This is what I ended up with for question 2.4 - I choose ATP as the small molecule to investigate and interestingly GrowEL came up as one of the molecules which binds to it. I covered this protein in one lecture and found it quite cool which is why it caught my attention. It is a chaperone protein so it helps other proteins fold by encasing them in the central pore shown in the picture included.
Both ends of the protein are capped by growes in this process and ATP is used when the growes is removed. Sadly I could not find the ATP binding sites as the protein is rather large but u can see in the central pore several little legs which stick out and interact with the protein being folded either hydrophobicly or electrostaticly if the protein has charged residues within it. These residues vary depending on the protein to be folded and help overcome energy barriers ect to prevent incorrect conformations being attained (which I think is really clever design to help the protein reach the desired conformation).
BOOOO =( cant get the picture working. It says successful but then just dosn't show up.
ReplyDeleteWell that's weird, I tried the same thing as before when I got home from work and . . well it worked.
ReplyDeleteNice work! And I can see it fine as well. Do you know which organism this GroEL is sourced from?
ReplyDeleteOn the topic of chaperones: does anyone happen to know the difference between a chaperone and a chaperonin? Is it to do with size, additional components (e.g. GroES caps), function - or something else entirely?
I was under the impression that the difference between a chaperone and chaperonin was the size...but I haven't actually checked this and it could be completely wrong.
ReplyDeleteGroEL has inspired a technique for refining computational structures of folded proteins by Prof. Alan Mark and a student H. Fan before Alan came to UQ. The technique works by modulating the electrostatic interactions between the protein and its environment periodically. This modulation seems to help the protein get out of unfavorable structures where it gets "stuck" to find the native state. See:
ReplyDelete1) Fan & Mark. Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures. Protein Science (2006) vol. 15 (3) pp. 441-448
2)Fan & Mark. Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. Protein Science (2004) vol. 13 (4) pp. 992-999