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how to predict transmembrane protein structure

transmembrane protein protein tag

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#1 Thomson

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Posted 13 November 2017 - 11:27 PM

Hi all,

 

What is the accurate way to predict structure/orientation of a transmembrane protein, I want to knock in a tag into the transmembrane protein for detection purpose and am having trouble as of the ideal position to knock in the peptide tag gene. 

 

Thx.

 



#2 bob1

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Posted 14 November 2017 - 02:27 PM

Check the tools at ExPASy: https://www.expasy.o...t:transmembrane



#3 Thomson

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Posted 15 November 2017 - 04:28 PM

Check the tools at ExPASy: https://www.expasy.o...t:transmembrane

Thanks bob1. How accurate was it to predict using computational tool? Is there anything we shall take into account beside amino acid sequence? Eg signal peptide etc?



#4 bob1

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Posted 16 November 2017 - 07:45 PM

As accurate as any of these sorts of tools are. Basically they look for regions of hydrophobic residues flanked by regions of hydrophilic residues, often in groups of 3 or more and with a certain number of residues spacing the phobic/philic parts ( I can't remember how many).

 

I think there are some structural considerations, something along the lines of hydrophobic alpha helices separated by hydrophilic loops.






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