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In Silico Mutation and Binding Studies of Human FVIIa γ‑Carboxyglutamic Acid-Domain to Endothelial Protein C Receptor: A Molecular Dynamics Simulation Approach

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journal contribution
posted on 08.01.2019 by Suparna Banerjee, Ramesh Prasad, Prosenjit Sen
Endothelial cell protein C receptor (EPCR), a multifunctional and multicellular receptor, is known to interact with protein C through its γ-carboxyglutamic acid (GLA)-rich domain. Being homologous to protein C, factor (F)­VIIa (activated form) also binds to EPCR through its GLA-domain. FXa also has a GLA-domain like FVIIa and protein C; however, there is a variation in FVIIa/FXa GLA-domain binding with EPCR in different species such as human (h) and mouse (m). The key differences present in the GLA-domain of these two species are the disposition of the residues located at fourth, eighth, and ninth positions. Recently, it was shown that phenylalanine (Phe) at the fourth position of hFVIIa GLA-domain is responsible for EPCR binding; however, hFXa has the same Phe at the fourth position, although the binding affinity of hFXa with EPCR is different. Atomistic illustration underlying the GLA-domain-binding mechanism toward EPCR remains unclear. Here, we employed molecular dynamics simulation to get insight into the structural alteration of interacting proteins. Free-energy profiles of all systems [wild-type (WT) and mutants] using the potential of mean force were computed. Phe4-mediated protein–protein (Phe4–Try154) and protein–lipid (Phe4–PCh) local interactions are prominently found in WT hFVIIa; however, these interactions get impaired in hFXa–EPCR interactions. Mutational studies in hFVIIa based on hFXa delineate the residue located at eighth and ninth positions and further guide the Phe4-based local interactions. Our findings considerably enrich the understanding of the protein structure–function relationship for FVIIa-based EPCR studies.