Understanding the Dynamics of Full-Length Tissue Factor (TF_1-263) in the Context of Allosteric Modulation of Factor VIIa : A Molecular Dynamics Simulation Approach

Tissue factor (TF) mediated blood clot is the key event in cellular physiology. During vascular injury or endothelial cell rupture, factor VII (FVII) which is present normally in flowing blood as zymogenic form, upon binding with its cofactor TF (present beneath endothelial cell), get converted into its activated form, FVIIa; makes TF-FVIIa protease complex for the conversion of downstream protease members into activated form. Upon successful transformation of FX to FXa, prothrombin to thrombin, soluble fibrinogen get converted into its insoluble form fibrin, which accumulates at the site of vascular injury in the presence of platelets, resulting into the blood clot.

Recent studies have shown that TF is solely responsible for the structural modulation of FVIIa. However, due to lack of well-resolved crystal structure of the zymogenic form of FVII and full-length TF-FVIIa binary complex, the actual allosteric mechanism induced by TF and structural changes observed in FVIIa is not fully understood at atomic resolution. Molecular dynamic simulation is the only way to visual the potential interaction between protein-protein and protein-lipid at atomistic resolution. Here we did the simulation of complex and free FVIIa to understand the causative effect of TF in terms of allosteric modulation occurred in FVIIa. The present study was carried out to investigate the domain-wise structural modulation of FVIIa in the presence of full-length TF. We have done the comparative study among full-length (FL) TF_1-263-FVIIa, sTF_1-219-FVIIa and free FVIIa. Measurements of intrinsic dynamic changes clearly suggest that TF not only made changes in the allosteric modulation of FVIIa but inter as well intradomain communication made between FLTF and FVIIa is also responsible for the structural modulation in the protease domain of FVIIa. Among interdomain communication, two interactions between EGF2 domain and FLTF (Glu94-Ser47 and Asp104-Thr51) guide the potential effect of TF in the structural modulation of FVIIa. Examining the catalytic triad localization reveals that single as well as double interaction regulates the dynamism of protease part in substrate recognition and substrate catalysis, however in the case of no interaction the movement of CT is much higher and in a wide range. In a case of sTF-FVIIa complex, few inter-domain communications ware missing, which causes reduced affinity of sTF towards FVIIa and thus sTF-FVIIa shows less activity compare to FLTF. We proposed the hypothesis that binding of FLTF not only changes the allosteric alteration of SP domain but also induces the structural alteration in each domain of FVIIa, and these alterations in combination contribute to the enhancement of FLTF-FVIIa activity in which two interactions may be the controller for such dynamic changes in FVIIa. In summary, our study provides valuable information to understand the blood coagulation more intrinsically.