Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane

State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane

Pentameric ligand-gated ion channels (pLGICs) are receptor proteins that are sensitive to their membrane environment, but the mechanism for how lipids modulate function under physiological conditions in a state dependent manner is not known. The glycine receptor is a pLGIC whose structure has been resolved in different functional states. Using a realistic model of a neuronal membrane coupled with coarse-grained molecular dynamics simulations, we demonstrate that some key lipid-protein interactions are dependent on the receptor state, suggesting that lipids may regulate the receptor's conformational dynamics. Comparison with existing structural data confirms known lipid binding sites, but we also predict further protein-lipid interactions including a site at the communication interface between the extracellular and transmembrane domain. Moreover, in the active state, cholesterol can bind to the binding site of the positive allosteric modulator ivermectin. These protein-lipid interaction sites could in future be exploited for the rational design of lipid-like allosteric drugs.

Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter

The human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transporter with the highest quality using the X-ray crystal structure of mouse ABCB1 (Pgp1), a close homologue of ABCB5 and a well-studied member of the ABC family. Molecular dynamics simulations were used to validate the atomistic model of ABCB5 and characterise its structural properties in model cell membranes. Molecular docking simulations of known ABCB5 substrates such as taxanes, anthracyclines, camptothecin and etoposide were then used to identify at least three putative binding sites for chemotherapeutic drugs transported by ABCB5. The location of these three binding sites is predicted to overlap with the corresponding binding sites in Pgp1. These findings will serve as the basis for future in vitro studies to validate the nature of the identified substrate-binding sites in the full-length ABCB5 transporter.

Probing cholesterol binding and translocation in P-glycoprotein

P-glycoprotein (Pgp) is a biomedically important member of the ABC transporter superfamily that mediates multidrug resistance in various cancer types. Substrate binding and transport in Pgp are modulated by the presence of cholesterol in the membrane. Structural information on cholesterol binding sites and mechanistic details of its redistribution are, however, largely unknown. In this study, a set of 40 independent molecular dynamics (MD) simulations of Pgp embedded in cholesterol-rich lipid bilayers are reported, totaling 8 μs, enabling extensive sampling of cholesterol-protein interactions in Pgp. Clustering analyses of the ensemble of cholesterol molecules (∼5740) sampled around Pgp in these simulations reveal specific and asymmetric cholesterol-binding regions formed by the transmembrane (TM) helices TM1-6 and TM8. Notably, not all the putative cholesterol binding sites identified by MD can be predicted by the primary sequence based cholesterol-recognition amino acid consensus (CRAC) or inverted CRAC (CARC) motifs, an observation that we attribute to inadequacy of these motifs to account for binding sites formed by remote amino acids in the sequence that can still be spatially adjacent to each other. Binding of cholesterol to Pgp occurs more frequently through its rough β-face formed by the two protruding methyl groups, whereas the opposite smooth α-face prefers packing alongside the membrane lipids. One full and two partial cholesterol flipping events between the two leaflets of the bilayer mediated by the surface of Pgp are also captured in these simulations. All flipping events are observed in a region formed by helices TM1, TM2, and TM11, featuring two full and two partial CRAC/CARC motifs, with Tyr49 and Tyr126 identified as key residues interacting with cholesterol during this event. Our study is the first to report direct observation of unconventional cholesterol translocation on the surface of Pgp, providing a secondary transport model for the known flippase activity of ABC exporters of cholesterol. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.