Studies of the Conformational Dynamics of Ligand and Nucleotide Bound P-Glycoprotein

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A major factor contributing to the therapeutic effectiveness of a drug is whether it will be a substrate for efflux transporter proteins such as P-glycoprotein (P-gp). P-gp is an ATP-binding cassette transporter that is able to expel a remarkable range of therapeutic drugs from their target cells. Despite this, surprisingly little is known about the mechanism with which it exports drugs. Following drug binding within P-gp's transmembrane domain (TMD) binding cavity, export to the cell exterior is believed to be driven by ATP binding and/or hydrolysis at the cytoplasmic nucleotide binding domains (NBDs). We have been using atomistic molecular dynamics simulation to study the interactions of experimentally characterized ligands with the binding cavity of P-gp and their influence on P-gp NBD dynamics.Available structures of P-gp display large separations of their NBDs. We observed tighter association of the NBDs in our simulations even in the absence of nucleotide. The degree of association and ATP binding site conformations were dependent on whether substrate or inhibitor was bound in the TMD binding cavity. In addition, conformational changes in the binding cavity coupled with ligand dynamics allowed formation of protein-ligand contacts that agreed with previous mutational studies but could not be predicted from just the crystal structure. Finally we explored the effects of ATP binding and hydrolysis to better understand how this process is coupled to substrate transport.