Solution structure of the VEGF-binding domain of Flt-1: Comparison of its free and bound states

Journal of Molecular Biology

Volumn 293, Issue 3, 1999, Pages 531-544

  Starovasnik, Melissa A ^a   Christinger, Hans W ^a   Wiesmann, Christian ^a   Champe, Mark A ^a   De Vos, Abraham M ^a   Skelton, Nicholas J ^a  

^a GENENTECH INC   (United States)

Author keywords

Flt 1; Immunoglobulin like domain; NMR; VEGF receptor; X ray crystallography

Indexed keywords

FLT1; GROWTH FACTOR RECEPTOR; IMMUNOGLOBULIN; NITROGEN 15; PLATELET DERIVED GROWTH FACTOR; PROTON; UNCLASSIFIED DRUG; VASCULOTROPIN; VASCULOTROPIN RECEPTOR;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; HUMAN; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 0032735130     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3134     Document Type: Article

References (58)

1. Aho A. V., Kernighan B. W., Weinberger P. J. The AWK Programming Language. 1988;Addison-Wesley, Reading.
2. 15N with side-chain Hβ resonances in larger proteins. J. Magn. Reson. 95:1991;636-641.
3. Barleon B., Totzke F., Herzog C., Blanke S., Kremmer E., Siemeister G., Marmé D., Martiny-Baron G. Mapping of the sites for ligand binding and receptor dimerization at the extracellular domain of the vascular endothelial growth factor receptor FLT-1. J. Biol. Chem. 272:1997;10382-10388.
4. Bartels C., Billeter M., Güntert P., Wüthrich K. Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J. Biomol. NMR. 7:1996;207-213.
5. Blechman J. M., Lev S., Barg J., Eisenstein M., Vaks B., Vogel Z., Givol D., Yarden Y. The fourth immunoglobulin domain of the stem cell factor receptor couples ligand binding to signal transduction. Cell. 80:1995;103-113.
6. Brünger A. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature. 355:1992;472-475.
7. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 235:1987;458-460.
8. Carmeliet P., Ferreira V., Breier G., Pollefeyt S., Kieckens L., Gertsenstein M., Fahrig M., Vandenhoeck A., Harpal K., Eberhardt C., Declercq C., Pawling J., Moons L., Collen D., Risau W., Nagy A. Abnormal blood vessel development and lethality in embryos lacking a single VEGF allele. Nature. 380:1996;435-439.
9. Carter P., Nilsson B., Burnier J. P., Burdick D., Wells J. A. Engineering subtilisin BPN′ for site-specific proteolysis. Proteins: Struct. Funct. Genet. 6:1989;240-248.
10. Cavanagh J., Fairbrother W., Palmer A. III, Skelton N. Protein NMR Spectroscopy: Principles and Practice. 1995;Academic Press, San Diego.
11. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
12. Christinger H., Muller Y., Berleau L., Keyt B., Cunningham B., Ferrara N., de Vos A. Crystallization of the receptor binding domain of vascular endothelial growth factor. Proteins: Struct. Funct. Genet. 26:1996;353-357.
13. 13C-separated rotating frame Overhauser spectroscopy. J. Biomol. NMR. 1:1991;13-22.
14. Cunningham S. A., Stephan C. C., Arrate M. P., Ayer K. G., Brock T. A. Identification of the extracellular domains of Flt-1 that mediate ligand interactions. Biochem. Biophys. Res. Commun. 231:1997;596-599.
15. Davis-Smyth T., Chen H., Park J., Presta L. G., Ferrara N. The second immunoglobulin-like domain of the VEGF tyrosine kinase receptor Flt-1 determines ligand binding and may initiate a signal transduction cascade. EMBO J. 15:1996;4919-4927.
16. de Vries C., Escobedo J. A., Ueno H., Houck K., Ferrara N., Williams L. T. The fms-like tyrosine kinase, a receptor for vascular endothelial growth factor. Science. 255:1992;989-991.
17. 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor. Protein Sci. 6:1997;2250-2260.
18. Ferrara N., Davis-Smyth T. The biology of vascular endothelial growth factor. Endocrine Rev. 18:1997;4-25.
19. Ferrara N., Carver-Moore K., Chen H., Dowd M., Lu L., O'Shea K. S., Powell-Braxton L., Hillan K. J., Moore M. W. Heterozygous embryonic lethality induced by targeted inactivation of the VEGF gene. Nature. 380:1996;439-442.
20. Fong G.-H., Rossant J., Gertsenstein M., Breltman M. L. Role of the Flt-1 receptor tyrosine kinase in regulating the assembly of vascular endothelium. Nature. 376:1995;66-70.
21. Fuh G., Li B., Crowley C., Cunningham B., Wells J. A. Requirements for binding and signaling of the kinase domain receptor for vascular endothelial growth factor. J. Biol. Chem. 273:1998;11197-11204.
22. Graña D., Gardella T., Susskind M. M. The effects of mutations in the ant promoter of phage P22 depend on context. Genetics. 120:1988;319-327.
23. Gronwald W., Willard L., Jellard T., Boyko R. F., Rajarathnam K., Wishart D. S., Sönnichsen F. D., Sykes B. D. CAMRA: chemical shift based computer aided protein NMR assignments. J. Biomol. NMR. 12:1998;395-405.
24. 2O in protein NMR. Applications to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115:1993;12593-12594.
25. Harpaz Y., Chothia C. Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains. J. Mol. Biol. 238:1994;528-539.
26. Havel T. F. An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog. Biophys. Mol. Biol. 56:1991;43-78.
