Crystal structure of human fibrinogen

Biochemistry

Volumn 48, Issue 18, 2009, Pages 3877-3886

  Kollman, Justin M ^a,c   Pandi, Leela ^a   Sawaya, Michael R ^b   Riley, Marcia ^a   Doolittle, Russell F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

C-DOMAIN; COILED COIL; CRYSTAL PACKINGS; DATA COLLECTION; DEAE CELLULOSE; ELECTRON DENSITIES; ETHANOL PRECIPITATION; GEL ELECTROPHORESIS; HUMAN BLOOD PLASMAS; NEIGHBORING MOLECULES; SDS-POLYACRYLAMIDE GEL; SUGAR RESIDUES; TERMINAL SEQUENCING; WEAK FORCE; X RAY CRYSTALS;

AMINES; BLOOD; CHROMATOGRAPHIC ANALYSIS; CRYSTALS; DIFFUSERS (OPTICAL); ELECTROPHORESIS; ETHANOL; GELATION; GELS; SUGAR (SUCROSE); SUGARS;

CRYSTAL STRUCTURE;

ALCOHOL; CARBOHYDRATE; FIBRINOGEN;

ALPHA CHAIN; AMINO TERMINAL SEQUENCE; ARTICLE; BETA CHAIN; CHICKEN; CRYSTAL STRUCTURE; HUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRECIPITATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN PURIFICATION; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

CHROMATOGRAPHY, DEAE-CELLULOSE; CRYSTALLOGRAPHY, X-RAY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FIBRINOGEN; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

BOVINAE;

EID: 66149138396     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi802205g     Document Type: Article

References (60)

