Detection of pairwise residue proximity by covariation analysis for 3D-structure prediction of G-protein-coupled receptors.
G-protein-coupled receptor (GPCR) is one of the most important targets for medicines. Homology modeling based on the crystal structure of bovine rhodopsin is currently the most frequently used method for GPCR targeted drug design. Information about residue-residue contacts and the structural specificity in the subfamily is essential for constructing more precise 3D structures, to distinguish the structural differences between the template and targets. In this study, we adopted the covariation analysis to extract information about residue-residue interactions from the amino acid sequence. In the opsin family, a large number of adjacent covarying residue pairs were detected. The detected residue pairs have a strong tendency to gather in some regions important for the structure and function. These results suggest that the covariation analysis is practically utilized to detect adjacent residue pairs and also to apply for predicting functional sites. Analyses of other GPCR subfamilies, olfactory receptor and chemokine receptor families, demonstrated that some adjacent covarying residue pairs were common. Thus, the covariation analysis has possibilities in the substantial improvement of the 3D-structure modeling of GPCRs and in the detection of functional sites such as the ligand-binding sites.
Nemoto
Wataru
W
Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
Imai
Takashi
T
Takahashi
Takuya
T
Kikuchi
Takeshi
T
Fujita
Norihisa
N
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D008024:Ligands; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods; D012243:Rhodopsin / Q000737:chemistry; D017299:Rod Opsins / Q000737:chemistry; D012984:Software; D013223:Statistics as Topic
D008024:Ligands; D017299:Rod Opsins; D012243:Rhodopsin