Identification of Putative Binding Sites of P‐glycoprotein Based on its Homology Model

Abstract

A homology model of P-glycoprotein based on the crystal structure of the multidrug transporter Sav1866 is developed, incorporated into a membrane environment, and optimized. The resulting model is analyzed in relation to the functional state and potential binding sites. The comparison of modeled distances to distances reported in experimental studies between particular residues suggests that the model corresponds most closely to the first ATP hydrolysis step of the protein transport cycle. Comparison to the protein 3D structure confirms this suggestion. Using SiteID and Site Finder programs three membrane related binding regions are identified: a region at the interface between the membrane and cytosol and two regions located in the transmembrane domains. The regions contain binding pockets of different size, orientation, and amino acids. A binding pocket located inside the membrane cavity is also identified. The pockets are analyzed in relation to amino acids shown experimentally to influence the protein function. The results suggest that the protein has multiple binding sites and may bind and/or release substrates in multiple pathways.

Lipid Regulation of the ABCB1 and ABCG2 Multidrug Transporters

“…All the computational methods discussed here, such as MD simulation or in silico docking, require high-resolution 3D structure of the protein under investigation. While murine Abcb1 has been crystallized in an apo state (Aller et al, 2009), and sufficient homology models can be built for its ATP-bound conformation (Globisch et al, 2008;O'Mara & Tieleman, 2007;Pajeva, Globisch, & Wiese, 2009), structural or homology models of human ABCG2 are insufficient for in silico studies because of the low-resolution structure information (cryoelectron microscopy, >5 Å ) (Rosenberg et al, 2010) and the very low (<20%) sequence similarity of the TMD with any existing ABC structure that could be applied as a possible template. s0110 5.1.…”

Human P-glycoprotein Contains a Greasy Ball-and-Socket Joint at the Second Transmission Interface

“…Models of human P-gp in a closed conformation have been built (23,24) using the Sav1866 crystal structure (25) as a template. Sav1866 is a homodimeric bacterial ABC drug pump that is predicted to have a similar architecture to human P-gp.…”

“…To address this question, we first tested whether the F1086A mutation blocked interactions with ATP or verapamil. (24) conformations are shown. C, histidine-tagged Cys-less P-gp or mutants A266C/F1086C, A266C, and F1086C (in Cys-less background) as well as wild-type P-gp and mutant F1086A ( in wild-type background) were isolated, and ATPase activities were measured in the presence of verapamil.…”

Identification of Residues in the Drug Translocation Pathway of the Human Multidrug Resistance P-glycoprotein by Arginine Mutagenesis

“…Fig. 1 (B-D) shows the models for N-half (residues 36 -631) C-half (residues 696 -1276), and full-length human P-gps, respectively (6). The models were based on the crystal structure of the Sav1866 multidrug transporter that was in the "closed conformation" (NBDs close together with TMDs in an outward facing conformation) (7).…”