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Biophys. J. BioFAST: First Published September 30, 2005. doi:10.1529/biophysj.105.070722
© 2005 by the Biophysical Society.

A more recent version of this article appeared on December 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

Modeling Flexible Loops in the Dark-Adapted and Activated States of Rhodopsin, a Prototypical GPCR

Gregory V Nikiforovich 1 and Garland R Marshall 1*

1 Washington University

* To whom correspondence should be addressed. E-mail: niki4ov{at}biochem.wustl.edu.

Submitted on July 13, 2005
Revised on August 10, 2005
Accepted on 23 August 2005


  Abstract
Conformational possibilities of flexible loops in rhodopsin, a prototypical GPCR, 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 (Nikiforovich, G.V., Marshall, G.R. Biochemistry (2003) 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 3D structures of the loops in rhodopsin.

Key Words: G-protein coupled receptors, conformational transitions, modeling loops, rhodopsin, transduction




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Copyright © 2005 by the Biophysical Society.