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Molecular modeling studies give hint for the existence of a symmetric hβ2R-Gαβγ-homodimer

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Abstract

Several experimental studies suggest that GPCR dimers or oligomers may play an important role in signal transduction. In 2011 the crystal structure of a hβ2R-Gαβγ-complex was published and crystal structures of GPCR dimers are known. But until now, no crystal structure of a GPCR dimer including the Gαβγ-complex is available. In order to obtain detailed insights into interactions within hβ2R dimers including the Gαβγ-complex we performed a potential-energy-surface scan in order to identify favored asymmetric and symmetric hβ2R-Gαβγ-homodimers. This potential energy surface scan suggests, besides the existence of asymmetric dimers, the existence of a symmetric hβ2R-Gαβγ-homodimer with a TM I/VII-contact. A subsequent 20 ns MD simulation of the symmetric homodimer revealed large asymmetric conformational changes of both hβ2Rs, especially regarding TM VII and the interaction network between Asp2.50, Val7.44, Ser7.46 and Tyr7.43. Since similar conformational changes were not observed during the molecular dynamic simulation of the monomeric hβ2R-Gαβγ-complex, it may be suggested that the conformational changes in the symmetric homodimer are related to the presence of the second hβ2R-Gαβγ-complex. Due to the limitations of simulation time, conformational changes within a time scale of μs or ms may of course not be observed. However, the detected conformational changes, especially in TM VII, correspond to minima on the potential energy surface and thus, this study gives new insights into GPCR dimers on molecular level and furthermore, gives suggestions for site-directed mutagenesis studies.

Symmetric hβ2R-Gαβγ-homodimer

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Acknowledgments

This work was supported by DFG (STR 1125/1-1) of the Deutsche Forschungsgemeinschaft.

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Authors and Affiliations

  1. Department of Pharmaceutical and Medicinal Chemistry II, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93040, Regensburg, Germany

    Andrea Straßer

  2. Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, 93040, Regensburg, Germany

    Hans-Joachim Wittmann

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  1. Andrea Straßer
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Correspondence to Andrea Straßer.

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Andrea Straßer and Hans-Joachim Wittmann contributed equally to this work

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Fig. S1

Total energy of the whole simulation box and box volume during the productive phase of the simulations for the monomer and the symmetric homodimer. (JPEG 50 kb)

High resolution image (TIFF 1805 kb)

Fig. S2

Relative density profile of water and the lipid bilayer. The relative density profile of water and the nitrogens of the POPC lipid bilayer are given as mean value with respect to time for the productive simulation phase of the symmetric homodimer. The relative density is calculated independently for the water and the POPC-nitrogen in such a manner that the maximum for both curves is 1. The gray line behind the curve for water indicates the relative water density at 200 different time frames in 100 ps steps within the productive simulation. (JPEG 60 kb)

High resolution image (TIFF 4072 kb)

Fig. S3

Lipids between both hβ2Rs at different times of equilibration and productive phase. For clarity, only the tube models of the hβ2Rs are shown, but not the G proteins. (JPEG 381 kb)

High resolution image (TIFF 10736 kb)

Fig. S4

Interaction between the ligand P0G and the hβ2R. A, Snapshot of the ligand in the binding pocket of the hβ2R (hβ2R (r2symdim), complex II) of the symmetric dimer. Besides a direct H-bond interaction between the ligand and hβ2R, water molecules, which are present in the binding pocket, mediate the interaction between the ligand and hβ2R. Exemplary, three water molecules are shown. Due to a high fluctuation of the water molecules into the binding pocket and back into the extracellular part, they exchange with each other during the simulation. B, Direct H-bonds between the ligand and hβ2R (rmono) of the monomeric hβ2R-Gαβγ-complex and both hβ2Rs (r1symdim and r2symdim) of the symmetric homodimeric hβ2R-Gαβγ- hβ2R-Gαβγ-complex. The red dots indicated the presence of a direct H-bond between P0G and the hβ2R. (JPEG 181 kb)

High resolution image (TIFF 6749 kb)

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Straßer, A., Wittmann, HJ. Molecular modeling studies give hint for the existence of a symmetric hβ2R-Gαβγ-homodimer. J Mol Model 19, 4443–4457 (2013). https://doi.org/10.1007/s00894-013-1923-8

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  • DOI: https://doi.org/10.1007/s00894-013-1923-8

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