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Susume's picture
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Joined: 10/02/2011

This is a very cool video exploring the spike protein in VR and looking at how to re-design a natural compound (linoleic acid) that has some ability to keep the spike from opening.

https://youtu.be/mZY-TIEwNI0

alcor29's picture
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Joined: 11/16/2012
Very ccol video

Is this pocket identifiable in the spike segments we are given for our binder puzzles?

Joined: 09/29/2016
Groups: Gargleblasters
TL;DR - I'm not able to, based on their camera work :(

It doesn't look like it's in our workable area. There's actually a whole Helix in the uncropped "Spike" subdomain that wasn't included in our puzzle (for valid reasons: it's way outside of where they want us to be working), and while it's hard to say for sure with it all folded up in all of their images, I think that may be where it is located. If not, my other thinking was that it's near Locked segments 7, 8, 9 on our puzzle.

But it's really hard to tell, since as I said, their reference model is the entire binding part of Coronavirus, which has 3 spikes that can --at least according to other animations-- independently hinge open and closed. It's quite a fascinating structure to see how it can function and convert itself the way it does, in very much the same way as a Docking Clamp works for a space station of underwater submersible.

To further make it harder to tell though, aside form those Spike domains being seeming to be "closed" in their model, is that OUR model does not have the same exact SS that other models are using. A key example is that in their model, I CAN make out where our puzzle is on their model with the other colored domains. In theirs, that 'outcropping' near where we design out Binder? Theirs has only 2 sheets, whereas ours has "3". Granted, one of the sheets in ours is just a single segment in length, but it still illustrates that our model isn't directly comparable to others on the internet. Or even the model in the LCB1 protein on the PDB website which is also from Baker Lab.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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