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fourth-year undergrad here so any help is super appreciated! Also this is not something I am working on for a grade, so pls don't think I am just looking for someone to do my homework lol!

In a gist, the project I am currently working on requires me to compare the same proteins involved in the Calvin cycle from both an extremophile and a mesophile. Specifically, I am supposed to figure out if the extremophile (which lives in the Arctic) protein's are more hydrophobic than the mesophile. I am expected just to use in sillico/bioinformatic techniques to figure this out

So far, all I have done is run the amino acid sequences through various hydrophobicity scales so each residue is given a ranking of hydrophobicity, then calculated an average from that. Obviously, this has a lot of flaws and is not proving to be very effective

If anyone has any ideas of programs or methodologies that could produce more accurate results I would be so grateful! I have been going in circles with this for a while now

Thank-you!

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  • $\begingroup$ Please explain what flaws you think the method you are currently using has and what you mean by "is not proving to be very effective". Effective in what? Do you just mean you can't find any differences? And it hardly seems that "getting more accurate results" can be your problem — why would you think the measures of hydrophobicity are inaccurate? And are you just averaging values of amino acids for each protein, or plotting values graphically across a whole protein, as is possible? $\endgroup$
    – David
    Commented Aug 10, 2023 at 11:40
  • $\begingroup$ Perhaps try to see if the protein is expected to be embedded in a membrane? See if hydrophobic parts are clustered, or if there is a signal sequence giving hints. $\endgroup$ Commented Sep 25, 2023 at 11:27

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I believe that the standard hydrophobicity measure is protein GRAVY.

However, as David comments, I don't see any particular reason to expect that its estimates would deviate from what you find by other means, as it's just taking the average across the protein rather than considering any other aspects of structure:

Protein GRAVY returns the GRAVY (grand average of hydropathy) value for the protein sequences you enter. The GRAVY value is calculated by adding the hydropathy value for each residue and dividing by the length of the sequence (Kyte and Doolittle; 1982).

There are more recent, more elaborate methods that quantify different features of hydrophobicity, but I don't imagine that your professors are asking for these somewhat less readily interpretable measures.

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