1. Scheraga, H. A., and Laskowski, M.Jr. (1957) The fibrinogen-fibrin conversion. Adv. Protein Chem. 12, 1-131.
2. Doolittle, R. F. (1973) Structural aspects of the fibrinogen to fibrin conversion. Adv. Protein Chem. 27, 1-109.
3. Weisel, J. (2006) Fibrinogen and fibrin. Adv. Protein Chem. 77, 247-299. (Pubitemid 40544785)
4. Yee, V. C., Pratt, K. P., Cote, H. C., LeTrong, I., Chung, D. W., Davie, E. W., Stenkamp, R. E., and Teller, D. C. (1997) Crystal structure of a 30 kDa C-terminal fragment from the γ chain of human fibrinogen. Structure 5, 125-138. (Pubitemid 27102863)
5. Spraggon, G., Everse, S. J., and Doolittle, R. F. (1997) Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin. Nature 389, 455-462. (Pubitemid 27435313)
6. EC domain from human fibrinogen-420. Proc. Natl. Acad. Sci. U.S.A. 95, 9099-9104.
7. Everse, S. J., Spraggon, G., Verrapandian, L., Riley, M., and Doolittle, R. F. (1999) Crystal structure of fragment double-D from human fibrin with two different bound ligands. Biochemistry 38, 2941-2946.
8. Everse, S. J., Spraggon, G., Veerapandian, L., and Doolittle, R. F. (1999) Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide. Biochemistry 38, 2941-2946. (Pubitemid 129501348)
9. Madrazo, J., Brown, J. H., Litvinovich, S., Dominguez, R., Yakovlev, S., Medved, L., and Cohen, C. (2001) Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4 angstroms resolution. Proc. Natl. Acad. Sci. U.S.A. 98, 11967-11972. (Pubitemid 32959810)
10. Yang, Z., Spraggon, G., Pandi, L., Everse, S. J., Riley, M., and Doolittle, R. F. (2002) Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide. Biochemistry 41, 10218-10224.
11. Yang, Z., Pandi, L., and Doolittle, R. F. (2002) The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface. Biochemistry 41, 15610-15617. (Pubitemid 36062465)
12. Kostelansky, M. S., Betts, L., Gorkkun, O. V., and Lord, S. T. (2002) 2.8 Å crystal structures of recombinant fibrinogen fragment D with and without two peptide ligands: GHRP binding to the "b" site disrupts its nearby calcium-binding site. Biochemistry 41, 12124-12132.
13. Pechik, I., Madrazo, J., Mosesson, M., Hernandez, I., Gilliland, G. J., and Medved, L. (2004) Crystal structure of the complex between thrombin and the central "E" region of fibrin. Proc. Natl. Acad. Sci. U.S.A. 101, 2718-2723.
14. Kostelansky, M. S., Bollinger-Stucki, B., Betts, L., Gorkun, O. V., and Lord, S. T. (2004) BβGlu397 and BβAsp398 but not BβAsp432 are required for "B:b" interactions. Biochemistry 43, 2465-2474.
15. Doolittle, R. F., Chen, A., and Pandi, L. (2006) Differences in binding specificity for the homologous γ- and β-chain "holes" on fibrinogen: Exclusive binding of Ala-His-Arg-Pro-amide by the β-chain hole. Biochemistry 45, 13962-13969.
16. Doolittle, R. F., and Pandi, L. (2007) Probing the β-chain holes of fibrinogen with synthetic peptides that differ at their amino termini. Biochemistry 46, 10033-10038. (Pubitemid 47378594)
17. Yang, Z., Mochalkin, I., Veerapandian, L., Riley, M., and Doolittle, R. F. (2000) Crystal structure of native chicken fibrinogen at 5.5 Å resolution. Proc. Natl. Acad. Sci. U.S.A. 97, 3907-3912. (Pubitemid 30226060)
18. Yang, Z., Kollman, J. M., Pandi, L., and Doolittle, R. F. (2001) Crystal structure of a native chicken fibrinogen at 2.7 Å resolution. Biochemistry 40, 12515-12523. (Pubitemid 32979704)
19. Weissbach, L., and Grieninger, G. (1990) Bipartite mRNA for chicken α-fibrinogen potentially encodes an amino acid sequence homologous to β- and γ-fibrinogens. Proc. Natl. Acad. Sci. U.S.A. 87, 5198-5202. (Pubitemid 20224300)
20. Brown, J. H., Volkmann, N., Jun, G., Henschen-Edman, A., and Cohen, C. (2000) The crystal structure of modified bovine fibrinogen. Proc. Natl. Acad. Sci. U.S.A. 97, 85-90. (Pubitemid 30055788)
21. Doolittle, R. F. (2003) Some notes on crystallizing fibrinogen and fibrin fragments. Biophys. Chem. 100, 307-313. (Pubitemid 36338048)
22. Williams, R. C. (1981) Morphology of bovine fibrinogen and fibrin polymers. J. Mol. Biol. 150, 399-408.
23. Yang, Z. (2000) A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides. Proc. Natl. Acad. Sci. U.S.A. 97, 14156-14161. (Pubitemid 32016546)
24. Doolittle, R. F., and Pandi, L. (2006) Binding of synthetic B knobs to fibrinogen changes the character of fibrin and inhibits its ability to activate tissue plasminogen activator and its destruction by plasmin. Biochemistry 45, 2657-2667. (Pubitemid 43297325)
25. Merrifield, R. B. (1964) Solid phase peptide synthesis. 3. An improved synthesis of bradykinin. Biochemistry 3, 1385-1390.
26. Doolittle, R. F., Schubert, D., and Schwartz, S. A. (1967) Amino acid sequence studies on artiodactyls fibrinopeptides. I. Dromedary camel, mule deer and Cape Buffalo. Arch. Biochem. Biophys. 118, 456-467.
27. Finlayson, J. S., and Mosesson, M. W. (1963) Heterogeneity of human fibrinogen. Biochemistry 2, 42-46.
28. Mosesson, M. W., Finlayson, J. S., Umfleet, R. A., and Galanakis, D. (1972) Human fibrinogen heterogeneities. I. Structural and related studies of plasma fibrinogens which are high solubility catabolic intermediates. J. Biol. Chem. 247, 5210-5219.
29. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326. (Pubitemid 27085611)