27. Hiratsuka S., Minowa O., Kuno J., Noda T., Shibuya M. Flt-1 lacking the tyrosine kinase domain is sufficient for normal development and angiogenesis in mice. Proc. Natl Acad. Sci. USA. 95:1998;9349-9354.
28. Holden H. M., Ito M., Hartshorne D. J., Rayment I. X-ray structure determination of telokin, the C-terminal domain of myosin light chain kinase at 2.8 Å resolution. J. Mol. Biol. 227:1992;840-851.
29. Hyberts S. G., Goldberg M. S., Havel T. F., Wagner G. The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci. 1:1992;736-751.
30. Kessler H., Griesinger C., Lautz J., Müller A., van Gunsteren W. F., Berendsen H. J. C. Conformational dynamics detected by nuclear magnetic resonance NOE values and J coupling constants. J. Am. Chem. Soc. 110:1988;3393-3396.
31. Klagsbrun M., D'Amore P. A. Vascular endothelial growth factor and its receptors. Cytokine Growth Factor Rev. 7:1996;259-270.
32. Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallog. 24:1991;946-950.
33. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
34. Lemmon B. A., Pinchasi D., Zhou M., Lax I., Schlessinger J. Kit receptor dimerization is driven by bivalent binding of stem cell factor. J. Biol. Chem. 272:1997;6311-6317.
35. Mahadevan D., Yu J.-C., Saldanha J. W., Thanki N., McPhie P., Uren A., LaRochelle W. J., Heidaran M. A. Structural role of the extracellular domain-1 of α-platelet-derived growth factor (PDGF) receptor for PDGF-AA and PDGF-BB binding. J. Biol. Chem. 270:1995;27595-27600.
36. Meadows R. P., Olejniczak E. T., Fesik S. W. A computer-based protocol for semiautomated assignments and 3D structure determination of proteins. J. Biomol NMR. 4:1994;79-96.
37. 2O solution. J. Magn. Reson. 85:1989;608-613.
38. Mumenthaler C., Güntert P., Braun W., Wüthrich K. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR. 10:1997;351-362.
39. 13C labeling. Biochemistry. 28:1989;7510-7516.
40. Park J. E., Chen H. H., Winer J., Houck L. A., Ferrara N. Placenta growth factor. Potentiation of vascular growth factor bioactivity, in vitro and in vivo, and high affinity binding to Flt-1 but not Flk-1/KDR. J. Biol. Chem. 269:1994;25646-25654.
41. Rossman M. G. The Molecular Replacement Method: A Collection of Papers on the Use of Non-crystallographic Symmetry. 1972;Gordon and Breach, New York.
42. Seetharam L., Gotoh N., Maru Y., Neufeld G., Yamaguchi S., M S. A unique signal transduction pathway for the FLT tyrosine kinase, a receptor for vascular endothelial growth factor. Oncogene. 10:1995;135-147.
43. 13C labeling. FEBS Letters. 249:1989;113-118.
44. Shalaby F., Rossant J., Yamaguchi R. P., Gertsenstein M., Wu W.-F., Breitman M. L., Schuh A. C. Failure of blood-island formation and vasculogenesis in flk-1 deficient mice. Nature. 376:1995;62-66.
45. Shibuya M., Yamaguchi S., Yamane A., Ikeda T., Tojo A., Matsushime H., Sato M. Nucleotide sequence and expression of a novel human receptor-type tyrosine kinase gene (flt) closely related to the fms family. Oncogene. 5:1990;519-524.
46. Skelton N. J., Akke M., Kördel J., Palmer A. G. P., Rance M., Chazin W. J. Practical aspects of the measurement of heteronuclear relaxation parameters. J. Magn. Reson. B. 102:1993;253-264.
47. Starovasnik M. A., Skelton N. J., O'Connell M. P., Kelley R. F., Reilly D., Fairbrother W. J. Solution structure of the E-domain of Staphylococcal protein A. Biochemistry. 35:1996;15558-15569.
48. 15N NMR relaxation measurements. Biochemistry. 31:1992;4394-4406.
49. Terman B. C., Dougher-Vermazen M., Carrion M. E., Dimitrov D., Armellino D. C., Gospodarowicz D., Böhlen P. Identification of the KDR tyrosine kinase as a receptor for vascular endothelial growth factor. Biochem. Biophys. Res. Commun. 187:1992;1579-1586.
50. Van der Greer P., Hunter T., Lindberg R. A. Receptor protein-tyrosine kinases and their signal transduction pathways. Annu. Rev. Cell Biol. 10:1994;251-337.
51. Waltenberger J., Claesson-Welsh L., Siegbahn A., Shibuya M., Heldin D.-H. Different signal transduction properties of KDR and Flt1, two receptors for vascular endothelial growth factor. J. Biol. Chem. 269:1994;26988-26995.
52. Weiner S. J., Kollman P. A., Case D. A., Singh U. C., Ghio C., Alagona G. S., Profeta J., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
53. Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:1986;230-252.
54. Wiesmann C., Fuh G., Christinger H. W., Eigenbrot C., Wells J. A., de Vos A. M. Crystal structure at 1.7 Å resolution of VEGF in complex with domain 2 of the Flt-1 receptor. Cell. 91:1997;695-704.
55. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;J. Wiley and Sons, New York.
56. 13C-labeled proteins. J. Biomol. NMR. 7:1996;99-106.
57. Zimmerman D., Montelione G. Automated analysis of nuclear magnetic resonance assignments for proteins. Curr. Opin. Struct. Biol. 5:1995;664-673.
58. Zimmerman D., Kulikowski C., Huang Y., Feng W., Tashiro M., Shimotakahara S., Chien C., Powers R., Montelione G. Automated analysis of protein NMR assignments using methods from artificial intelligence. J. Mol. Biol. 269:1997;592-610.