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montelena montelena
wrote...
Posts: 5
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9 years ago
I've been given an amino acid sequence, and I need to determine what features of the sequence suggest that it's a transmembrane protein. I then have to draw a schematic diagram of it to show where each amino acid is.

Here's the sequence:
glu-arg-arg-gln-leu-lys-his-his-lys-ser-glu-pro-glu-ile-leu-leu-ile-ile-phe-gly-val-met-ala-gly-val-ile-gly-gly-ile-leu-ile-leu-ile-ser-his-gly-ile-arg-arg-leu-ile-lys-lys-ser-pro-ser-asp-val-lys-pro-leu-pro

I'm not really sure where to start.
I took a look at each amino acid's polarity/charge, but from what I can tell it doesn't make any sense (I'm not really sure exactly what pattern I'm looking for, anyway). The chain is mostly non-polar, but the placement of charged AA and polar AA don't follow any pattern that would make sense for a transmembrane protein.

I'd love any assistance as to what I should look for in the sequence, what are some hallmarks of transmembrane protein AA sequences, or anything else that may help me figure this (and future) problems out.

Thanks!
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wrote...
Valued Member
9 years ago
Transmembrane proteins span the cell membrane. The amino acids in the middle, therefore, should be non-polar, whereas the ones at the ends should be polar.
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montelena Author
wrote...
9 years ago
That's what I thought, but the sequence I was given doesn't show that sort of pattern. I also considered that perhaps the protein folds within the membrane, so there would be amino acids in the "center" of the sequence that would be polar with some level of symmetry, but there isn't. And what's with the randomly placed charged amino acids? I thought they may be part of a transmembrane channel, but again, it doesn't seem like their pattern makes any sense.

So either it's some freaky looking odd-ball shaped folded transmembrane protein, or I'm crazy and this sequence is not transmembrane at all (despite that being the very topic this paper is covering).

Any ideas?
wrote...
Valued Member
9 years ago Edited: 9 years ago, ThePsychic
I suppose what you could do is download a protein viewer and add the sequence to it. Based on the amino acids in the sequence, it will determine its shape mathematically and give you an idea how it looks.

http://www.bioblender.eu/
http://jmol.sourceforge.net/download/

We used a program like this in undergrad. and it was spot on.
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wrote...
9 years ago
go to signalp software it will tell whether it has a signal peptide based on the hydrophobicity value etc
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