30. Kabsch, W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell contants. J. Appl. Crystallogr. 26, 795-800.
31. Navaza, J. (2001) Implementation of molecular replacement in AmoRe. Acta Crystallogr. D57, 1367-1372. (Pubitemid 36117184)
32. Collaborative Computational Project Number 4 (1994) Acta Crystallogr. D50, 760-763.
33. McCoy, A. J., Grosse-Kunstleve, R. W., Storone, L. C., and Read, R. J. (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr. D61, 458-464. (Pubitemid 43934606)
34. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110-119.
35. Brunger, A. T., Adams, P. D., Chlore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905-921. (Pubitemid 28443603)
36. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255. (Pubitemid 27235885)
37. Hodel, A., Kim, S.-H., and Brunger, A. T. (1992) Model bias in macromolecular crystal structures. Acta Crystallogr. A48, 851-858.
38. Delano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA..
39. Strong, M., Sawaya, M. R., Wang, S., Phillips, M., Cascio, D., and Eisenberg, D. (2006) Toward a structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 103, 8060-8065. (Pubitemid 43801052)
40. Winn, M. D., Isupov, M. N., and Murshudov, G. N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D57, 122-133. (Pubitemid 32062682)
41. Painter, J., and Merritt, E. A. (2006) TLSMD web server for the generation of multi-group TLS models. J. Appl. Crystallogr. 39, 109-111.
42. Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132. (Pubitemid 41742764)
43. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
44. Read, R. J., and Kleywegt, G. J. (2009) Case-controlled stucture validation. Acta Crystallogr. D65, 140-147.
45. Hanss, M., and Biot, F. (2001) A database for human fibrinogen variants. Ann. N.Y. Acad. Sci. 936, 89-90. (Pubitemid 32613894)
46. Doolittle, R. F., and Kollman, J. M. (2006) Natively unfolded regions of the vertebrate fibrinogen molecule. Proteins 63, 391-397.
47. Burton, R. A., Tsurupa, G., and Medved, L..; et al. (2006) Identification of an ordered compact structure within the recombinant bovine fibrinogen αC domain fragment by NMR. Biochemistry 45, 2257-2266. (Pubitemid 43271325)
48. Burton, R. A., Tsurupa, G., and Hantgan, R. R..; et al. (2007) NMR solution structure, stability and interaction of the recombinant bovine fibrinogen αC domain fragment. Biochemistry 46, 8550-8560.
49. Townsend, R. R., Hilliker, E., Li, Y.-T., Laine, R. A., Bell, W. R., and Lee, Y. C. (1982) Carbohydrate structure of human fibrinogen. J. Biol. Chem. 257, 9704-9710.
50. Wu, P., Lee, K. B., Lee, Y. C., and Brand, L. (1996) Solution conformations of a biantennary glycopeptide and a series of its exoglycosidase products from sequential trimming of sugar residues. J. Biol. Chem. 271, 1470-1474. (Pubitemid 26028632)
51. Langer, B. G., Weisel, J. W., Dinauer, P. A., Nagaswami, C., and Bell, W. R. (1988) Deglycosylation of fibrinogen accelerates polymerization and increases lateral aggregation of fibrin fibers. J. Biol. Chem. 263, 15056-15063. (Pubitemid 18251937)
52. Okude, M., Yamanaka, A., Morimoto, Y., and Akihama, S. (1993) Sialic acid in fibrinogen: Effects of sialic acid on fibrinogen-fibrin conversion by thrombin and properties of asialofibrin clot. Biol. Pharm. Bull. 16, 448-452. (Pubitemid 23208660)
53. Doolittle, R. F., Goldbaum, D. M., and Doolittle, L. R. (1978) Designation of sequences involved in the "coiled-coil" interdomainal connections if fibrinogen: Construction of an atomic scale model. J. Mol. Biol. 120, 311-325.
54. Doolittle, R. F., Cassman, K. G., Cottrell, B. A., Friezner, S. J., and Takagi, T. (1977) Amino acid sequence studies on the α chain of human fibrinogen. Covalent structure of the α-chain portion of fragment D. Biochemistry 16, 1710-1715.
55. Marchi, R. C., Meyer, M. H., de Bosch, N. B., Arocha-Pinango, C. L., and Weisel, J. W. (2004) A novel mutation (deletion of Aα-Asn 80) in an abnormal fibrinogen: Fibrinogen Caracas VI. Consequences of disruption of the coiled-coil for the polymerization of fibrin: Peculiar clot structure and diminished stiffness of the clot. Blood Coagulation Fibrinolysis 15, 550-567.
56. Okumura, N., Terasawa, F., Hirota-Kawadobora, M., Yamauchi, K., Nakanishi, K., Shia, S., Ichiyama, S., Saito, M., Kawai, M., and Nakahata, T. (2005) A novel variant fibrinogen, deletion of Bβ111Ser in coiled-coil region, affecting lateral aggregation. Clin. Chim. Acta 365, 160-167. (Pubitemid 43196433)
57. Guthold, M., Liu, W., Sparks, E. A., Jawert, L. M., Peng, L., Falvo, M., Superfine, R., Hantgan, R. R., and Lord, S. T. (2007) A comparison of the mechanical and structural properties of fibrin fibers with other protein fibers. Cell Biochem. Biophys. 49, 165-181. (Pubitemid 350242577)
58. Brown, A. E., Litvinov, R. I., Discher, D., and Weisel, J. W. (2007) Forced unfolding of coiled-coils in fibrinogen by single-molecule AFM. Biophys. J. Lett. 92, L09-L41. (Pubitemid 46393457)
59. Lim, B. B., Lee, E. H., Sotomeyer, M., and Schulten, K. (2007) Structural basis of fibrin clot elasticity. Structure 16, 449-459.
60. Medved, L., and Weisel, J. W. (2009) Recommendations for nomenclature on fibrinogen and fibrin. J. Thromb. Haemostasis 7, 355-359.