A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.
BACKGROUND
G- Protein coupled receptors (GPCRs) comprise the largest group of eukaryotic cell surface receptors with great pharmacological interest. A broad range of native ligands interact and activate GPCRs, leading to signal transduction within cells. Most of these responses are mediated through the interaction of GPCRs with heterotrimeric GTP-binding proteins (G-proteins). Due to the information explosion in biological sequence databases, the development of software algorithms that could predict properties of GPCRs is important. Experimental data reported in the literature suggest that heterotrimeric G-proteins interact with parts of the activated receptor at the transmembrane helix-intracellular loop interface. Utilizing this information and membrane topology information, we have developed an intensive exploratory approach to generate a refined library of statistical models (Hidden Markov Models) that predict the coupling preference of GPCRs to heterotrimeric G-proteins. The method predicts the coupling preferences of GPCRs to Gs, Gi/o and Gq/11, but not G12/13 subfamilies.


RESULTS
Using a dataset of 282 GPCR sequences of known coupling preference to G-proteins and adopting a five-fold cross-validation procedure, the method yielded an 89.7% correct classification rate. In a validation set comprised of all receptor sequences that are species homologues to GPCRs with known coupling preferences, excluding the sequences used to train the models, our method yields a correct classification rate of 91.0%. Furthermore, promiscuous coupling properties were correctly predicted for 6 of the 24 GPCRs that are known to interact with more than one subfamily of G-proteins.


CONCLUSIONS
Our method demonstrates high correct classification rate. Unlike previously published methods performing the same task, it does not require any transmembrane topology prediction in a preceding step. A web-server for the prediction of GPCRs coupling specificity to G-proteins available for non-commercial users is located at http://bioinformatics.biol.uoa.gr/PRED-COUPLE.
Sgourakis
Nikolaos G
NG
Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece. nsgourakis@biol.uoa.gr
Bagos
Pantelis G
PG
Papasaikas
Panagiotis K
PK
Hamodrakas
Stavros J
SJ
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008024:Ligands; D008390:Markov Chains; D008954:Models, Biological; D008956:Models, Chemical; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D025941:Protein Interaction Mapping; D011956:Receptors, Cell Surface; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000235:genetics*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software
D008024:Ligands; D011956:Receptors, Cell Surface; D043562:Receptors, G-Protein-Coupled