![]() ![]() 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. 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. Bovine rhodopsin modelled using this method showed 3.31 Å RMSD to its crystal structure for 198 Cα atom pairs, suggesting the utility of the method even when starting with idealised structures such as the Baldwin template. In particular, for most GPCRs, a rotation of helix VII by 240–300° resulted in improved scores. For most GPCRs in the set, changes in the rotational position of one or more helices resulted in significant improvement in the compatibility scores. The arrangement of helices in the helix bundle of the 493 models was then altered systematically by rotating the individual helices. The compatibility scores increased significantly using REPIMPS because it takes into account the physicochemical properties of the (lipid) environment surrounding the helix bundle. Multi-pass TPs are notably hard to isolate due to their complicated architectures with numerous hydrophobic transmembrane sections and low expression levels in host cells, yet they have emerged as. 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. As the new protein is made by the ribosome, it enters the endoplasmic reticulum membrane where it folds into the correct shape. ![]() 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. Transmembrane proteins are synthesized by ribosomes protein-making machines that are on the surface of a cell compartment called the endoplasmic reticulum. 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. Because of this, considerable effort has been expended on developing in silico tools for refining structures of individual GPCRs. 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. 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. ![]()
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