Thromb Haemost 2000; 84(05): 849-857
DOI: 10.1055/s-0037-1614127
Review Article
Schattauer GmbH

Three-dimensional Model of Coagulation Factor Va Bound to Activated Protein C

Jean-Luc Pellequer
1   From the Department of Molecular Biology and The Skaggs Institute for Chemical Biology, California, USA
,
Andrew J. Gale
2   Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
,
Elizabeth D. Getzoff
1   From the Department of Molecular Biology and The Skaggs Institute for Chemical Biology, California, USA
,
John H. Griffin
2   Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
› Author Affiliations
This work was supported by the National Institutes of Health HL21544, GM48495, HL07695 and HL52246 and the National Science Foundation BIR9631436. AJG is a Fellow of the Leukemia and Lymphoma Society. The FVa coordinates are deposited in the Protein Data Bank (code IFV4).
Further Information

Publication History

Received 08 March 2000

Accepted after revision 05 June 2000

Publication Date:
13 December 2017 (online)

Summary

A complete molecular model of blood coagulation factor Va (FVa) bound to anticoagulant activated protein C (APC) and to a phospholipid membrane was constructed. The three homologous A domains and the two homologous C domains of FVA were modeled based on the X-ray crystallographic structures of ceruloplasmin and C2 domain of factor V, respectively. The final arrangement of the five domains in the complete FVa model bound to a membrane incorporated extensive published experimental data. FVa binds the phospholipid membrane through its C2 domain while the A-domain trimer is located from 40 through 100 Å above the membrane plane. From our model we infer a probable role for metal ions at the interface between FVa light and heavy chains, provide an explanation for the slower APC cleavage at Arg306 relative to Arg506, and predict specific interactions between positively and negatively charged exosites in APC and FVa, respectively.

