ArticleBiophysical journal2005
Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Structure prediction of the second extracellular loop in G-protein-coupled receptors.Biophysical journal · 2014Article
- Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking.BMC biophysics · 2014Article
- The cytoplasmic rhodopsin-protein interface: potential for drug discovery.Current drug targets · 2012Review
- Conserved residues in the extracellular loops of short-wavelength cone visual pigments.Biochemistry · 2011Article
- Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor.Proteins · 2011Article
- Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors.Proteins · 2010Article
- Progress in elucidating the structural and dynamic character of G Protein-Coupled Receptor oligomers for use in drug discovery.Current pharmaceutical design · 2009Review
- Modulating G-protein coupled receptor/G-protein signal transduction by small molecules suggested by virtual screening.Journal of medicinal chemistry · 2008Article
- Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.Biophysical journal · 2008Article
- Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors.Expert opinion on drug discovery · 2008Article
- Loop modeling: Sampling, filtering, and scoring.Proteins · 2008Article
- Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin.Biophysical journal · 2007Article
- Membrane protein prediction methods.Methods (San Diego, Calif.) · 2007Review
- How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations.Proteins · 2007Article
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2 authors.
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Abstract
Conformational possibilities of flexible loops in rhodopsin, a prototypical G-protein-coupled receptor, were studied by modeling both in the dark-adapted (R) and activated (R*) states. Loop structures were built onto templates representing the R and R* states of the TM region of rhodopsin developed previously (G. V. Nikiforovich and G. R. Marshall. 2003. Biochemistry. 42:9110). Geometrical sampling and energy calculations were performed for each individual loop, as well as for the interacting intracellular loops IC1, IC2, and IC3 and the extracellular loops EC1, EC2, and EC3 mounted on the R and R* templates. Calculations revealed that the intra- and extracellular loops of rhodopsin possess low-energy structures corresponding to large conformational movements both in the R and R* states. Results of these calculations are in good agreement with the x-ray data available for the dark-adapted rhodopsin as well as with the available experimental biophysical data on the disulfide-linked mutants of rhodopsin. The calculated results are used to exemplify how the combined application of the results of independent calculations with emerging experimental data can be used to select plausible three-dimensional structures of the loops in rhodopsin.
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