Consider the following protein sequence. Circle the regions of the protein that

you think will either be an internal part of a protein, or found as a transmembrane domain.

MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASW

SSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAK

QTKRMLDMKVNPIQGLASKWDYEKNEWKK

I have no idea how to do this. I did a google search, and I found something that said the internal parts of a protein are more likely to be hydrophobic. I went through and found all the hydrophobic amino acids. For the most part, it seemed like hydrophobic were distributed randomly throughout the sequence, except for one part, identified in bold below:

MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASW

SSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAK

QTKRMLDMKVNPIQGLASKWDYEKNEWKK

 

 

Am I correct in thinking that the bolded part is the region that's part of the internal part of the protein? And that everything else is part of the transmembrane domain?

Edited March 24, 201312 yr by TeenieBopper

That sounds very reasonable to me. If it is not correct, I'd like to know why.

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Do we know whether this protein has a single alpha helix as the transmembrane domain, or are there multiple alpha helices? A few proteins have beta transmembrane domains also, but perhaps we can ignore them. I think your answer might be backwards.

Based on the available info the answer as well as the reasoning sound reasonable to me. Bonus if you want to do some digging: it is a cytochrome c oxidase subunit.

 

Edit: After re-reading it appears that I may have misunderstood OP. To clarify, the hyrdrophobic run is the part that is located within the membrane. the rest would be intra- or extracellular, respectively.

Edited April 10, 201312 yr by CharonY