Capturing Large-Scale Conformational Dynamics of P-Glycoprotein by MD Simulations

Abstract

P-glycoprotein is one of the most biomedically relevant ABC transporters, due to its frequent over-expression in cancer cells and involvement in their multidrug resistance. The crystal structure of murine P-glycoprotein has been reported in the nucleotide-free state. Employing molecular dynamics simulations we have investigated its conformation, dynamics and transport mechanism in a membrane environment. The simulation results show that, surprisingly, P-glycoprotein is capable of adopting an unusually wide range of conformations under the nucleotide-free conditions, highlighted by the degree of separation between the two nucleotide-binding domains (NBDs). During the equilibrium simulations, the distance between the two NBDs fluctuates over a range of at least 20 A, exhibiting both wider and narrower NBD openings than what is captured in the crystal structure. Moreover, we have been able to successfully dock ATP and Mg2+ in the Walker A motif, and generate an ATP-bound state that remains stable throughout the following 50 ns simulations. Interestingly, the presence of ATP and Mg2+ does not significantly alter the distribution of P-glycoprotein between open and closed conformations during the simulations, implying that the closed dimeric NBDs might be an innate conformation already existing in the nucleotide-free form, and the presence of nucleotide only stabilizes such a closed form. These results are in very close agreement, and in fact rationalize the reported high fluctuations at the NBDs measured in several other ABC exporters, which is possibly representing a fundamental difference in the transport mechanisms between ABC exporters and importers.