Discussions with Dr. Lynn Thursday Night (Halloween)
Setting the stage here - what am I doing in the Lynn lab?
I'm doing three rotations in three labs before choosing one. I'm now in my second six week rotation, the Lynn lab. Click the link on the right tab to see his home page website!
Basically, to start the rotation, Dr. Lynn requires students to come up with their own project - an idea I love and originally attracted me to his lab. I have been interested in figuring out applications for Lisa's peptide nanotubes since back in February when I heard about them. She made a peptide nanotube - a hollow tube out of a peptide repeat (a short piece of what makes up protein) that forms a bilayer structure (see photo at bottom of this post). The outer layer is negatively charged and the inner layer is positively charged. Such a nicely setup charge separation seems as if it should have some interesting uses, but no one has thought of any yet. I wanted to try to think of some. I've been thinking of this off and on since then.
The peptides form nanotubes by essentially stacking together in layers, than curling up into ribbons and finally closing up into a tube. You can see this idea if you look at a paper towel tube out of cardboard - it has the same twisted design into a tube - something Allisandra showed me.
A question: what sets the diameter of the tubes
I asked Dr. Lynn what formed the basis of the diameter size that the peptide nanotubes would form. That spawned an interesting discussion about different peptides and their nanotube diameters upon assembly. Their diameter appears to be determined by the N-terminal amino acid residue, I think.
And, in discussions with Allisandra, I learned it’s the phenylalanine di-peptide hydrophobic stacking interaction that dominates when nanotubes are formed. That’s a key principle it seems.
A modeling article I read: tubes within tubes; their rotation and frictional forces
I was looking up articles and found one of computationalists modeling two nanotubes inside each other rotating like some kind of shaft setup. There were atoms of opposite charges on either side of the inner tube and they placed the whole thing in an electric field, resulting in the inner tube spinning. However, the charged atoms in the field resulted in deformation of the tube. They were modeling frictional forces and stuff.
How does one get a tube inside a tube?
Several thoughts came from this paper – first was – how would one get a nanotube inside a nanotube in real life? I’m not sure how it would be done. Dr. Lynn said if you had a positive and negatively charged one of different peptide sequence that forms differently sized nanotubes, it’s possible they would form inside each other. That’s an interesting thought. (Mixed peptides still form separate tubes.)
Attaching a peptide nanotube to a nanorod
I was wondering if one could attach a nanotube on a nanorod that was magnetic, then spin the nanorod, resulting in spinning of the tube, like a shaft. But, I’m not sure what that would be used for. Also, I was worried such a shaft would unravel, unless it were spinning in the same direction that these peptides wind to form a tube.
Dr. Lynn actually liked this idea, for some reason, and said that shafts of peptide nanotubes would be unique, in that if they break, they can self-heal, unlike carbon nanotubes. I hadn’t thought of that. So we talked about how one could functionalize a tube onto a nanorod.
1. There’s a peptide sequence he mentioned with two his on one end. I thought why not lengthen this to six his and coordinate the peptide to a Ni-NTA? It might work.
2. Dr. Lynn had a fantastic idea that I really like related to DNA nucleated templating. They have these peptides that will only form tubes in the presence of DNA monomers. He said you could maybe functionalize DNA on the surface of a nanorod, then add the peptides along with a low concentration of DNA monomers. The peptides would nucleate a tube on the rod surface and potentially grow outward. SWEET! Except, very little is known about these tubes yet. I asked if they would still be stable as tubes upon the removal of the DNA monomers and Dr. Lynn said he didn’t know.
Conclusion to discussion
In conclusion to this discussion, which included a bit more than I’ve written about here, and much expansions of the same, Dr. Lynn said that I was good at asking why questions. […] *lifts hands up in sign of victory* I never expected to hear that and it really blessed me. I was so relieved. I consider it to be the Lord’s goodness to me – He did bless our conversation and give me favor with Dr. Lynn, exactly as I had been fervently asking for that day. I told him that was very comforting, which was true. Previously in the morning, he had been most obviously annoyed with me, but all that disappeared after this conversation.
He said I should discuss the ideas we’d talked about with Lisa and Allisandra to see if they could find flaws. I think I can try several of them at once, since some of them would take a long time to see if they worked.
Then he said he was going to hand out candy to kids, because he loved doing that on Halloween. I approve. We love doing that too at our house. We also make candy apples. This is the Halloween tradition.
Later, More Thinking
I was wondering if you could stand tubes up on a surface, make a “forest of tubes” that could potentially act as artificial cilia. I talked to Kevin about this on Friday and all the things I'd talked to Dr. Lynn about. There was one article I read about injecting (+) charge into carbon nanotubes that would expand the tube and bend it. Removal of the charge would unbend the tube – hence – wavy motion. I *think* it was fueled by hydrogen peroxide – that universal and problematic fuel. Still the concept is interesting.
I found articles tonight about such applications – at least – people studying this idea.
Interestingly, it seems people have been able to template “forests of tubes” onto surfaces by vapor deposition. Most of the examples of this I have seen so far are making nanotubes with a dipeptide of phenylalanine – the basic nanotube unit. However, I’m not if this makes uniform hollow tubes or not. They also make “nanobelts” that look like grass.
Interestingly, these tubes have piezoelectric and ferroelectric properties – even quantum confined phenomena. I wasn’t sure you could get that kind of thing. I’m not sure if that’s because they’re using only phe-phe dipeptides or what. More reading required.
FIN: Thoughts this weekend
So, I read a two of those articles this evening and one about nanomotors that I emailed to myself from Kevin’s laptop.
Unfortunately, I’m feeling really ill, with a low-grade fever. I don’t have time to be sick. So, if you would, pray I get better. Next week is stacking up to be just as busy if not busier than last week. *sigh* I just want to make sure I can get things done well, not doing anything slipshod. We’ll see how tomorrow goes.
Hmm... here's an interesting article about peptide nanotubes for application in sensing viruses, partially based on some of their electrical properties...