Figure 2.

MD simulation of warfarin binding to VKOR. (A) The initial position of warfarin and the 3-TM VKOR in 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) lipid bilayer in the ionic water environment. For clarity, water molecules and ions are not shown. Warfarin was added to the ER lumen of VKOR (structure of the last snapshot of the 62-nanosecond simulation according to Wu et al¹⁷), and equilibrated for 40 nanoseconds using unconstrained conventional MD simulation. (B) Snapshots of the steered MD simulation of warfarin accessing the putative binding site of VKOR during 448 picoseconds. For clarity, water, ions, and lipids molecules are not shown. Key residues, encountered during warfarin accessing the binding site in VKOR, are labeled and displayed using stick diagrams.