Table S1 Reactions and parameter values
Reaction / Reaction rate / Parameter a / Initial value / Adjusted value / Ref.1 / VIII -> VIIIa (IIa) / v1=Vmax1∙IIa∙[VIII]Km1+[IIa] / Vmax1
Km1 / 70
10 / --
-- / 1, 2
2 / IX -> IXa (XIa) / v2=Vmax2∙XIa∙[IX]Km2+[XIa] / Vmax2
Km2 / 7
10 / --
-- / 3, 4
3 / XI -> XIa (XIIa) / v3=Vmax3∙XIIa∙[XI]Km3+[XIIa] / Vmax3
Km3 / 70
1 / --
-- / 5
4 / XI -> XIa (IIa) / v4=Vmax4∙IIa∙[XI]Km4+[IIa] / Vmax4
Km4 / 10
10 / --
-- / 6
5 / VII -> VIIa (IIa) / v5=Vmax5∙IIa∙[VII]Km5+[IIa] / Vmax5
Km5 / 1
10 / --
-- / 5
6 / X -> Xa (IXa) / v6=Vmax6∙IXa∙[X]Km6+[IXa] / Vmax6
Km6 / 3
178 / --
-- / 2, 5, 7
7 / X -> Xa (IXa:VIIIa) / v7=Vmax7∙IXa:VIIIa∙[X]Km7+[IXa:VIIIa] / Vmax7
Km7 / 74
10 / --
-- / 2, 5, 7
8 / X -> Xa (VIIa) / v8=Vmax8∙VIIa∙[X]Km8+[VIIa] / Vmax8
Km8 / 1×10-3
10 / --
-- / 5
9 / V -> Va (IIa) / v9=Vmax9∙IIa∙[V]Km9+[IIa] / Vmax9
Km9 / 70
10 / --
-- / 5
10 / II -> IIa (Xa:Va) / v10=Vmax10∙Xa:Va∙[II]Km10+[Xa:Va] / Vmax10
Km10 / 70
10 / --
-- / 8
11 / II -> IIa (Xa) / v11=Vmax11∙Xa∙[II]Km11+[Xa] / Vmax11
Km11 / 7
10 / --
-- / 8, 9
12 / Fg -> F (IIa) / v12=Vmax12∙IIa∙[Fg]Km12+[IIa] / Vmax12
Km12 / 7
10 / 3000
-- / assumed
5
13 / Fg -> DP (P) / v13=Vmax13∙[P]∙[Fg]Km13+[P] / Vmax13
Km13 / 7
100 / --
-- / 5
14 / F -> XF (XIIIa) / v14=Vmax14∙[XIIIa]∙[F]Km14+[XIIIa] / Vmax14
Km14 / 7
10 / --
-- / 5
15 / F -> DP (P) / v15=Vmax15∙[P]∙[F]Km15+[P] / Vmax15
Km15 / 7
10 / --
-- / 5
16 / XF -> DP (P) / v16=Vmax16∙[P]∙[XF]Km16+[P] / Vmax16
Km16 / 7
1 / --
-- / 5
17 / XIII -> XIIIa (IIa) / v17=Vmax17∙[IIa]∙[XIII]Km17+[IIa] / Vmax17
Km17 / 7
1 / --
-- / 5
18 / Pg -> P (IIa) / v18=Vmax18∙[IIa]∙[Pg]Km18+[IIa] / Vmax18
Km18 / 7
1 / --
-- / 5
19 / Pg -> P (F) / v19=Vmax19∙[F]∙[Pg]Km19+[F] / Vmax19
Km19 / 70
1 / --
-- / 5
20 / VIIIa + IXa -> IXa:VIIIa / v20=VIIIa∙[IXa]c20 / c20 / 1×10-2 / -- / 10
21 / Xa + Va -> Xa:Va / v21=Xa∙[Va]c21 / c21 / 0.5 / -- / 10
22 / VIIa + TF -> VIIa:TF / v22=VIIa∙[TF]c22 / c22 / 0.5 / -- / 10
23 / VII + TF -> VII:TF / v23=VII∙[TF]c23 / c23 / 0.1 / -- / 10
24 / Xa:TFPI + VIIa:TF -> VIIa:TF:Xa:TFPI / v24=Xa:TFPI∙[VIIa:TF]c24 / c24 / 0.5 / -- / 10
25 / Xa + TFPI -> Xa:TFPI / v25=Xa∙[TFPI]c25 / c25 / 0.5 / -- / 10