 
  • References

  • 1 Davie EW, Ratnoff OD. Waterfall sequence for intrinsic blood clotting. Science 1964; 145: 1310-2.
  • 2 MacFarlane RG. An enzyme cascade in the blood clotting mechanism, and its function as a biochemical amplifier. Nature 1964; 202: 498-9.
  • 3 Stenn KS, Blout ER. Mechanism of bovine prothrombin activation by an insoluble preparation of bovine factor Xa (Thrombokinase). Biochemistry 1972; 11: 4502-15.
  • 4 Subbaiah PV, Bajwa SS, Smith CM, Hanahan DJ. Interactions of the components of the prothrombinase complex. Biochim Biophys Acta 1976; 444: 131-46.
  • 5 Rosing J, Tans G, Govers-Riemslag JWP, Zwaal RFA, Hemker HC. The role of phospholipids and factor Va in the prothrombinase complex. J Biol Chem 1980; 255: 274-83.
  • 6 Nesheim ME, Taswell JB, Mann KG. The contribution of bovine factor V and factor Va to the activity of prothrombinase. J Biol Chem 1979; 254: 10952-62.
  • 7 Kane WH, Davie EW. Blood coagulation factors V and VIII: Structure and functional similarities and their relationship to hemorrhagic and thrombotic disorders. Blood 1988; 71: 539-55.
  • 8 Rosing J, Tans G. Coagulation factor V: An old star shines again. Thromb Heamostas 1997; 78: 427-33.
  • 9 Papahadjopoulos D, Hanahan DJ. Observations on the interaction of phospholipids and certain clotting factors in prothrombin activator formation. Biochim Biophys Acta 1964; 90: 436-9.
  • 10 Pusey ML, Mayer LD, Wei GJ, Bloomfield VA, Nelsestuen GL. Kinetic and hydrodynamic analysis of blood clotting factor V-membrane binding. Biochemistry 1982; 21: 5262-9.
  • 11 van de Waart P, Bruls H, Hemker HC, Lindhout T. Interaction of bovine blood clotting factor Va and its subunits with phospholipid vesicles. Biochemistry 1983; 22: 2427-32.
  • 12 Krishnaswamy S, Mann KG. The binding of factor Va to phospholipid vesicles. J Biol Chem 1988; 263: 5714-23.
  • 13 Cutsforth GA, Koppaka V, Krishnaswamy S, Wu JR, Mann KG, Lentz BR. Insights into the complex association of bovine factor Va with acidic-lipidcontaining synthetic membranes. Biophys J 1996; 70: 2938-49.
  • 14 Skogen WF, Esmon CT, Cox AC. Comparison of coagulation factor Xa and Des-(1-44)factor Xa in the assembly of prothrombinase. J Biol Chem 1984; 259: 2306-10.
  • 15 Sunnerhagen M, Forsén S, Hoffrén A-M, Drakenberg T, Teleman O, Stenflo J. Structure of the Ca2+-free GLA domain sheds light on membrane binding of blood coagulation proteins. Nature Struct Biol 1995; 02: 504-9.
  • 16 Freedman SJ, Blostein MD, Baleja JD, Jacobs M, Furie BC, Furie B. Identification of the phospholipid binding site in the vitamin K-dependent blood coagulation protein factor IX. J Biol Chem 1996; 271: 16227-36.
  • 17 Zaitseva I, Zaitsev V, Card G, Moshkov K, Bax B, Ralph A, Lindley P. The X-ray structure of human serum ceruloplasmin at 3.1A: Nature of the copper centres. J Biol Inorg Chem 1996; 01: 15-23.
  • 18 Pellequer J-L, Gale AJ, Griffin JH. Getzoff Homology modeling of Factor Va, a cofactor of the prothrombinase complex. Protein Sci 1998; 07 (Suppl. 01) 159.
  • 19 Villoutreix BO, Dahlback B. Structural investigation of the A domains of human blood coagulation factor V by molecular modeling. Protein Sci 1998; 07: 1317-25.
  • 20 Pan Y, DeFay T, Gitschier J, Cohen FE. Proposed structure of the A domains of factor VIII by homology modelling. Nature Struct Biol 1995; 02: 740-4.
  • 21 Pemberton S, Lindley P, Zaitsev V, Card G, Tuddenham EGD, Kemball-Cook G. A molecular model for the triplicated A domains of human factor VIII based on the crystal structure of human ceruloplasmin. Blood 1997; 89: 2413-21.
  • 22 Pellequer J-L, Gale AJ, Griffin JH. Getzoff Homology models of the C domains of blood coagulation factors V and VIII: A proposed membrane binding mode for FV and FVIII C2 domains. Blood Cells Mol Dis 1998; 24: 448-61.
  • 23 Villoutreix BO, Bucher P, Hofmann K, Baumgartner S, Dahlbäck B. Molecular models for the two discoidin domains of human blood coagulation factor V. J Mol Model 1998; 04: 268-75.
  • 24 Ito N, Phillips SEV, Yadav KDS, Knowles PF. Crystal structure of a free radical enzyme, galactose oxidase. J Mol Biol 1994; 238: 794-814.
  • 25 Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, Fuentes-Prior P. Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Nature 1999; 402: 434-9.
