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Collect the cytoplasmic loop segments from 7TM receptors

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Collect the cytoplasmic loop segments from 7TM receptors

Postby studentbio » Mon Mar 19, 2012 6:00 pm

Hello, I am new to this forum as well to bioinformatics, however I have this project to do and I am completley blank... I am asking for help/advice from any kind people who know more than me about that subject.

My project objective is to find out whether cytoplasmic loops of '7-transmembrane helix' receptor proteins show structural homology/conserved features. I have chosen Class C (or 3) Metabotropic glutamate receptors to work on, I know roughly what genes encode different types of that receptor family proteins but I DO NOT know how to isolate sequences of cytoplasmic loops.

Is there any way I can find this from entire sequence of the protein gene? OR there is some other ways?

Please help.

Thank you for all replies ;)
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Postby JackBean » Mon Apr 02, 2012 10:07 am

You need to determine, which segments are membrane-spanning helices. The rest are the extra-membranous loops. What I remember about 7TM proteins, one of them should be considerably longer and that's the one you are looking for ;)

Cis or trans? That's what matters.
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