Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors?

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Abstract

Molecular modelling is of major help to understand structure–function data on G-protein-coupled receptors (GPCRs). Since the first determination of the structure of rhodopsin, at high resolution, the view has emerged that it will be now easy to automatically obtain realistic models for any GPCR by homology modeling. Our experience on cholecystokinin CCK1 receptor modelling together with available data on other GPCRs leads us to rule out this opinion. We believe that construction of realistic models of certain GPCRs still remains time-consuming and requires many refinements of the models in close association with experiments. This conclusion has important consequences for modelling orphan GPCRs.

Section snippets

Homology modelling: an important, evolving methodology for GPCR modelling

Homology modelling is a computer-assisted method used to obtain a three-dimensional (3-D) model of a protein with an unknown structure, based on the structures of related proteins that are used as templates in the modelling procedure. This important method relies on an alignment between the target amino acid sequence and that of the template, and on the availability of a high-resolution structure of the template. For a long time, the only available 3-D structure of a 7-TM segment protein was

Rhodopsin: the first crystallized GPCR provides a new template for homology modelling

The publication in 2000 of the X-ray structure of rhodopsin at high resolution [8] has created the opportunity to compare data from this 3-D structure to indirect structural data from earlier studies, yielding the first detailed mechanisms of how rhodopsin propagates its signal 15, 16. More generally, the rhodopsin template was further applied to amine receptors such as dopamine D2 receptors and muscarinic acetylcholine M1 receptors to interpret structure–function data 17, 18. At last,

Construction of a CCK1 receptor model using the rhodopsin crystal as a template

The rhodopsin-derived CCK1 receptor model was built using Insight II modules (Homology, Discover and Biopolymer; Accelrys, San Diego, CA, USA). Alignment of the human CCK1 receptor sequence on the bovine rhodopsin sequence was performed using an alignment procedure [19], followed by manual refinement so that motifs common to GPCRs (e.g. E/DRY and NPXXY) and conserved amino acids between the two sequences matched precisely. The coordinates of the CCK1 receptor were then assigned to those of the

Testing of the rhodopsin-derived model by docking of CCK

A way to test the accuracy of the rhodopsin-derived CCK1 receptor model is to determine whether the receptor groove formed by the TM helices could receive its natural ligand CCK in a position compatible with experimental data that identify contact points between CCK and its binding site on the CCK1 receptor.

Validity of rhodopsin-derived models of other GPCRs?

Data suggesting that the rhodopsin structure could not be applied directly to the CCK1 receptor raise the double question: ‘why is the rhodopsin structure not directly applicable to the CCK1 receptor, and is this structure not directly applicable to many other GCPRs’. A first point that must be considered is the template itself. The template structure corresponds to an inactive conformation of the rhodopsin crystal. However, this conformation was used to build a CCK1 receptor model in a

Concluding remarks

Homology modelling of the CCK1 receptor using the rhodopsin structure as a template, together with emerging data on GPCRs, lead us to rule out the very attractive view that following the determination of the crystal structure of rhodopsin, it would now be easy and fast to automatically construct a realistic model of any GPCR. We believe that construction of realistic models of certain GPCRs still remains time-consuming and requires many refinements of the primary models on the basis of

Acknowledgements

This study was supported by grants from the Association pour la Recherche sur le Cancer 5481 and 4430.

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