GMoS (GPCRs Motif Searcher) searches for conserved sequence motifs in the most recent sequence alignment of Class A GPCRs, obtained from the GPCRDB. The results are classified according to the percentage of occurrences within subfamilies. The core code was written by Joffre Heredia, and the different utilities and web interface have been created by Marlous Hoogstraat and Marc Perea. For questions or comments, contact Xavier Deupi.
The GMoS algorithm is highly flexible and allows for a number of different types of searches to be performed. So far, we have developed two extensive utilities:
GMoS (search of a sequence motif at a particular position)
Correlated GMoS (simultaneous search of two sequence motifs at two different positions throughout the sequence)
Applications
There is no publication presenting this program yet, although it has been used in many of our publications. For a very basic (albeit useful) usage, you can check ref. [1], where GMoS is used to show that the highly conserved (D/E)R(Y/W) amino acid sequence of Class A GPCRs is present in ~72% of the sequences.
In a more elaborate application, GMoS has been used to study the presence of motifs associating Pro with either Ser or Thr in Class A GPCRs [2]. The results suggest that association of Ser and Thr with Pro is commonly used in transmembrane helices of specific subfamilies to accommodate the structural needs of specific functions (ref. [3]). GMoS can also be used to detect subfamily-specific residues involved in ligand selectivity.
References
[1] Kobilka, B., Deupi, X. "Conformational complexity of G Protein Coupled Receptors." Trends in Pharmacological Sciences 2007 28:397-406
[2] Deupi X, Olivella M, Govaerts C, Ballesteros JA, Campillo M, Pardo L. Ser and Thr residues modulate the conformation of Pro-kinked transmembrane alpha-helices. Biophys J. 2004 86:105-15.
[3] Govaerts, C., Blanpain, C., Deupi, X., Ballet, S., Ballesteros, JA., Wodak, SJ., Vassart, G., Pardo, L., Parmentier, M. "The TXP motif in the second transmembrane helix of CCR5. A structural determinant of chemokine-induced activation." Journal of Biological Chemistry 2001 276(16):13217-25
Last modified: March 11 2011.
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