Completed Three-Dimensional Model of Human Coagulation Factor Va. Molecular Dynamics Simulations and Structural Analyses

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Factor Va is the critical cofactor for prothrombinase assembly required for timely and efficient prothrombin activation. In the absence of a complete crystal structure for the cofactor, Pellequer et al. [(2000) Thromb. Haemostasis 84, 849−857] proposed an incomplete homology model of factor Va (it lacks 46 amino acids from the carboxyl terminus of the heavy chain), which is a static model in a vacuum. A recently published X-ray structure of activated protein C (APC) inactivated bovine factor Vai (without the A2 domain) suggests a completely new arrangement of the C1 and C2 domains as compared with the previously published structure of the recombinant C1 and C2 domains. Our aims were (a) to exchange the C1 and C2 domains of the homology model with the modified bovine C1 and C2 domains using the X-ray structure as a template, (b) to determine by computation the three-dimensional model for the carboxyl-terminal peptide of the factor Va heavy chain (Ser664−Arg709) and incorporate it into the incomplete model, (c) to obtain a complete model of the cofactor folded in solution that might account for its physiological functions and interactions with other components of prothrombinase, and (d) to use the model in order to understand the mechanism of factor Va inactivation by APC. In the first step a sequence alignment of the human and bovine C1 and C2 domains was performed followed by amino acid changes in the three-dimensional structure where the sequences were not identical. The new model of the C1 and C2 domains was then attached to the homology model. The analysis of the MD simulation data revealed that several domains of the cofactor were significantly displaced during simulation. Using our completed model of human factor Va, we are also demonstrating for the first time that cleavage of membrane-bound normal factor Va as well as membrane-bound factor VLEIDEN by APC at Arg306 is required for the dissociation of the A2 domain from the rest of the molecule. Thus, differences in the inactivation rates of the two cofactor molecules are due to differences in the rate of cleavage at Arg306. The data demonstrate that our model represents the foundation for the establishment of a complete prothrombinase complex model, which might be successful in describing accurately the ternary protein−protein interaction and thus accounts for experimental observations.