  Leahy, Daniel J ^a   Aukhil, Ikramuddin ^b   Erickson, Harold P ^c  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGINYL-GLYCYL-ASPARTIC ACID; ARGINYLGLYCYLASPARTIC ACID; FIBRONECTIN; OLIGOPEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; CRYSTALLOGRAPHY; HUMAN; IMAGE PROCESSING; MOLECULAR GENETICS; PROTEIN CONFORMATION; ULTRASTRUCTURE; BINDING SITE; CELL ADHESION; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY; FIBRONECTINS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MOLECULAR SEQUENCE DATA; OLIGOPEPTIDES; PROTEIN CONFORMATION;

EID: 0030050396     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81002-8     Document Type: Article

References (59)

1. Adler, M., Lazarus, R.A., Dennis, M.S., and Wagner, G. (1991). Solution structure of kistrin, a potent platelet aggregation inhibitor and GP IIb-IIIa antagonist. Science 253, 445-448.
2. Aota, S., Nagai, T., and Yamada, K.M. (1991). Characterization of regions of fibronectin besides the arginine-glycine-aspartic acid sequence required for adhesive function of the cell-binding domain using site-directed mutagenesis. J. Biol. Chem. 266, 15938-15943.
3. Aota, S., Nomizu, M., and Yamada, K.M. (1994). The short amino acid sequence Pro-His-Ser-Arg-Asn in human fibronectin enhances cell-adhesive function. J. Biol. Chem. 269, 24756-24761.
4. Aukhil, I., Joshi, P., Yan, Y., and Erickson, H.P. (1993). Cell-and heparin-binding domains of the hexabrachion arm identified by tenascin expression proteins. J. Biol. Chem. 268, 2542-2553.
5. Bork, P., and Doolittle, R. (1992). Proposed acquisition of an animal protein domain by bacteria. Proc. Natl. Acad. Sci. USA 89, 8990-8994.
6. a (platelet GPIIb-IIIa) recognizes multiple sites in fibronectin. J. Biol. Chem. 266, 23323-23328.
7. 3 integrins. J. Biol. Chem. 269, 10856-10863.
8. Brünger, A.T. (1990). Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta Crystallogr. A46, 46-57.
9. Brünger, A.T. (1992a). The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-474.
10. Brünger, A.T. (1992b). XPLOR, Version 3.1: A System for X-Ray Crystallography and NMR (New Haven, Connecticut: Department of Molecular Biophysics and Biochemistry, Yale University).
11. Carrell, N.A., Fitzgerald, L.A., Steiner, B., Erickson, H.P., and Phillips, D.R. (1985). Structure of human platelet membrane glycoproteins IIb and IIIa as determined by electron microscopy. J. Biol. Chem. 260, 1743-1749.
12. Chan, A.W.E., Hutchinson, E.G., Harris, D., and Thornton, J.M. (1993). Identification, classification, and analysis of β-bulges in proteins. Protein Sci. 2, 1574-1590.
13. Constantine, K.L., Madrid, M., Banyai, L., Trexler, M., Patthy, L., and Llinas, M. (1992). Refined solution structure and ligand-binding properties of PDC-109 domain b: a collagen-binding type II domain. J. Mol. Biol. 223, 281-298.
14. Craig, W.S., Cheng, S., Mullen, D.G., Blevitt, J., and Pierschbacher, M.. (1995). Concept and progress in the development of RGD-containing peptide pharmaceuticals. Biopolymers 37, 157-175.
15. Deisenhofer, J. (1981). Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B from Staphylococcus aureus at 2.9 and 2.8 Å resolution. Biochemistry 20, 2361-2370.
16. DeVos, A.M., Ultsch, M., and Kossiakoff, A.A. (1992). Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 255, 306-312.
17. Dickinson, C.D., Veerapandian, B., Dai, X.P., Hamlin, R.C., Xuong, N.H., Ruoslahti, E., and Ely, K.R. (1994). Crystal structure of the tenth type III cell adhesion module of human fibronectin. J. Mol. Biol. 236, 1079-1092.
