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PEDS Advance Access published online on March 24, 2006
Protein Engineering Design and Selection, doi:10.1093/protein/gzl010
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received September 6, 2005
Revised January 17, 2006
Accepted February 20, 2006

Article

Statistical analysis and prediction of functional residues effective for GPCR-G-protein coupling selectivity

Takahiko Muramatsu 1 * and Makiko Suwa 1

1 Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8915-5 Takayama, Ikoma, Nara 630-1010, Japan; Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Waterfront BIO-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan

* To whom correspondence should be addressed.
Takahiko Muramatsu, E-mail: taka-mu{at}is.naist.jp


  Abstract

One of the important issues in G-protein-coupled receptor (GPCR) functional analysis is the mechanism of GPCR-G-protein coupling selectivity. G-proteins are classified into Gi/o, Gq/11 and Gs families. Although several experimental and computational analyses have been attempted, the mechanism remains unknown to this day. In this study, we have analyzed the multiple sequence alignments of GPCRs of known coupling selectivities by mapping onto the tertiary structure of rhodopsin. We identified several functional residue sites in GPCRs related to coupling selectivity, which are located mainly at the intracellular loops, and found that the occurrence of positively/negatively charged amino acids of the characteristic residues varies depending on the G-protein coupling selectivity. Especially, the occurrence of positively charged amino acids in receptors coupling to Gs family is less than that in receptors coupling to Gi/o and Gq/11 families. It is interesting that some characteristic residues are located near the extracellular terminus of transmembrane helices, which is far from the GPCR/G-protein binding interface. In most of the receptors coupling to Gs family, the occurrence of proline on the position corresponding to the 170th residue on rhodopsin is rare. These findings are vital to improving our understanding of the mechanism of G-protein coupling selectivity.

Keywords: G-protein-coupled receptor; functional residue site; correlation coefficient; rhodopsin; protein-protein interaction.
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