Science Buddies: "Ask an Expert"

Hello ScienceBuddies community,
I need a bit of help wrapping my head around what amino acids are and how protein folding works. I get that all amino acids have in common a basic structure consisting of a carboxyl group -COOH, an amine group -NH2, an atom of hydrogen -H, and a variable R group, all bound to an alpha Carbon. These R groups can be Positively Charged Side Chains, Negatively Charged Side Chains, Hydrophobic Side Chains, Polar Uncharged Side Chains, or Special Cases (not sure about these? Like Glycine or Proline?), and are what determine the tertiary structure of a protein. That said, I don't understand 1) What is the difference between any two amino acids with the same property? As in, couldn't you just take any Hydrophobic side chain, replace it with another such side chain, and have the same resulting tertiary structure and a functionally identical protein? Or if this isn't true, what makes each amino acid unique beyond these groupings? and 2) Are there different ways of folding the same folds/creating a protein with the same tertiary structure and shape but with more unique primary structure?
Basically, I'm trying to identify proteins that fold similarly to a certain domain that I'm looking at, and I think understanding these concepts better would be helpful in doing so. Thank you.

Hi, antarcticUrbanite, these are great questions!

1. The difference between amino acids with the same property is the molecular structure of their R groups and how that influences other amino acids' ability to interact with them.
For example, alanine, leucine, and phenylalanine are all non-polar, hydrophobic amino acids. All of their R groups are composed entirely of carbon and hydrogen. However, they are different sizes and shapes. This means that other amino acids will have different abilities to fold around them. Say a protein normally had an alanine in a particular spot in its primary structure. Alanine's R group is hydrophobic and quite small, so it's likely that other parts of the protein would fold around it. If you replaced the alanine with a leucine, other parts of the protein might have a harder time folding into their normal positions around it, since leucine is a little bigger than alanine. And if you replaced the alanine with a phenylalanine, you would expect to interfere even more with the protein's normal folding around that spot, since phenlalanine is much larger than alanine. This could therefore have quite an important impact on the overall protein's tertiary structure and function.

2. How proteins fold into their tertiary structures is a very complicated puzzle that scientists are still trying to figure out. Right now, given the primary structure of a protein, we still don't know for the most part how it will fold into a 3-dimensional protein. However, certain types of amino acid sequences can suggest that a given domain of the protein folds into secondary structures like alpha helices and beta sheets. We also use similarities between the primary structures of portions of proteins with known and unknown tertiary structure to predict or make an educated guess about the tertiary structure of potions of the unknown protein. So the short answer to your question is yes, although it's currently difficult to design new proteins with desired structures or function.
...That said, we're getting closer to being able to do this. Here is a recent-ish article from the New York Times sort of on this subject that you might find interesting:
https://www.nytimes.com/2017/12/26/scie ... baker.html

Good luck, and let me know if I can help explain anything further!