18. Doolittle, R.F. (1986). Of URFs and ORFs (Mill Valley, California: University Science Books).
19. Engel, J., Odermatt, E., Engel, A., Madri, J.A., Furthmayr, H., Rohde, H., and Timpl, R. (1981). Shapes, domain organizations and flexibility of laminin and fibronectin, two multifunctional proteins of the extracellular matrix. J. Mol. Biol. 150, 97-120.
20. Erickson, H.P., and Carrell, N.A. (1983). Fibronectin in extended and compact conformations: electron microscopy and sedimentation analysis. J. Biol. Chem. 258, 14539-14544.
21. Erickson, H.P., Carrell, N., and McDonagh, J. (1981). Fibronectin molecule visualized in electron microscopy: a long, thin flexible strand. J. Cell Biol. 91, 673-678.
22. Gurrath, M., Muller, G., Kessler, H., Aumailley, M., and Timpl, R. (1992). Conformation/activity studies of rationally designed potent anti-adhesive RGD peptides. Eur. J. Biochem. 210, 911-921.
23. Hendrickson, W.A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58.
24. Hendrickson, W.A., Horton, J.R., and LeMaster, D.M. (1990). Seleno-methionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665-1672.
25. Hodel, A., Kim, S.-H., and Brünger, A.T. (1992). Model bias in macromolecular crystal structures. Acta Crystallogr. A48, 851-858.
26. Huber, A.H., Wang, Y.M., Bieber, A.J., and Bjorkman, P.J. (1994). Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 Å. Neuron 12, 717-731.
27. Hynes, R.O. (1990). Fibronectins (New York: Springer-Verlag).
28. Jones, E.Y., Davis, S.J., Williams, A.F., Harlos, K., and Stuart, D.I. (1992). Crystal structure at 2.8Å resolution of a soluble form of the cell adhesion molecule CD2. Nature 360, 232-239.
29. Jones, T.A., and Kjeldgaard, M. (1991). Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110-119.
30. Joshi, P., Chung, C.Y., Aukhil, I., and Erickson, H.P. (1993). Endothelial cells adhere to the RGD domain and the fibrinogen-like terminal knob of tenascin. J. Cell Sci. 106, 389-400.
31. Kabsch, W., and Sander, C. (1983). Dictionary of protein secondary structures: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 1-17.
32. Kornblihht, A.R., Umezawa, K., Vibe-Pedersen, K., and Baralle, F.E. (1985). Primary structure of human fibronectin: differential splicing may generate at least 10 polypeptides from a single gene. EMBO J. 4, 1755-1759.
33. Kossiakoff, A.A., Randal, M., Guenot, J., and Eigenbrot, C. (1992). Variability of conformations at crystal contacts in BPTI represent true low-energy structures: correspondence among lattice packing and molecular dynamics structures. Proteins 14, 65-74.
34. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of proteins. J. Appl. Crystallogr. 24, 946-950.
35. Krezel, A.M., Wagner, G., Seymour-Ulmer, J., and Lazarus, R.A. (1994). Structure of the RGD protein decorsin: conserved motif and distinct function in leech proteins that affect blood clotting. Science 264, 1944-1947.
36. Kunkel, T.A., Roberts, J.D., and Azkour, R.A. (1987). Rapid and efficient site-specific mutagenesis without phenotype selection. Meth. Enzymol. 154, 367-384.
37. Lai, C.S., Wolff, C.E., Novello, D., Griffone, L., Cuniberti, C., Molina, F., and Rocco, M. (1993). Solution structure of human plasma fibronectin under different solvent conditions: fluorescence energy transfer, circular dichroism, and light-scattering studies. J. Mol. Biol. 230, 625-640.
38. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993). PROCHECK: a program to check stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
39. Leahy, D.J., Hendrickson, W.A., Aukhil, I., and Erickson, H.P. (1992). Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. Science 258, 987-991.
40. Leahy, D.J., Erickson, H.P., Aukhil, I., Joshi, P., and Hendrickson, W. A. (1994). Crystallization of a fragment of human fibronectin: introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine. Proteins 19, 48-54.
41. Litvinovich, S.V., and Ingham, K.C. (1995). Interactions between type III domains in the 110 kDa cell-binding fragment of fibronectin. J. Mol. Biol. 248, 611-626.
