Question

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

Answer 1

To obtain more accurate results when comparing the hydrophobicity of proteins from an extremophile and a mesophile, you can use molecular dynamics simulations, analyze the amino acid sequences using machine learning algorithms, and consider the secondary and tertiary protein structures.

Step-by-step explanation:

When comparing the hydrophobicity of proteins involved in the Calvin cycle from an extremophile and a mesophile, there are several bioinformatic techniques you can use to obtain more accurate results. One approach is to use molecular dynamics simulations, which can provide information on the behavior of the proteins in a water environment. You can also analyze the amino acid sequences using machine learning algorithms trained on experimentally determined hydrophobicity data. Additionally, considering the secondary and tertiary protein structures can give you insights into their hydrophobic properties.