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Re: Ideal helices

On Tue, Jun 18, 2002 at 01:43:17PM +0300, Dan Thomas Major wrote:
> Hi,
> I'm modelling G-protein coupled receptors using rhodopsin as a template.
> When I compare the Ramachandran plot of the models vs that of rhodopsin,
> the models have much more ideal helices than the rhodopsin X-ray
> structure (2.8 A).

I am also modelling a GPCR using rhodopsin as a template.
There is a kink in one of the helices in rhodopsin caused by
met308-met309-asn310-lys311. Because the kink isn't caused by
something like proline, dihedral angles must probably incur some

> Is this because:
> 1) The homology is relatively low (20-30%) and the distance constraints
> receive a low weight in the pdf function??
> 2) The helices in rhodopsin are less regular than the globular proteins
> used in the pdf parametrization??
> 3) None of the above...
> Sincerely,
> Dan
> --
> Dan Thomas Major (at Dr. B. Fischer's lab)
> Bar-Ilan University
> Ramat-Gan, Israel
> Phone: 972-3-5317785
> Fax:   972-3-5348730

Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology | Undergraduate Research Assistant
Yale Medical School
Center for Medical Informatics | Summer Research Assistant