Journal of Molecular Biology
Volume 272, Issue 1, 12 September 1997, Pages 144-164
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An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors1

https://doi.org/10.1006/jmbi.1997.1240Get rights and content

Abstract

A model for the alpha-carbon positions in the seven transmembrane helices in the rhodopsin family of G-protein-coupled receptors is presented. The model incorporates structural information derived from the analysis of ∼500 sequences in this family. The location, relative to the centre of the lipid bilayer, of each of the seven helical sequence segments and their probable lengths are deduced from sequence analysis, along with the orientation, relative to the centre of the helix bundle, of each helical segment around its axis. The packing of the helices in the model is guided by the density in a three-dimensional map of frog rhodopsin determined by electron cryo-microscopy. The model suggests which of the residues that are highly conserved in this family of receptors interact with each other. Helices III, V and VI are predicted to protrude more than the others from the central lipid core towards the aqueous phase on the intracellular side of the membrane. This feature could be a property of the receptor structure in some but not all of the conformations that it adopts, since recent studies suggest that relative movement occurs between these helices on photoactivation of rhodopsin. Results from other techniques, including the creation of metal-binding sites and disulphide bridges, site-directed spin-labelling studies, the substituted-cysteine accessibility method and other site-directed mutagenesis studies, are discussed in terms of the model.

Introduction

The rhodopsin family of G-protein-coupled receptors includes many of great medical importance. Besides the visual pigments, this family includes receptors for neurotransmitters, peptide and glycoprotein hormones, chemokines and adenine nucleotides. A large body of information on the function of these receptors has been accumulated Baldwin 1994, Khorana 1993, Strader et al 1995, van Rhee and Jacobson 1996, Wess et al 1995 and a knowledge of their structure is a preliminary step towards an understanding of signal transduction mechanisms and rational drug design. The direct determination, by X-ray crystallography or electron microscopy, of the atomic structure of any member of this family of membrane proteins has not yet been achieved. For the moment, useful structural insights can be obtained by combining sequence and other information with the low-resolution structural data that are currently available.

This family of receptors is characterised by amino acid sequences that have seven hydrophobic segments, each of which contains a distinct pattern of two or three conserved residues. Structural information derived from the analysis of ∼200 sequences of the family was used to derive a model (Baldwin, 1993) that established the arrangement of seven membrane-spanning helical segments that was compatible with a low-resolution projection density map of bovine rhodopsin obtained by electron cryo-microscopy (Schertler et al., 1993). The model specified the orientation of each of the seven helical segments with respect to the centre of the helical bundle, assigned the segments of sequence to the peaks of density in the projection map and suggested how these segments might be arranged in three dimensions. In the proposed arrangement, the seven helical sequence segments are arranged sequentially in a clockwise manner when viewed from the intracellular side, and helix III is the most buried helix, particularly on the intracellular side. Projection maps of frog rhodopsin (Schertler & Hargrave, 1995) and of squid rhodopsin (Davies et al., 1996) and a map of bovine rhodopsin with some resolution in the direction perpendicular to the membrane (Unger & Schertler, 1995) have since been determined and these maps have been discussed in terms of the model.

There are now many more sequences available for the rhodopsin family of G-protein-coupled receptors, enabling an updated model based on an analysis of ∼500 clearly alignable sequences to be presented. The location of the helical sequence segments relative to the plane of the membrane, and the probable limits to which the helices extend outside the lipid bilayer core, can now be predicted from sequence information, in addition to the orientation of the helical segments relative to the centre of the helix bundle. There is also a new low-resolution density map of frog rhodopsin (Unger et al., 1997) that has significant resolution perpendicular to the membrane plane. This map verifies the general features of the previous three-dimensional model but shows that the angles at which some of the helices are inclined to the membrane normal were underestimated. The positions and inclinations of the helix axes incorporated in this updated model are compatible with the density in the new map but are not uniquely specified by it. The new model provides probable alpha-carbon positions within the seven helical segments, over the lengths that appear common to all the receptors in the rhodopsin family.

Recent studies indicate that there is relative movement between some of the helices when rhodopsin is photoactivated (Farrens et al., 1996) and that G-protein activation is prevented if this movement is suppressed Farrens et al 1996, Sheikh et al 1996. The existence of such a conformation change, presumably common to the mechanism of all receptors in the family, means that the conservation patterns revealed by the sequence analysis are not necessarily indicative of the ground-state structure of a receptor but may belong to a conformation that is stabilised by the binding of agonist and/or G-protein.

Section snippets

Helix axes parameters

For the previous model (Baldwin, 1993), the positions and inclinations of the helix axes were estimated from the projection map of bovine rhodopsin (Schertler et al., 1993). The new three-dimensional map of frog rhodopsin (Unger et al., 1997) gives a clearer indication of these helix axes parameters, although the interpretation of the map is not entirely clear. It is now established which side of the map corresponds to the intracellular side of the membrane. This was determined during the data

Helix orientations, locations and lengths

The orientation of each helix with respect to the centre of the bundle of helices is clear from Figure 2. Conclusions can also be drawn concerning the location of each helical segment relative to the centre of the lipid bilayer and the limits of each helix in the intracellular and extracellular directions.

Conclusions

We present an alpha-carbon template for the helical parts of the structure of rhodopsin-like receptors. The parts of the molecule that lie in the core of the lipid bilayer and the extensions of the helices on the intracellular side where G-proteins bind are more certain than the extensions of the helices on the extracellular side where more variation in structure is expected between family members. The model is compatible with many recent results and it makes predictions that could be tested by

Acknowledgements

We thank Richard Henderson for helpful discussion and encouragement. We are grateful to the organisers of the SwissProt and EMBL databanks, and to the authors of sequence information for making their data available through the databanks.

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    Edited by R. Huber

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    Present address: V. M. Unger, The Scripps Research Institute, Department of Cell Biology, 10666 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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