Information Technology Reference
In-Depth Information
Fig. 7.5. Dynamics of rhodopsin predicted by the GNM and ANM. (a) Experimental(black),
GNM (red) and ANM (dashed blue) predicted thermal B-factors. (b) Distribution of square
displacements of residues predicted by GNM (blue) and ANM (black). The non-TM regions exhibit
higher mobilities, in general. ANM yields two additional minima: Pro180 and Cys187 near the EC
entrance to the chromophore binding pocket. (c) The global mode eigenvector calculated with the
GNM, indicating relative motions of different regions of the proteins along the principal mode
coordinate. Positive and negative regions delineate structural blocks subject to concerted motions.
The locations of the helices (1-8) are indicated on the upper abscissa and distinguished by gray
bands. (d) Ribbon diagram of rhodopsin color-coded according to the relative motions in (b) in
order of increasing mobilities: blue (lowest mobility), cyan, green, yellow, orange, red (highest
mobility). Side chains are shown for the seven GNM hinges labeled in (b) and 11- cis -retinal is
shown in light blue space-filling representation.
Rhodopsin: An activation mechanism coupling the EC and CP domains . As the
only structurally determined member of the G-protein coupled receptors (GPCR)
family, rhodopsin has been widely studied by both experimental and
computational techniques. Capture of the substrate G-protein triggers a highly
cooperative conformational change in rhodopsin accompanied by the
isomerization of its chromophore (11- cis -retinal) at the TM region. The
chromophore binding pocket is a highly packed region. The perturbation of the
structure at this region drives the propagation of the conformational change via
cooperative rearrangements of TM helices to the cytoplasmic (CP) domain, to
induce the active state of rhodopsin, metarhodopsin II (Meta-II) (Isin et al .,
2006). The application of GNM to two dark state structures of rhodopsin 1L9H
(Okada et al ., 2002) and 1U19A (Okada et al. , 2004) yielded the B-factor profile
( Fig. 7 .5A) in close agreement with the experimental data (correlation coefficient
Search WWH ::




Custom Search