  • 26 Kisiel W, Canfield WM, Ericsson LH, Davie EW. Anticoagulant properties of bovine plasma protein C following activation by thrombin. Biochemistry 1977; 16: 5824-31.
  • 27 Walker FJ, Sexton PW, Esmon CT. The inhibition of blood coagulation by activated Protein C through the selective inactivation of activated Factor V. Biochim Biophys Acta 1979; 571: 333-42.
  • 28 Marlar RA, Kleiss AJ, Griffin JH. Mechanism of action of human activated protein C, a thrombin-dependent anticoagulant enzyme. Blood 1982; 59: 1067-72.
  • 29 Fisher CL, Greengard JS, Griffin JH. Models of the serine protease domain of the human antithrombotic factor activated protein C and its zymogen. Protein Sci 1994; 03: 588-99.
  • 30 Mather T, Oganessyan V, Hof P, Huber R, Foundling S, Esmon C, Bode W. The 2.8A crystal structure of gla-domainless activated protein C. EMBO J 1996; 15: 6822-31.
  • 31 Walker FJ. Regulation of activated protein C by a new protein. A possible function for bovine protein S. J Biol Chem 1980; 255: 5521-4.
  • 32 Suzuki K, Stenflo J, Dahlbäck B, Teodorsson B. Inactivation of human coagulation factor V by activated protein C. J Biol Chem 1983; 258: 1914-20.
  • 33 Bakker HM, Tans G, Janssen-Claessen T, Thomassen MCLGD, Hemker HC, Griffin JH, Rosing J. The effect of phospholipids, calcium ions and protein S on rate constants of human factor Va inactivation by activated human protein C. Eur J Biochem 1992; 208: 171-8.
  • 34 Kalafatis M, Mann KG. Role of the membrane in the inactivation of factor Va by activated protein C. J Biol Chem 1993; 268: 27246-57.
  • 35 Tuffery P, Etchebest C, Hazout S, Lavery R. A new approach to the rapid determination of protein side chain conformations. J Biomol Struct Dynam 1991; 08: 1267-89.
  • 36 McRee DE. XtalView: A visual protein crystallographic software system for X11/XView. J Mol Graph 1992; 10: 44-7.
  • 37 Roussel A, Cambillau C. TURBO-FRODO. Silicon Graphics geometry partners directory. Mountain View, California: Silicon Graphics; 1989: 77-8.
  • 38 Brünger AT. X-PLOR Manual. Version 3.0. New Haven: Yale University; 1992
  • 39 Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations. J Comp Chem 1983; 04: 187-217.
  • 40 Brünger AT, Karplus M. Polar hydrogen positions in proteins: empirical energy function placement and neutron diffraction comparison. Proteins 1988; 04: 148-56.
  • 41 Powell MJD. Restart procedures for the conjugate gradient method. Math Program 1977; 12: 241-54.
  • 42 Rost B, Sander C. Prediction of protein structure at better than 70% accuracy. J Mol Biol 1993; 232: 584-99.
  • 43 Rost B, Sander C, Schneider R. PHD - an automatic mail server for protein secondary structure prediction. Comput Applic Biosci 1994; 10: 53-60.
  • 44 van de Locht A, Bode W, Huber R, Le Bonniec BF, Stone SR, Esmon CT, Stubbs MT. The thrombin E192Q-BPTI complex reveals gross structural rearrangements: Implications for the interaction with antithrombin and thrombomodulin. EMBO J 1997; 16: 2977-84.
  • 45 Soriano-Garcia M, Padmanabhan K, de Vos AM, Tulinsky A. The Ca2+ ion and membrane binding structure of the Gla domain of Ca-prothrombin fragment 1. Biochemistry 1992; 31: 2554-66.
  • 46 Banner DW, D’Arcy A, Chène C, Winkler FK, Guha A, Konigsberg WH, Nemerson Y, Kirchhofer D. The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature 1996; 380: 41-6.
  • 47 Brandstetter H, Kuhne A, Bode W, Huber R, von der Saal W, Wirthensohn K, Engh RA. X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition. J Biol Chem 1996; 271: 29988-92.
  • 48 Brandstetter H, Bauer M, Huber R, Lollar P, Bode W. X-ray structure of clotting factor IXa: Active site and module structure related to Xase activity and hemophilia B. Proc. Natl Acad Sci USA 1995; 92: 9796-800.
  • 49 Castagnetto JM, Hennessy SH, Pique M, Tainer JA. Getzoff The metalloprotein site database and browser (Release 1.3): The metalloprotein structure and design group at the Scripps research institute. 1999
  • 50 Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 1993; 26: 283-91.
  • 51 EU 3-D Validation Network. Who Checks the checkers? Four validation tools applied to eight atomic resolution structures. J Mol Biol 1998; 276: 417-36.
