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@ARTICLE{Isin:54914,
      author       = {Isin, B. and Rader, A.J. and Dhiman, H. K. and
                      Klein-Seetharaman, J. and Bahar, I.},
      title        = {{P}redisposition of the {T}hree-{D}imensional {D}ark
                      {S}tate {S}tructure of {R}hodopsin for {F}unctional
                      {C}onformational {C}hanges},
      journal      = {Proteins},
      volume       = {65},
      issn         = {0887-3585},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {PreJuSER-54914},
      pages        = {970 - 983},
      year         = {2006},
      note         = {Record converted from VDB: 12.11.2012},
      abstract     = {As the only member of the family of G-protein-coupled
                      receptors for which atomic coordinates are available,
                      rhodopsin is widely studied for insight into the molecular
                      mechanism of G-protein-coupled receptor activation. The
                      currently available structures refer to the inactive, dark
                      state, of rhodopsin, rather than the light-activated
                      metarhodopsin II (Meta II) state. A model for the Meta II
                      state is proposed here by analyzing elastic network normal
                      modes in conjunction with experimental data. Key mechanical
                      features and interactions broken/formed in the proposed
                      model are found to be consistent with the experimental data.
                      The model is further tested by using a set of Meta II
                      fluorescence decay rates measured to empirically
                      characterize the deactivation of rhodopsin mutants. The
                      model is found to correctly predict $93\%$ of the
                      experimentally observed effects in 119 rhodopsin mutants for
                      which the decay rates and misfolding data have been
                      measured, including a systematic analysis of Cys-->Ser
                      replacements reported here. Based on the detailed comparison
                      between model and experiments, a cooperative activation
                      mechanism is deduced that couples retinal isomerization to
                      concerted changes in conformation, facilitated by the
                      intrinsic dynamics of rhodopsin. A global hinge site is
                      identified near the retinal-binding pocket that ensures the
                      efficient propagation of signals from the central
                      transmembrane region to both cytoplasmic and extracellular
                      ends. The predicted activation mechanism opens the
                      transmembrane helices at the critical G-protein binding
                      cytoplasmic domain. This model provides a detailed,
                      mechanistic description of the activation process, extending
                      experimental observations and yielding new insights for
                      further tests.},
      keywords     = {Algorithms / Binding Sites / Hydrogen Bonding / Isomerism /
                      Ligands / Light / Models, Molecular / Neural Networks
                      (Computer) / Periodicity / Protein Conformation / Receptors,
                      G-Protein-Coupled: metabolism / Retinaldehyde: chemistry /
                      Retinaldehyde: metabolism / Rhodopsin: chemistry /
                      Rhodopsin: metabolism / Structure-Activity Relationship /
                      Ligands (NLM Chemicals) / Receptors, G-Protein-Coupled (NLM
                      Chemicals) / Retinaldehyde (NLM Chemicals) / metarhodopsins
                      (NLM Chemicals) / Rhodopsin (NLM Chemicals) / J (WoSType)},
      cin          = {IBI-2},
      ddc          = {540},
      cid          = {I:(DE-Juel1)VDB58},
      pnm          = {Funktion und Dysfunktion des Nervensystems},
      pid          = {G:(DE-Juel1)FUEK409},
      shelfmark    = {Biochemistry $\&$ Molecular Biology / Biophysics},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:17009319},
      UT           = {WOS:000242056500018},
      doi          = {10.1002/prot.21158},
      url          = {https://juser.fz-juelich.de/record/54914},
}