26 / VII:TF -> VIIa:TF (Xa) / v26=Vmax26∙[Xa]∙[VII:TF]Km26+[Xa] / Vmax26
Km26 / 70
1 / --
-- / 10
27 / X -> Xa (VIIa:TF) / v27=Vmax27∙[VIIa:TF]∙[X]Km27+[VIIa:TF] / Vmax27
Km27 / 9×102
2×102 / --
-- / 10
28 / IX -> IXa (VIIa:TF) / v28=Vmax28∙[VIIa:TF]∙[IX]Km28+[VIIa:TF] / Vmax28
Km28 / 70
1 / --
-- / 10
29 / VII:TF -> VIIa:TF (TF) / v29=Vmax29∙[TF]∙[VII:TF]Km29+[TF] / Vmax29
Km29 / 1×103
1 / --
-- / 10
30 / VII -> VIIa (Xa) / v30=Vmax30∙[Xa]∙[VII]Km30+[Xa] / Vmax30
Km30 / 1
10 / --
-- / 10
31 / VII -> VIIa (VIIa:TF) / v31=Vmax31∙[VIIa:TF]∙[VII]Km31+[VIIa:TF] / Vmax31
Km31 / 1
10 / --
-- / 10
32 / VII -> VIIa (IXa) / v32=Vmax32∙[IXa]∙[VII]Km32+[IXa] / Vmax32
Km32 / 0.2
10 / --
-- / 10
33 / XII -> XIIa (CA) / v33=Vmax33∙[CA]∙[XII]Km33+[CA] / Vmax33
Km33 / 7
1 / --
-- / 10
34 / XII -> XIIa (K) / v34=Vmax34∙[K]∙[XII]Km34+[K] / Vmax34
Km34 / 70
1 / --
-- / 10
35 / PK -> K (XIIa) / v35=Vmax35∙[XIIa]∙[PK]Km35+[XIIa] / Vmax35
Km35 / 7
1 / --
-- / 10
36 / ATIII + Xa -> Xa:ATIII / v36=ATIII∙[Xa]c36 / c36 / 5.4×10-3 / -- / 11
37 / IXa + ATIII -> IXa:ATIII / v37=IXa∙[ATIII]c37 / c37 / 1.76×10-3 / -- / 11
38 / ATIII + IIa -> IIa:ATIII / v38=ATIII∙[IIa]c38 / c38 / 2.56×10-2 / -- / 11
39 / VIIa:TF + ATIII -> VIIa:TF:ATIII / v39=VIIa:TF∙[ATIII]c39 / c39 / 8.28×10-4 / -- / 11
40 / XIIa + ATIII -> XIIa:ATIII / v40=XIIa∙[ATIII]c40 / c40 / 7.78×10-5 / -- / 12
41 / XIa + ATIII -> XIa:ATIII / v41=XIa∙[ATIII]c41 / c41 / 1.15×10-3 / -- / 13
42 / XII -> null / v42=k42∙[XII] / k42 / 1.2×10-2 / -- / 14
43 / XIIa -> null / v43=k43∙[XIIa] / k43 / 20 / -- / 5, 15
44 / XI -> null / v44=k44∙[XI] / k44 / 9.9×10-3 / -- / 5
45 / XIa -> null / v45=k45∙[XIa] / k45 / 20 / -- / 5
46 / VIII -> null / v46=k46∙[VIII] / k46 / 5.8×10-2 / -- / 16
47 / VIIIa -> null / v47=k47∙[VIIIa] / k47 / 20 / -- / 7
48 / IX -> null / v48=k48∙[IX] / k48 / 2.9×10-2 / -- / 18
49 / IXa -> null / v49=k49∙[IXa] / k49 / 20 / -- / 5
50 / IXa:VIIIa -> null / v50=k50∙[IXa:VIIIa] / k50 / 20 / -- / 5
51 / VIIa + Xa -> VIIa:Xa / v51=VIIa∙[Xa]c51 / c51 / 0.5 / -- / 10
52 / VII -> null / v52=k52∙[VII] / k52 / 0.12 / -- / 18
53 / VIIa -> null / v53=k53∙[VIIa] / k53 / 20 / -- / 5