  • 52 Novotny J, Rashin AA, Bruccoleri RE. Criteria that disriminate between native proteins and incorrectly folded models. Proteins 1988; 04: 19-30.
  • 53 Chiche L, Gregoret LM, Cohen FE, Kollman P. Protein model structure evaluation using the solvation free energy of folding. Proc Natl Acad Sci USA 1990; 87: 3240-3.
  • 54 Sanner MF, Spehner J-C, Olson AJ. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996; 38: 305-20.
  • 55 Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986; 319: 199-203.
  • 56 Stoylova S, Mann KG, Brisson A. Structure of membrane-bound human factor Va. FEBS Lett 1994; 351: 330-4.
  • 57 Isaacs BS, Husten EJ, Esmon CT, Johnson AE. A domain of membranebound blood coagulation factor Va is located far from the phospholipid surface. A fluorescence energy transfer measurement. Biochemistry 1986; 25: 4958-69.
  • 58 Yegneswaran S, Wood GM, Esmon CT, Johnson AE. Protein S alters the active site location of activated protein C above the membrane surface. A fluorescence resonance energy transfer study of topography. J Biol Chem 1997; 272: 25013-21.
  • 59 Mann KG, Lawler CM, Vehar GA, Church WR. Coagulation factor V contains copper ion. J Biol Chem 1984; 259: 12949-51.
  • 60 Greenquist AC, Colman RW. Bovine factor V: A calcium-containing metalloprotein. Blood 1975; 46: 769-82.
  • 61 Esmon CT. The subunit structure of thrombin-activated factor V: Isolation of activated factor V, separation of subunits, and reconstitution of biological activity. J Biol Chem 1979; 254: 964-73.
  • 62 Mann KG, Hockin MF, Begin KJ, Kalafatis M. Activated protein C cleavage of factor Va leads to dissociation of the A2 domain. J Biol Chem 1997; 272: 20678-83.
  • 63 Fay PJ, Smudzin TM, Walker FJ. Activated protein C-catalyzed inactivation of human factor VIII and factor VIIIa. J Biol Chem 1991; 266: 20139-45.
  • 64 Fay PJ, Smudzin TM. Characterization of the interaction between the A2 subunit and A1/A3-C1-C2 dimer in human factor VIIIa. J Biol Chem 1992; 267: 13246-50.
  • 65 Krishnaswamy S, Church WR, Nesheim ME, Mann KG. Activation of human prothrombin by human prothrombinase: Influence of factor Va on the reaction mechanism. J Biol Chem 1987; 262: 3291-9.
  • 66 Bloom JW, Nesheim ME, Mann KG. Phospholipid-binding properties of bovine factor V and factor Va. Biochemistry 1979; 18: 4419-25.
  • 67 Higgins DL, Mann KG. The interaction of bovine factor V and factor V-derived peptides with phospholipid vesicles. J Biol Chem 1983; 258: 6503-8.
  • 68 Hubbard SJ, Eisenmenger F, Thornton JM. Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Protein Sci 1994; 03: 757-68.
  • 69 Zhang St E, Charles R, Tulinsky A. Structure of extracellular tissue factor complexed with factor VIIa inhibited with a BPTI mutant. J Mol Biol 1999; 285: 2089-104.
  • 70 Krishnaswamy S, Williams EB, Mann KG. The binding site of activated protein C to factors V and Va. J Biol Chem 1986; 261: 9684-93.
  • 71 Hockin MF, Cawthern KM, Kalafatis M, Mann KG. A model describing the inactivation of factor Va by APC: Bond cleavage, fragment dissociation, and product inhibition. Biochemistry 1999; 38: 6918-34.
  • 72 Shen L, Dahlbäck B. Factor V and protein S as synergistic cofactors to activated protein C in degradation of factor VIIIa. J Biol Chem 1994; 269: 18735-8.
  • 73 Thorelli E, Kaufman RJ, Dahlbäck B. Cleavage of factor V at Arg 506 by activated protein C and the expression of anticoagulant activity of factor V. Blood 1999; 93: 2552-8.
  • 74 Yegneswaran S. The molecular architecture of the anticoagulant membrane-bound activated protein C enzyme and its dependence on the cofactor protein and phospholipid composition. College Station: Texas A&M University; 1997
  • 75 Gale AJ, Heeb MJ, Griffin JH. The autolysis loop of activated protein C interacts with factor Va and differentiates between the Arg506 and Arg306 cleavage sites. Blood 2000; 96: 585-93.
  • 76 Reitsma PH, Poort SR, Bernardi F, Gandrille S, Long GL, Sala N, Cooper DN. Protein C deficiency: A database of mutations. Thromb Haemost 1993; 69: 77-84.
  • 77 Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991; 24: 946-50.
  • 78 Merritt EA, Bacon DJ. Raster3D: Photorealistic molecular graphics. Meth. Enzymol 1997; 277: 505-24.