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

Abstract

SummaryA 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.

Characterization of a Factor Xa Binding Site on Factor Va near the Arg-506 Activated Protein C Cleavage Site

“…After humanization of the bovine FVa side chains, missing loops were built by superimposing the previous human FVa model onto the humanized bovine FVa using two overlapping residues on each side of the loop. All replaced side chains were optimized (33) then Cartesian coordinates of all atoms were energy-minimized with X-PLOR using standard protocols (32).…”

“…6) contained residues 1-663 of the heavy chain and the entire light chain (1546 -2196). The C-terminal tail of the A2 domain (664 -709) was missing in this model because it could not be modeled based on ceruloplasmin (32). Our model placed the sequence 499 -505 on the surface, adjacent to the APC cleavage site at Arg-506 -Gly-507.…”

The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function

“…The lack of interactions between the A1 and C2 domains suggests that the association between the A1 domain and light chain is entirely mediated by means of interactions with the A3 domain. (45), the cryoEM structure of factor VIIIa (B) (47), and the crystal structure of bovine Va i (C). The sizes and orientation of the ovals were scaled to match the cryoEM C2 domain.…”

Defining the Factor Xa-binding Site on Factor Va by Site-directed Glycosylation

“…A recently created three-dimensional model of FVa was very helpful for the selection of adequate sites for the novel carbohydrate side chains (29,30). We focused on introducing the glycosylation sites at residues that are surface-exposed in the three-dimensional model of FVa.…”