Volume 8, Issue 13 p. 1527-1539
Full Paper

Prediction of the 3D Structure of FMRF-amide Neuropeptides Bound to the Mouse MrgC11 GPCR and Experimental Validation

Jiyoung Heo Dr.

Jiyoung Heo Dr.

Materials and Process Simulations Center (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1 )626-585-0918

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Sang-Kyou Han Dr.

Sang-Kyou Han Dr.

Division of Biology (147-75), California Institute of Technology, Pasadena, CA 91125, USA

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Nagarajan Vaidehi  Dr.

Nagarajan Vaidehi  Dr.

Materials and Process Simulations Center (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1 )626-585-0918

Present address: City of Hope Graduate School of Biological Sciences, Division of Immunology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA

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John Wendel

John Wendel

Materials and Process Simulations Center (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1 )626-585-0918

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Peter Kekenes-Huskey

Peter Kekenes-Huskey

Materials and Process Simulations Center (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1 )626-585-0918

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William A. Goddard III Prof.

William A. Goddard III Prof.

Materials and Process Simulations Center (139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA, Fax: (+1 )626-585-0918

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First published: 27 August 2007
Citations: 20

Graphical Abstract

Reliable forecast. The 3D structure of the mouse MrgC11 G protein-coupled receptor and the binding site of FMRFamide peptides were predicted. Three residues, Tyr110, Asp161, and Asp179 in transmembrane (TM) regions 3, 4, and 5, respectively (see figure), were predicted to be important to ligand binding; this was verified by subsequent mutation experiments.

Abstract

We report the 3D structure predicted for the mouse MrgC11 (mMrgC11) receptor by using the MembStruk computational protocol, and the predicted binding site for the F-M-R-F-NH2 neuropeptide together with four singly chirally modified ligands. We predicted that the R-F-NH2 part of the tetrapeptide sticks down into the protein between the transmembrane (TM) domains 3, 4, 5, and 6. The Phe (F-NH2) interacted favorably with Tyr110 (TM3), while the Arg makes salt bridges to Asp161 (TM4) and Asp179 (TM5). We predicted that the Met extends from the binding site, but the terminal Phe residue sticks back into an aromatic/hydrophobic site flanked by Tyr237, Leu238, Leu240, and Tyr256 (TM6), and Trp162 (TM4). We carried out subsequent mutagenesis experiments followed by intracellular calcium-release assays that demonstrated the dramatic decrease in activity for the Tyr110Ala, Asp161Ala, and Asp179Ala substitutions, which was predicted by our model. These experiments provide strong evidence that our predicted G protein-coupled receptor (GPCR) structure is sufficiently accurate to identify binding sites for selective ligands. Similar studies were made with the mMrgA1 receptor, which did not bind the R-F-NH2 dipeptide; we explain this to be due to the increased hydrophobic character of the binding pocket in mMrgA1.