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Mutations Affecting the Oligomerization Interface of G-Protein-Coupled Receptors Revealed by a Novel De Novo Protein Design Framework

Martin S. Taylor ^*, Ho K. Fung ^*, Rohit Rajgaria ^*, Marta Filizola , Harel Weinstein   and Christodoulos A. Floudas ^*

^* Department of Chemical Engineering, Princeton University, Princeton, New Jersey; Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York; Department of Physiology and Biophysics, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York

Correspondence: Address reprint requests to Christodoulos A. Floudas, Dept. of Chemical Engineering, Princeton University, Princeton, NJ 08544. Tel.: 609-258-4595; Fax: 609-258-0211; E-mail: floudas{at}titan.princeton.edu.

Specific functional and pharmacological properties have recently been ascribed to G-protein-coupled receptor (GPCR) dimers/oligomers. Because the association of two identical or two distinct GPCR monomers seems to be required to elicit receptor function, it is necessary to understand the exact nature of this interaction. We present here a novel method for de novo protein design and its application to the prediction of mutations that can stabilize or destabilize a GPCR dimer while maintaining the monomer's native fold. To test the efficacy of this new method, the dimer of the single-spanned transmembrane domain of glycophorin A was used as a model system. Experimental data from mutagenesis of the helix-helix interface are compared with computational predictions at that interface, and the model's results are found to be consistent with the experimental findings. A flexible template was developed for the rhodopsin homodimer at atomic resolution and used to predict sets of three and five mutations. The results are found to be consistent across eight case studies, with favored mutations at each position. Mutation sets predicted to be the most disruptive at the dimerization interface are found to be less specific to the flexible template than sets predicted to be less disruptive.