I have always heard a bunch of my friends who are studying for their masters and PhD always complaining about the difficulty of working with hydrophobic proteins compared to that of hydrophilic proteins. I have a basic understanding that these titles are related to non-polarity and polarity, but I am wondering what causes hydrophobic proteins to give them so much difficulty when they ar trying to, I think, purify and express them.
Hydrophobic proteins don’t like water. When you try to clone them they tend to fold poorly and form insoluble inclusion bodies. They also tend to fall out of solution, or denature, during purification. That forces people to include all sorts of odd detergents and salts in their buffers, just to keep the proteins happy. Of course soap is seldom a good substitute for a proteins natural environment, so even when you do get the things purified, it’s doubtful that they retain a native configuration or functionality.