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Modeling activated states of GPCRs: the rhodopsin template

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An Erratum to this article was published on 26 July 2007

Abstract

Activation of G Protein-Coupled Receptors (GPCRs) is an allosteric mechanism triggered by ligand binding and resulting in conformational changes transduced by the transmembrane domain. Models of the activated forms of GPCRs have become increasingly necessary for the development of a clear understanding of signal propagation into the cell. Experimental evidence points to a multiplicity of conformations related to the activation of the receptor, rendered important physiologically by the suggestion that different conformations may be responsible for coupling to different signaling pathways. In contrast to the inactive state of rhodopsin (RHO) for which several high quality X-ray structures are available, the structure-related information for the active states of rhodopsin and all other GPCRs is indirect. We have collected and stored such information in a repository we maintain for activation-specific structural data available for rhodopsin-like GPCRs, http://www.physiology.med.cornell.edu/GPCRactivation/gpcrindex.html. Using these data as structural constraints, we have applied Simulated Annealing Molecular Dynamics to construct a number of different active state models of RHO starting from the known inactive structure. The common features of the models indicate that TM3 and TM5 play an important role in activation, in addition to the well-established rearrangement of TM6. Some of the structural changes observed in these models occur in regions that were not involved in the constraints, and have not been previously tested experimentally; they emerge as interesting candidates for further experimental exploration of the conformational space of activated GPCRs. We show that none of the normal modes calculated from the inactive structure has a dominant contribution along the path of conformational rearrangement from inactive to the active forms of RHO in the models. This result may differentiate rhodopsin from other GPCRs, and the reasons for this difference are discussed in the context of the structural properties and the physiological function of the protein.

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Acknowledgements

We thank Dr. Luis Gracia for providing RMSD plugins, Dr. Marc Ceruso for the protonation states of rhodopsin residues, Dr. Evan Crocker and Dr. Steven O. Smith for providing NMR results prior to publication and Dr. Giuseppe A. Paleologo for helpful discussions. This work was supported by NIH grants DA00060, DA012923 (to HW) and DA017976, DA020032 (to MF) from the National Institute on Drug Abuse.

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Authors and Affiliations

  1. Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave., New York, NY, 10021, USA

    Masha Y. Niv, Lucy Skrabanek, Marta Filizola & Harel Weinstein

  2. HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Ave., New York, NY, 10021, USA

    Lucy Skrabanek & Harel Weinstein

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  1. Masha Y. Niv
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  2. Lucy Skrabanek
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Correspondence to Harel Weinstein.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s10822-007-9117-z

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Niv, M.Y., Skrabanek, L., Filizola, M. et al. Modeling activated states of GPCRs: the rhodopsin template. J Comput Aided Mol Des 20, 437–448 (2006). https://doi.org/10.1007/s10822-006-9061-3

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