Hello! I am donuts554. After a while, I have seen that in some proteins, especially the locked segments, there seems to be clusters of amino acids of the same type on the surface of them. I thought that there must be some special reason for why there are clusters in specific places in specific proteins.
So, several of the locked segments of the locked segments of Foldit puzzles were looked through, and I noticed that parts of the locked protein backbone tended to have been designated as a loop structure in Foldit, while there were several oxygen atoms &/or polar and uncharged amino acids surrounding those parts.
Here are some examples I have found:
Example B. https://fold.it/portal/files/chatimg/irc_902783_1591211878.png (the structures were set with the "Reset Structures" action
From these clusters I have found, I have made several hypotheses that I made that may explain how and why these clusters are. I will share three of them for now.
1. If oxygen's relatively strong electronegativity may leave an inductive effect on the atoms bonded to it, then this inductive effect may be what stabilizes the loop secondary structure, and cause the bends in the tertiary structure.
According to a study at https://pubmed.ncbi.nlm.nih.gov/10021421/ , it has been proved that the inductive effect caused by the oxygen atom present in hydroxyproline stabilizes the triple-helix collagen structure. This poly-proline helix is neither a alpha helix, nor a beta-sheet, so it is rendered as a loop secondary structure in Foldit.
This study has been referenced in an online paper that won the 2005 Emil Thomas Kaiser Award, at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242511/ .
2. If two hydrophilic, polar and uncharged amino acids with both of them each having a high enough polarity are strongly attracted to each other, and that they also would form a strong and stable hydrophilic bond, then this bond would be stable enough to stabilize the bends in the loops between the helixes and/or sheets.
According to https://authoring.concord.org/sequences/502/activities/9727/pages/125063/806c7dbd-d4d5-4a40-8f41-5c1ec10e9f7a , a credible site which has science simulations, it says that compounds with a high enough polarity are strongly attracted to each other, which greatly lowers the potential energy. Since uncharged and hydrophilic amino acids are very polar, those types of amino acids may be strongly attracted to each other.
3. If there are strong hydrophobic amino acids around the endpoints of the loop secondary structures (as in Example C), then those strong hydrophobic amino acids being brought together would cause the bend of the loop secondary structure, with the hydrophilic, polar and uncharged amino acids in the loop just contributing to stabilize the loop.
In my investigation, I used the 2D tool at http://mw.concord.org/nextgen/#interactives/biology/intermolecular-attractions-bio/protein-folding-bio . It shows hydrophilic, polar, and uncharged amino acids as forming a strong bond with each other. I think this tool is important in terms of the physics involved, not its structure, because it is in 2D.
I strongly encourage any questions or comments about my hypothesis and I will try to reply to them as soon as possible! Thank you for reading through my forum post! Good day and stay well!