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Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide.

Everse SJ, Spraggon G, Veerapandian L, Doolittle RF
Biochemistry 38 2941-6 (1999)
Related entries: 1fzf, 1fzg

Cited: 33 times
EuropePMC logo PMID: 10074346

Abstract

The structure of fragment double-D from human fibrin has been solved in the presence and absence of the peptide ligands that simulate the two knobs exposed by the removal of fibrinopeptides A and B, respectively. All told, six crystal structures have been determined, three of which are reported here for the first time: namely, fragments D and double-D with the peptide GHRPam alone and double-D in the absence of any peptide ligand. Comparison of the structures has revealed a series of conformational changes that are brought about by the various knob-hole interactions. Of greatest interest is a moveable "flap" of two negatively charged amino acids (Glubeta397 and Aspbeta398) whose side chains are pinned back to the coiled coil with a calcium atom bridge until GHRPam occupies the beta-chain pocket. Additionally, in the absence of the peptide ligand GPRPam, GHRPam binds to the gamma-chain pocket, a new calcium-binding site being formed concomitantly.

Articles - 1fze mentioned but not cited (1)

  1. A model of fibrin formation based on crystal structures of fibrinogen and fibrin fragments complexed with synthetic peptides. Yang Z, Mochalkin I, Doolittle RF. Proc Natl Acad Sci U S A 97 14156-14161 (2000)


Reviews citing this publication (7)

  1. A comparison of the mechanical and structural properties of fibrin fibers with other protein fibers. Guthold M, Liu W, Sparks EA, Jawerth LM, Peng L, Falvo M, Superfine R, Hantgan RR, Lord ST. Cell Biochem Biophys 49 165-181 (2007)
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  7. New insights into fibrin (ogen) structure and function. Everse SJ. Vox Sang 83 Suppl 1 375-382 (2002)

Articles citing this publication (25)

  1. Fibrinogen beta-chain tyrosine nitration is a prothrombotic risk factor. Parastatidis I, Thomson L, Burke A, Chernysh I, Nagaswami C, Visser J, Stamer S, Liebler DC, Koliakos G, Heijnen HF, Fitzgerald GA, Weisel JW, Ischiropoulos H. J Biol Chem 283 33846-33853 (2008)
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  3. Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution. Madrazo J, Brown JH, Litvinovich S, Dominguez R, Yakovlev S, Medved L, Cohen C. Proc Natl Acad Sci U S A 98 11967-11972 (2001)
  4. Crystal structure of native chicken fibrinogen at 5.5-A resolution. Yang Z, Mochalkin I, Veerapandian L, Riley M, Doolittle RF. Proc Natl Acad Sci U S A 97 3907-3912 (2000)
  5. Biochemical and structural analysis of the interaction between β-amyloid and fibrinogen. Zamolodchikov D, Berk-Rauch HE, Oren DA, Stor DS, Singh PK, Kawasaki M, Aso K, Strickland S, Ahn HJ. Blood 128 1144-1151 (2016)
  6. Alpha-helically constrained phage display library. Petrenko VA, Smith GP, Mazooji MM, Quinn T. Protein Eng 15 943-950 (2002)
  7. Modification of fibrinogen with poly(ethylene glycol) and its effects on fibrin clot characteristics. Barker TH, Fuller GM, Klinger MM, Feldman DS, Hagood JS. J Biomed Mater Res 56 529-535 (2001)
  8. A network-based multi-target computational estimation scheme for anticoagulant activities of compounds. Li Q, Li X, Li C, Chen L, Song J, Tang Y, Xu X. PLoS One 6 e14774 (2011)
  9. Fibrinogen variant BbetaD432A has normal polymerization but does not bind knob "B". Bowley SR, Lord ST. Blood 113 4425-4430 (2009)
  10. Atomic Structural Models of Fibrin Oligomers. Zhmurov A, Protopopova AD, Litvinov RI, Zhukov P, Weisel JW, Barsegov V. Structure 26 857-868.e4 (2018)
  11. Which knobs fit into which holes in fibrin polymerization? Weisel JW. J Thromb Haemost 5 2340-2343 (2007)
  12. Determining the crystal structure of fibrinogen. Doolittle RF. J Thromb Haemost 2 683-689 (2004)
  13. Letter The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE. Betts L, Merenbloom BK, Lord ST. J Thromb Haemost 4 1139-1141 (2006)
  14. Impaired protofibril formation in fibrinogen gamma N308K is due to altered D:D and "A:a" interactions. Bowley SR, Okumura N, Lord ST. Biochemistry 48 8656-8663 (2009)
  15. Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds. Litvinov RI, Kononova O, Zhmurov A, Marx KA, Barsegov V, Thirumalai D, Weisel JW. Proc Natl Acad Sci U S A 115 8575-8580 (2018)
  16. Functional analysis of recombinant Bbeta15C and Bbeta15A fibrinogens demonstrates that Bbeta15G residue plays important roles in FPB release and in lateral aggregation of protofibrils. Hirota-Kawadobora M, Kani S, Terasawa F, Fujihara N, Yamauchi K, Tozuka M, Okumura N. J Thromb Haemost 3 983-990 (2005)
  17. A neoantigenic determinant in the D-dimer fragment of fibrin. Lugovskoy EV, Kolesnikova IN, Gritsenko PG, Zolotareva EN, Gaffney P, Nieuwenhuizen W, Komisarenko SV. Thromb Res 107 151-156 (2002)
  18. Functional characterization of fibrinogen Bicêtre II: a gamma 308 Asn-->Lys mutation located near the fibrin D:D interaction sites. Marchi RC, Carvajal Z, Boyer-Neumann C, Anglés-Cano E, Weisel JW. Blood Coagul Fibrinolysis 17 193-201 (2006)
  19. Fibrinopeptide A release is necessary for effective B:b interactions in polymerisation of variant fibrinogens with impaired A:a interactions. Soya K, Terasawa F, Okumura N. Thromb Haemost 109 221-228 (2013)
  20. Functional role of Bbeta-chain N-terminal fragment in the fibrin polymerization process. Lugovskoy EV, Gritsenko PG, Kapustianenko LG, Kolesnikova IN, Chernishov VI, Komisarenko SV. FEBS J 274 4540-4549 (2007)
  21. Two monoclonal antibodies to D-dimer-specific inhibitors of fibrin polymerization. Lugovskoy EV, Gritsenko PG, Kolesnikova IN, Zolotarova EN, Chernishov VI, Nieuwenhuizen W, Komisarenko SV. Thromb Res 113 251-259 (2004)
  22. Novel monoclonal antibody that recognizes new neoantigenic determinant of D-dimer. Doh HJ, Song KS, Kang MS, Kim DS, Kim KA, Kang J, Jang Y, Chung KH. Thromb Res 118 353-360 (2006)
  23. Some notes on crystallizing fibrinogen and fibrin fragments. Doolittle RF. Biophys Chem 100 307-313 (2003)
  24. Fibrin protofibril packing and clot stability are enhanced by extended knob-hole interactions and catch-slip bonds. Asquith NL, Duval C, Zhmurov A, Baker SR, McPherson HR, Domingues MM, Connell SDA, Barsegov V, Ariëns RAS. Blood Adv 6 4015-4027 (2022)
  25. Mapping of the fibrinogen-binding site on the staphylocoagulase C-terminal repeat region. Maddur AA, Voehler M, Panizzi P, Meiler J, Bock PE, Verhamme IM. J Biol Chem 298 101493 (2022)


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