54 / TF -> null / v54=k54∙[TF] / k54 / 5×10-2 / -- / 10
55 / VII:TF -> null / v55=k55∙[VII:TF] / k55 / 0.7 / -- / 10
56 / VIIa:TF -> null / v56=k56∙[VIIa:TF] / k56 / 20 / -- / 10
57 / Xa:TFPI -> null / v57=k57∙[Xa:TFPI] / k57 / 20 / -- / 10
58 / VIIa:TF:Xa:TFPI -> null / v58=k58∙[VIIa:TF:Xa:TFPI] / k58 / 20 / -- / 10
59 / X -> null / v59=k59∙[X] / k59 / 1.8×10-2 / -- / 18,17
60 / Xa -> null / v60=k60∙[Xa] / k60 / 20 / -- / 7
61 / V -> null / v61=k61∙[V] / k61 / 4.3×10-2 / -- / 18,17
62 / Va -> null / v62=k62∙[Va] / k62 / 20 / -- / 5
63 / Xa:Va -> null / v63=k63∙[Xa:Va] / k63 / 20 / -- / 5
64 / TFPI -> null / v64=k64∙[TFPI] / k64 / 20 / -- / 10
65 / II -> null / v65=k65∙[II] / k65 / 1×10-2 / -- / 18,16
66 / IIa -> null / v66=k66∙[IIa] / k66 / 67.4 / -- / 17
67 / XIII -> null / v67=k67∙[XIII] / k67 / 3.6×10-3 / -- / 16
68 / XIIIa -> null / v68=k68∙[XIIIa] / k68 / 0.69 / -- / 17
69 / Pg -> null / v69=k69∙[Pg] / k69 / 5×10-2 / -- / 5
70 / P -> null / v70=k70∙[P] / k70 / 20 / -- / 5
71 / PK -> null / v71=k71∙[PK] / k71 / 5×10-2 / -- / 10
72 / K -> null / v72=k72∙[K] / k72 / 20 / -- / 10
73 / Fg -> null / v73=k73∙[Fg] / k73 / 6.4×10-3 / -- / 5
74 / F -> null / v74=k74∙[F] / k74 / 5×10-2 / -- / 5
75 / XF -> null / v75=k75∙[XF] / k75 / 5×10-2 / -- / 5
76 / DP -> null / v76=k76∙[DP] / k76 / 3.5 / -- / 5
77 / ATIII -> null / v77=k77∙[ATIII] / k77 / 1×10-2 / -- / 18
78 / Xa:ATIII -> null / v78=k78∙[Xa:ATIII] / k78 / 8.3 / -- / 19
79 / IXa:ATIII -> null / v79=k79∙[IXa:ATIII] / k79 / 1.4 / -- / 20
80 / XIa:ATIII -> null / v80=k80∙[XIa:ATIII] / k80 / 1 / -- / assumed
81 / XIIa:ATIII -> null / v81=k81∙[XIIa:ATIII] / k81 / 1 / -- / assumed
82 / IIa:ATIII -> null / v82=k82∙[IIa:ATIII] / k82 / 0.2 / -- / 5
a Units for Vmax values=1/h, for Km values=nM, for c values=nM*h, and for k=1/h.
Species -> null, the degradation reaction of species.
See the legend of Figure 2 for the abbreviations.
References
1. Donath, M.J.,Lenting, P.J.,Van Mourik, J.A.,Mertens, K. Kinetics of factor VIII light-chain cleavage by thrombin and factor Xa. A regulatory role of the factor VIII heavy-chain region Lys713-Arg740. Eur J Biochem 240, 365-372 (1996).
