The body's fight against COVID-19 explained using 3D printed models

00:04:22 Antibodies are a protein that take a Y like shape.

All of life has proteins.

So human cells have proteins, and the same is true for viruses.

Even though they're not cells, like we think of technically,

right, they have proteins,

A virus is kind of made up of kind of two main things.

One is, is a protein shell and then genetic material.

So this is a 3d printed model I made of proteins from the human papilloma virus.

And these proteins form together, each one of these kind of colored pieces is

made up of five different proteins, and you put a bunch of them together

to make this kind of icosahedral shell.

And then inside, I've represented the genetic material here as a red strand.

And that's basically essentially what viruses its structure is made up of.

So in this case, we can see, right the the protein is making, . its function is to make a shell, protective shell around it.

Some viruses also have a plasma membrane or lipid membrane around them.

I haven't quite figured out how to model it yet, . maybe a plastic bag or something.

Like I mentioned, the spike protein kind of has two main roles for the virus.

One is to recognize and bind to human cells.

And so that the top part of it is going to recognize another protein that's on the cell surface.

So if imagine my arm is the cell surface, it's going to connect to a protein there.

And the protein that it recognizes in human cells is called ACE-2.

Once it recognizes that ACE-2 protein,

there's a more kind of complicated process in which the spike protein actually

unfolds and makes like a long, thin structure, . and allows to kind of stick into the the plasma membrane,

and basically fuse the plasma membrane of the virus with the plasma membrane of the cell.

It all has to do with the shapes and particularities of the spike protein and the ACE protein.

And I don't know if you can see, but read the surface is all really bumpy

and each of those little kind of little bumps represents an individual atom.

And the structure of the spike protein is, you know, specific in that

the surface here is going to recognize that ACE-2 protein,

sort of like, a puzzle, right, you know, puzzle piece that fits just right,

or people kind of use the analogy of a locking the key, right.

and it all comes down to the shape of the proteins,

and also some with with charge, right?

So some amino acids have a positive charge, some have a negative charge,

so you can imagine, right, each of these dots might be kind of like a little magnet.

So that connection and finding the right shape, . and connections also kind of depend on surface charge.

Yeah, so this is where it's kind of cool is that, right? These are mRNA based vaccines

and I guess we should say what mRNA is.

mRNA is, you know, genetic material that's going to encode for protein

has instructions or information to make that protein.

So in the simplest case, we are using this red pipe cleaner . to represent the genetic material inside a virus.

And so for the spike protein, there's an mRNA, that carries instructions

for how to make that protein chain.

Our green chain of amino acids (which make up the protein), right?

to put all these little beads (each representing an amino acid) in the correct order.

So with these vaccines, what they do is that,

they take the mRNA sequence for the spike protein, right,

and they put in a special package,

and deliver that inside your into your human cell.

And once it's in the cell, your body is going to make that protein,

some of that protein is gonna end up on the surface of your cell.

And then that's where the immune system kind of takes action.

This is a foreign protein, right?

And we're gonna try to seek out and destroy that protein.

What I think is interesting is that the mechanism,

how do we get that mRNA into the cell,

in some ways is kind of like the way the viruses do it.

With a vaccine, it's encapsulating this kind of lipid droplet.

You can think of this as sort of like a plasma membrane.

In some ways It's very much like our virus, right?

It's a simple package with genetic material inside,

and then the role the viruses is to get that genetic material inside.

So let's talk about antibodies. Right?

So antibodies are another kind of protein. So I've got no 3d printed model.

And their job is to recognize things in your body that are formed like bacteria and viruses.

And how they do that?

Well, basically, the shape at the end, . the tips of the Y's here is slightly different from antibody to antibody.

So your body makes somewhere around like a billion different antibodies.

And mostly they differ here at the at the tips.

And this tip here is what's going to recognize the foreign particles in your body.

So as an example, right, we've got the SARS CoV-2 spike protein.

So there's hopefully an antibody floating around in your body. that's going to recognize the surface of that spike protein, right?

and the specific shape, little nooks and crannies and the. charge of that antibody has to match just right to the shape,

and positive negative charge on the surface of the spike protein. Right?

Once it recognizes it can have a direct role in that now it kind of blocks that virus protein.

So remember, this virus protein is trying to find your ACE protein, right?

So now if you got an antibody stuck on there, it can't do that anymore, right?

And so this is the process of what we call the ”neutralizing antibody,” right?

So it stops, stops it from attaching to the cell.

So the other thing it can do is once it's kind of attached, it acts like a flag.

And then your cell can recognize that flag and say,

“Okay, I you know, go eat this thing. This is a thing that's, you know, bad for your body.”

So it kinda has two main main roles.

It all has to do kind of floating around and bumping into each other,

which is maybe a little concerning that the fate of our health

depends on these molecules floating around and finding each other.

But you've got a lot of antibodies and you know, you're infected with a lot of viruses,

they'll float around and if they meet just the right surface and bump the right way,

then they'll attach to one another.