Computational study of coagulation factor VIIa’s affinity for phospholipid membranes

Abstract

The interaction between the gamma-carboxyglutamic acid-rich domain of coagulation factor VIIa (FVIIa), a vitamin-K-dependent enzyme, and phospholipid membranes plays a major role in initiation of blood coagulation. However, despite a high sequence and structural similarity to the Gla domain of other vitamin-K-dependent enzymes with a high membrane affinity, its affinity for negatively charged phospholipids is poor. A few amino acid differences are responsible for this observation. Based on the X-ray structure of lysophosphatidylserine (lysoPS) bound to the Gla domain of bovine prothrombin (Prth), models of the Gla domain of wildtype FVIIa and mutated FVIIa Gla domains in complex with lysoPS were built. Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on the complexes were applied to investigate the significant difference in the binding affinity. The MD simulation approach provides a structural and dynamic support to the role of P10Q and K32E mutations in the improvement of the membrane contact. Hence, rotation of the Gly11 main chain generated during the MD simulation results in a hydrogen bond with Q10 side chain as well as the appearance of a hydrogen bond between E32 and Q10 forcing the loop harbouring Arg9 and Arg15 to shrink and thereby enhances the accessibility of the phospholipids to the calcium ions. Furthermore, the application of the SMD simulation method to dissociate C6-lysoPS from a series of Gla domain models exhibits a ranking of the rupture force that can be useful in the interpretation of the PS interaction with Gla domains. Finally, adiabatic mapping of Gla6 residue in FVIIa with or without insertion of Tyr4 confirms the critical role of the insertion on the conformation of the side chain Gla6 in FVIIa and the corresponding Gla7 in Prth.

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

“…480 The GLA domain of coagulation factor VII (FVII-GLA) has also been studied using AA simulations, with SMD used to assess the rupture force of PS unbinding from wildtype and mutant FVII-GLA domains. 481 Ohkubo et al used SMD to simulate FVII-GLA binding to a 100% PS membrane, and later simulated spontaneous binding of the same domain to a PS-HMMM membrane. 176 This allowed for demonstration of hydrophobic keel binding to the membrane core, the importance of Ca 2+ ions in association of FVII-GLA with anionic lipids, and identification of protein residues with significant lipid contacts.…”

Distinct Structural and Adhesive Roles of Ca2+ in Membrane Binding of Blood Coagulation Factors

“…In the X-ray-and NMR-solved structures of the GLA domain of bovine prothrombin, charged side chains and Ca 2+ ions interact with a single molecule of 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine (lysophosphatidylserine, or, in short, lysoPS) (Huang et al, 2003). Taboureau and Olsen (2007) carried out simulations to pull out the lysoPS from the complex and investigated the role of protein side chains in membrane binding. McCallum et al (1996) estimated the distance from the membrane to the active site in the protease domain of human FVIIa along the membrane normal to be about 76 A ẘhen FVIIa is associated with TF.…”

Phosphatidylserine and phosphatidylethanolamine regulate the structure and function of FVIIa and its interaction with soluble tissue factor

“…However, we could not detect any noticeable change in the overall secondary structure of FVIIa in the presence of soluble lipids from the CD spectroscopic measurement (data not shown). Notably, Taboureau et al also reported no perturbation in FVIIa due to the insertion of C6Lyso-PS [30]. Both single and two lipid titrations with des Gla-FVIIa revealed the fact that at least one of the two lipid binding sites exists in the Gla domain.…”

“…Lysolipids are an emerging class of signaling lipids involved in inflammatory and autoimmune diseases [28]. Activated platelets secrete Lyso-PS [29] and lyso-PE [30] in vitro. Lyso-PS may be involved specifically in platelet activation in vivo, [31] yet its physiological function has not been fully elucidated.…”