1: Proteins. 2006 May 15;63(3):466-78. 

Predicting the three-dimensional structure of human P-glycoprotein in absence of
ATP by computational techniques embodying crosslinking data: Insight into the
mechanism of ligand migration and binding sites.

Vandevuer S, Van Bambeke F, Tulkens PM, Prevost M.

Bioinformatique Genomique et Structurale, Universite Libre de Bruxelles,
Bruxelles, Belgium.

P-glycoprotein is a membrane protein involved in the phenomenon of multidrug
resistance. Its activity and transport function have been largely characterized
by various biochemical studies and a low-resolution image has been obtained by
electron microscopy. Obtaining a high-resolution structure is, however, still
remote due to the inherent difficulties in the experimental determination of
membrane protein structures. We present here a three-dimensional (3D) atomic
model of P-glycoprotein in absence of ATP. This model was obtained using a
combination of computational techniques including comparative modeling and rigid
body dynamics simulations that embody all available cysteine disulfide
crosslinking data characterizing the whole protein in absence of ATP. The model
features rather well most of the experimental interresidue distances derived
both in the transmembrane domains and in the nucleotide binding domains. The
model is also in good agreement with electron microscopy data, particularly in
terms of size and topology. It features a large cavity detected in the protein
core into which seven ligands were successfully docked. Their predicted affinity
correlates well with experimental values. Locations of docked ligands compare
favorably with those suggested by cysteine-scanning data. The finding of
different positions both for a single ligand and for different ligands
corroborates the experimental evidence indicating the existence of multiple drug
binding sites. The interactions identified between P-glycoprotein and the docked
ligands reveal that different types of interactions such as H-bonds, pi-pi and
cation-pi interactions occur in agreement with a recently proposed pharmacophore
model of P-glycoprotein ligands. Furthermore, the model also displays a lateral
opening located in the transmembrane domains connecting the lipid bilayer to the
central cavity. This feature supports rather well the commonly admitted
mechanism of substrate uptake from the lipid bilayer. We propose that this 3D
model may be an important tool to understand the structure-function relationship
of P-glycoprotein. (c) 2006 Wiley-Liss, Inc.

PMID: 16463278 [PubMed - in process]