Human Coagulation Factor Va Interaction with Phospholipid Vesicles: A Molecular Dynamics Study.
Authors: Orban Tivadar , Kalafatis Michael 
Published: October 2019

Abstract
The prothrombinase complex, the enzyme responsible for the timely conversion of prothrombin to thrombin, is composed of factor Xa (the enzyme), factor Va (the cofactor) assembled on the activated cell surface in the presence of divalent metal ions. In our quest to propose a model of the prothrombinase complex we first created a homology model in solution of factor Va (pdb code 1y61). Next we created a mixed phospholipid bilayer model composed of 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) and 1-palmitoyl, 2-oleoyl-sn-glycero-3-phosphatidylserine (POPS) in a 4:1 ratio. The lipid bilayer was equilibrated for 10 ns. The data showed that the average area per head group and the deuterium order parameters of the fatty acyl chains compare well with the previously reported nuclear magnetic resonance data. We next created a system composed of factor Va, water molecules, phospholipid bilayer composed of POPS/POPC and sodium ions. Factor Va was placed at the near interface of the equilibrated POPC/POPS phospholipid bilayer but making sure that the two entities were not interacting. Molecular dynamics simulation was then performed on the entire system. Distance analysis performed between the center of masses of the factor Va molecule and the lipid bilayer revealed that during the 4.5 ns simulation time, the factor Va molecule gets inserted into the interface of the hydrophobic core of the bilayer. The distance between the two centers of masses decreased during the 4.5 ns simulation time from 92 Å to 78 Å. At the end of the 4.5 ns simulation time the indole moieties of Trp2063 and Trp2064 were found to be in the vicinity of the ester and the fatty acyl chain moieties of the phospholipids. Factor Va was found to participate in hydrogen bonds formation with both the carboxylate and the phosphate groups of POPS. Following 4.5 ns simulation time the farthest amino acid residue away from the membrane is located at ~ 100 Å from the lipid bilayer plane. This result is in agreement with previous fluorescence energy transfer studies that concluded that a domain of membrane-bound factor Va is positioned at a minimum distance of 90 Å above the membrane surface. It is noteworthy that the amino acid sequence comprising Pro1663 to Val1672 of factor Va had a root mean square displacemenent (RMSD) 4.5 times higher as the average RMSD of the other residues, i.e., 9 Å. This sequence is highly hydrophobic in nature and it was previously shown to contain a membrane binding site on factor Va. However, the present placement of factor Va on the lipid bilayer does not allow the insertion of this hydrophobic patch into the lipid bilayer. We next tested the hypothesis whether the region encompassing amino acid residues Glu323 to Val331 gets exposed to solvent following the interaction of factor Va with the phospholipids. This region was shown to contain a binding site of factor Xa on factor Va. Solvent accessible surface area calculated for each amino acid residue of the Glu323 to Val331 sequence revealed that during the 4.5 ns simulation time the solvent accessible surface area does not increase. In conclusion, our work proposes for the first time a model of factor Va bound to a mixed POPC/POPS lipid bilayer and provides the necessary framework that accounts for the presence of phospholipids as a major regulatory component of a protein complex. This model can be extrapolated to the study of the dynamics of other membrane associated complexes involved in blood coagulation.