Different Physical Parameters in the Bonds between Platelet Glycoprotein Ibalpha with von Willebrand factor and with Coagulant Factor XI -Results from the Molecular Dynamic Simulation-

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Background: Both von Willebrand factor (VWF) and coagulation factor XI (FXI) bind with platelet membrane glycoprotein (GP) Ibalpha. However, the differences in the physical parameters in the bonds between VWF-GPIbalpha and FXI-GPIbalpha mediating different biological functions are unclear. Methods: The FXI molecule was arranged in 9 different initial positions around the structure of GPIbalpha bound to VWF. The position coordinate and velocity vectors of all atoms constructing VWF, GPIbalpha, and FXI were calculated in each 2 femto (10-15) second using the Chemistry at HARvard Macromolecular Mechanics (CHARMM) force field. The physical parameters of VWF-GPIbalpha and FXI-GPIbalpha bonds were calculated by molecular dynamic (MD) simulations. Results: MD calculation revealed 2.8 to 11.3 times greater positional fluctuations in atoms constructing FXI-GPIbalpha as compared to those constructing VWF-GPIbapha (RMSDs: 5.9{plus minus}1.5 to 18.1{plus minus}7.9 Å for FXI-GPIbalpha vs 1.6{plus minus}0.1 to 2.1{plus minus}0.3 Å for VWF-GPIbalpha). The absolute value of non-covalent binding energy generated in FXI-GPIbalpha (65.5{plus minus}79.7 to 517.6{plus minus}54.2 kcal/mol) was smaller than that generated in VWF-GPIbalpha (678.5{plus minus}58.3 to 1000.4{plus minus}75.1 kcal/mol). The binding structure of VWF-GPIbalpha was stable and was only minimally influenced by the presence of FXI-GPIbalpha binding. Conclusions: Our MD calculation results revealed that atoms constructing the VWF-GPIbalpha bond are physically more stable and produce more non-covalent binding energy than the bond of FXI-GPIbalpha. The physical parameters in the VWF-GPIbalpha bond were not largely influenced by FXI binding with GPIbalpha.

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