Structural analysis of β2GPI–PF4 complex. This model was extracted from the dynamics docking simulation and then extensively minimized. Among the 70 best ranked structures extracted from the simulation trajectory, this model exhibited the most favorable binding energy. (A) The molecular surface representation of β2GPI is colored by its electrostatic potential (red indicates electronegative; blue, electropositive; gray, hydrophobic), whereas PF4 is shown in ribbons colored by its secondary structure. (B) The interaction interface of PF4 is colored by its electrostatic potential. It possesses electrostatic charges complementary to that of the interaction surface of β2GPI (shown as orange ribbons). (C) Representation of the hydrogen bonds formed between domains III, IV, and V of β2GPI (shown as green ribbons) and PF4 (shown as yellow ribbons). The residues involved in these interactions are displayed as CPK-colored ball/stick and labeled in the color of the corresponding chain. (D) Steric clash analysis of the N-glycans at residues Asn143, Asn174, and Asn234 of β2GPI (as determined by x-ray crystallography in PDB structure 1QUB) and PF4. The oligosaccharides are shown as blue sticks with dotted surface, whereas PF4 is displayed as a yellow ribbon. Only a bulky-complex sugar at Asn164 could interfere in ligand binding.