Conformational Transition Of Human P-gp Studied By Targeted Molecular Dynamics Simulations

Multidrug resistance in the treatment of cancers is caused by the over-expressionof human P-glycoprotein (P-gp). It transports anti-cancer drugs out of cancer cellsthrough the conformational transition, which causes the ineffectiveness ofchemotherapy. Therefore, studying the conformational transition of human P-gp hasimportant academic significance and application value. After building theinward-facing3D structure of human P-gp using homology modeling, the molecularmechanism of the conformational transition was investigated using the targetedmolecular dynamics (MD) simulations.Taking the X-ray crystal structure of mouse P-gp as a template,100structures ofhuman P-gp are established using Modeller software. Three scoring functions wereused to screen and Ramachandran Plots were used to evaluate the final model ofhuman P-gp. The results show that the obtained model is better than the reportedmodels. So, it is dependable to be used in the further MD simulations. The MDsimulations were used to establish the inward/outward-facing protein/membranesystems, which were then minimized and equilibrated.Targeted MD simulations were performed to investigate the conformationaltransition from the inward-to the outward-facing states of human P-gp. The resultsshow that two nucleotide-binding domains (NBDs) move both on the two directions(x and y), which induces the close of them and adjusts their conformations to form thecorrect ATP binding pockets. The movements of NBDs triggered the movement ofkey segments (KSs) at the end of TMDs. The motion between KSs in y directioninduces the outward open of human P-gp conformation through the α-helix.Using conventional MD simulations, the study on outward-facing andinward-facing protein/membrane systems was performed to analyze the interactionsbetween KSs and NBDs. The interaction networks in the interface between NBDs andTMDs are more complex in outward-facing system, which is beneficial to the stabilityof human P-gp structure. The results indicate that x-loops play key roles in theformation of outward-facing conformation, and highly conservative key residue pairscontribute to the interactions between NBDs and TMDs mostly.