42. Main, A.L., Harvey, T.S., Baron, M., Boyd, J., and Campbell, I.D. (1992). The three-dimensional structure of the tenth type III molule of fibronectin: an insight into RGD-mediated interactions. Cell 71, 671-678.
43. Otwinowski, Z. (1993). Oscillation data reduction program. In Data Collection and Processing, L. Sawyer, N. Isaacs, and S. Bailey, eds. (Warrington, England: Science and Engineering Research Council/ Daresbury Laboratory), pp. 56-62.
44. Petersen, T.E., Thogersen, H.C., Skorstengaard, K., Vibe-Pedersen, K., Sahl, P., Sottrup-Jensen, L., and Magnusson, S. (1983). Partial primary structure of bovine plasma fibronectin: three types of internal homology. Proc. Natl. Acad. Sci. USA 80, 137-141.
45. Pierschbacher, M.D., and Ruoslahti, E. (1984). Cell attachment activity of fibronectin can be duplicated by small synthetic fragments of the molecule. Nature 309, 30-33.
46. Pierschbacher, M.D., and Ruoslahti, E. (1987). Influence of stereo-chemistry of the sequence Arg-Gly-Asp-Xaa on binding specificity in cell adhesion. J. Biol. Chem. 262, 17294-17298.
47. Potts, J.R., and Campbell, I.D. (1994). Fibronectin structure and assembly. Curr. Opin. Cell Biol. 6, 648-655.
48. Richardson, J.S. (1981). The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167-339.
49. Rocco, M., Carson, M., Hantgan, R., McDonagh, J., and Hermans, J. (1983). Dependence of the shape of the plasma fibronectin molecule on solvent composition, ionic strength and glycerol content. J. Biol. Chem. 258, 14545-14549.
50. Ruoslahti, E., and Pierschbacher, M.D. (1987). New perspectives in cell adhesion: RGD and integrins. Science 238, 491-497.
51. Ryu, S.-E., Kwong, P.D., Truneh, A., Porter, T.G., Arthos, J., Rosenberg, M., Dai, X., Xuong, N.-H., Axel, R., Sweet, R.W., and Hendrickson, W.A. (1990). Crystal structure of an HIV-binding recombinant fragment of human CD4. Nature 348, 419-426.
52. Ryu, S.-E., Truneh, A., Sweet, R.W., and Hendrickson, W.A. (1994). Structures of an HIV and MHC binding fragment from human CD4 as refined in two crystal lattices. Structure 2, 59-74.
53. Saudek, V., Atkinson, R.A., and Pelton, J.T. (1991). Three-dimensional structure of echistatin, the smallest active RGD protein. Biochemistry 30, 7369-7372.
54. Studier, F.W., Rosenberg, A.H., Junn, J.J., and Dubendorff, J.W. (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Meth. Enzymol. 185, 60-89.
55. Tamkun, J.W., Schwarzbauer, J.E., and Hynes, R.O. (1984). A single rat fibronectin gene generates three different mRNAs by alternative splicing of a complex exon. Proc. Natl. Acad. Sci. USA 81, 5140-5144.
56. Wang, J., Yan, Y., Garrett, T.P. J., Liu, J., Rodgers, D.W., Garlick, R. L., Tarr, G.E., Husain, Y., Reinherz, E.L., and Harrison, S.C. (1990). Atomic structure of a fragment of human CD4 containing two immunoglobulin-like domains. Nature 348, 411-418.
57. Williams, M.J., Phan, I., Harvey, T.S., Rostagno, A., Gold, L.I., and Campbell, I.D. (1994). Solution structure of a pair of fibronectin type 1 modules with fibrin binding activity. J. Mol. Biol. 235, 1302-1311.
58. Wu, H., Lustbader, J.W., Liu, Y., Canfield, R.E., and Hendrickson, W.A. (1994). Structure of human chorionic gonadotropin at 2.6 Å resolution from MAD analysis of the selenomethionyl protein. Structure 2, 545-558.
59. Yamada, T., Song, H., Inaka, K., Shimada, Y., Kikuchi, M., and Matsushima, M. (1995). Structure of a conformationally constrained Arg-Gly-Asp sequence inserted into human lysozyme. J. Biol. Chem. 270, 5687-5690.