Comparison of the transmembrane helices of bovine rhodopsin in the crystal structure and the C α template based on cryo-electron microscopy maps and sequence analysis of the G protein-coupled receptors

Modelling the structures of G protein-coupled receptors aided by three-dimensional validation

Background

G protein-coupled receptors (GPCRs) are abundant, activate complex signalling and represent the targets for up to ~60% of pharmaceuticals but there is a paucity of structural data. Bovine rhodopsin is the first GPCR for which high-resolution structures have been completed but significant variations in structure are likely to exist among the GPCRs. Because of this, considerable effort has been expended on developing in silico tools for refining structures of individual GPCRs. We have developed REPIMPS, a modification of the inverse-folding software Profiles-3D, to assess and predict the rotational orientation and vertical position of helices within the helix bundle of individual GPCRs. We highlight the value of the method by applying it to the Baldwin GPCR template but the method can, in principle, be applied to any low- or high-resolution membrane protein template or structure.

Results

3D models were built for transmembrane helical segments of 493 GPCRs based on the Baldwin template, and the models were then scored using REPIMPS and Profiles-3D. The compatibility scores increased significantly using REPIMPS because it takes into account the physicochemical properties of the (lipid) environment surrounding the helix bundle. The arrangement of helices in the helix bundle of the 493 models was then altered systematically by rotating the individual helices. For most GPCRs in the set, changes in the rotational position of one or more helices resulted in significant improvement in the compatibility scores. In particular, for most GPCRs, a rotation of helix VII by 240–300° resulted in improved scores. Bovine rhodopsin modelled using this method showed 3.31 Å RMSD to its crystal structure for 198 C^α atom pairs, suggesting the utility of the method even when starting with idealised structures such as the Baldwin template.

Conclusion

We have developed an in silico tool which can be used to test the validity of, and refine, models of GPCRs with respect to helix rotation and vertical position based on the physicochemical properties of amino acids and the surrounding environment. The method can be applied to any multi-pass membrane protein and potentially can be used in combination with other high-throughput methodologies to generate and refine models of membrane proteins.

Molecular Dynamics Simulation of Dark-adapted Rhodopsin in an Explicit Membrane Bilayer: Coupling between Local Retinal and Larger Scale Conformational Change

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.