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How Much Bovine Rhodopsin Crystal Structure is Useful for Modeling Human GPCRs? - ß2-Adrenergic Receptor as a Test Case

Availability of realistic models for human G-Protein Coupled Receptors (hGPCRs) will aid structure-based drug design (SBDD), thus shortening the time period needed for drug development and minimizing crossreactivity of drugs with other hGPCRs. Many researchers have constructed models for hGPCRs with homology modeling techniques based on the X-ray structure of bovine rhodopsin and recently to β2adrenergic receptor which are the only two GPCRs that have high resolution crystal structures. In this study, we evaluate the usefulness of the bovine rhodopsin crystal structures for modeling hGPCRs by analysis of large database of human G-protein coupled receptors that are members of family A (rhodopsin family). The recently released structure of β2-adrenergic receptor was used as a test case for validation purposes of our findings. From pair-wise sequence alignment of each of the receptors in the database to bovine rhodopsin, we come to the conclusion that only for few hGPCRs, X-ray structure of rhodopsin could be used as a template for modeling the trans-membrane domains (TMDs).The detailed analysis of the whole database shows that in general, similarity to bovine rhodopsin is found more in the middle/endoplasmic part than in the exoplasmic part. The shift in the cytoplasmic end of TMD-6 that has been seen in the recently released crystal structure of β2-adrenergic receptor could be understood well from our bioinformatics study. On the basis of our results from this research, we propose to regard specific parts from the endoplasmic domain of the rhodopsin helices as appropriate template for constructing models of other GPCRs, while most of the exoplasmic parts of GPCRs in this family require other techniques for their modeling, due to the low sequence similarity between the receptors and rhodopsin in that region.