2. Fay, P.J. Regulation of factor VIIIa in the intrinsic factor Xase. Thromb. Haemost. 82, 193-200 (1999).
3. Sun, Y.,Gailani, D. Identification of a factor IX binding site on the third apple domain of activated factor XI. J Biol Chem 271, 29023-29028 (1996).
4. Gailani, D.,Ho, D.,Sun, M.F.,Cheng, Q.,Walsh, P.N. Model for a factor IX activation complex on blood platelets: dimeric conformation of factor XIa is essential. Blood 97, 3117-3122 (2001).
5. Tanos, P.P.,Isbister, G.K.,Lalloo, D.G.,Kirkpatrick, C.M.,Duffull, S.B. A model for venom-induced consumptive coagulopathy in snake bite. Toxicon 52, 769-780 (2008).
6. von dem Borne, P.A.,Meijers, J.C.,Bouma, B.N. Feedback activation of factor XI by thrombin in plasma results in additional formation of thrombin that protects fibrin clots from fibrinolysis. Blood 86, 3035-3042 (1995).
7. Qiao, Y.H. et al. The kinetic model and simulation of blood coagulation--the kinetic influence of activated protein C. Med. Eng. Phys. 26, 341-347 (2004).
8. Krishnaswamy, S.,Jones, K.C.,Mann, K.G. Prothrombinase complex assembly. Kinetic mechanism of enzyme assembly on phospholipid vesicles. J Biol Chem 263, 3823-3834 (1988).
9. Brufatto, N.,Nesheim, M.E. Analysis of the kinetics of prothrombin activation and evidence that two equilibrating forms of prothrombinase are involved in the process. J Biol Chem 278, 6755-6764 (2003).
10. Wajima, T.,Isbister, G.K.,Duffull, S.B. A comprehensive model for the humoral coagulation network in humans. Clin. Pharmacol. Ther. 86, 290-298 (2009).
11. Chatterjee, M.S.,Denney, W.S.,Jing, H.,Diamond, S.L. Systems biology of coagulation initiation: kinetics of thrombin generation in resting and activated human blood. PLoS Comput. Biol. 6, (2010).
12. Pixley, R.A.,Schapira, M.,Colman, R.W. The regulation of human factor XIIa by plasma proteinase inhibitors. J Biol Chem 260, 1723-1729 (1985).
13. Wuillemin, W.A. et al. Modulation of contact system proteases by glycosaminoglycans. Selective enhancement of the inhibition of factor XIa. J Biol Chem 271, 12913-12918 (1996).
14. Lalloo, D.G. et al. Coagulopathy following bites by the Papuan taipan (Oxyuranus scutellatus canni). Blood Coagul. Fibrinolysis 6, 65-72 (1995).
15. Mann, K.G.,Brummel, K.,Butenas, S. What is all that thrombin for? Journal of thrombosis and haemostasis : JTH 1, 1504-1514 (2003).
16. Isbister, G.K. et al. Clinically applicable laboratory end-points for treating snakebite coagulopathy. Pathology 38, 568-572 (2006).
17. Eastham, R.D.,Slade, R.R. Clinical haematology. 7th edn. (Butterworth-Heinemann: Jordan Hill, Oxford ; Boston, 1992).
18. Collen, D.,Schetz, J.,de Cock, F.,Holmer, E.,Verstraete, M. Metabolism of antithrombin III (heparin cofactor) in man: effects of venous thrombosis and of heparin administration. Eur. J. Clin. Invest. 7, 27-35 (1977).
19. Narita, M.,Rudolph, A.E.,Miletich, J.P.,Schwartz, A.L. The low-density lipoprotein receptor-related protein (LRP) mediates clearance of coagulation factor Xa in vivo. Blood 91, 555-560 (1998).
20. Takahashi, I. et al. Activated factor IX-antithrombin III complexes in human blood: quantification by an enzyme-linked differential antibody immunoassay and determination of the in vivo half-life. J Lab Clin Med 118, 317-325 (1991).
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