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Next, we're going to look at
what's the second most common type of protein domain
and these are the protein domains
that consist only of β strands.
According to connectivity and adjacency of these β strands,
there's really three different motifs
that the β strands can pack into.
They can either pack into
what's known as a β barrel domain
or it can pack into the Greek key barrel
or the jelly roll barrel.
And again, these are all classified as we'll see
according to the topology diagrams.
Let's start with the up-and-down β barrel.
The up-and-down β barrel is really a chemical container,
and if you just follow from the N terminus
to the C terminus you can see that its, ah,
strand followed by a β turn,
the β turn is that tight turn that we talked about
in one of our previous webcasts that turns into a β strand,
loops around again with a very tight β turn
and, and forms alternating or antiparallel
β sheet structures.
Once again, the sheet comes back and loops onto itself
to form a completely closed cylinder kind of structure.
These tend to be used for receptors of proteins.
They're basically, in this case,
the interior of the barrel usually has some space
that can accommodate a guest molecule.
Here's the retinol binding protein.
It binds the structure retinol, which is shown there,
and you can see the β strands, they come in pairs.
They're paired up so you have this very long yellow strand
connected to another very long yellow strand
and then some shorter strands
and so all of the β strands that are,
there are eight of them in the β barrel,
tend to come together, um, in, in pairs.
Now we're looking, we were looking at a side view
and here's a view down the barrel axis
and you can see it's not perfectly round.
It's got this oblong shape to it, but nonetheless,
it looks like it forms the cylinder of a barrel.
Let's take a look at what are the hydrophobic segments.
As you might guess, in the interior of that barrel
is going to be hydrophobic segments,
and here you can see in the blue structure
is actually the molecule of retinol
and the hydrophobic amino acids are colored white.
The polar hydrophilic amino acids are colored red.
So that's down, looking down that barrel axis.
It's a similar view as to what you see over here.
And, ah, now let's take a look at, um,
how that, ah, interior looks.
So here we're going to carve away the interior
from a side view
and you can see as we've sliced through this, ah, barrel
that we can see the retinol molecule that fits snugly
into a compartment inside that barrel
that's carved out by the amino acid side chains
that fill that interior space.
The Greek key barrel has a topology
that is reminiscent of the ancient Greek key pattern.
You've probably seen this pattern decorating walls,
and the reason that we, ah, name this motif
the Greek key barrel is because
if you look at the adjacency of strands that appear,
then their, their following the exact same pattern
that show up in this Greek key motif.
So, strand 1 is connected to strand 2 and 4
and so the way that works
is that if you just follow the connectivity,
1 is connected to 2 is connected to 3,
but then there's a long loop region
that comes back to strand 4, which is adjacent to strand #1.
If we look, Greek key barrel is actually important
in the eye lens protein. It's a, a protein that's, um,
that actually forms a very large volume fraction
of the eye lens.
It helps to adjust the optical properties of the eye lens.
But you can see from the person with a cataract
that there has been degradation of that eye lens protein
and they begin to aggregate together
and form large objects that ends up scattering light
and that's the gist of what a, a cataract is.
Well, let's follow the connectivity
that you see in this three-dimensional diagram.
Starting with the end terminus, the N terminus,
and then you notice that the, ah, strand #1 is connected to 2
and it was adjacent to strand #2 and strand #4.
So how does that look?
Well, the other thing to notice is actually in this, ah,
Greek key barrel domain of the eye lens protein,
there are actually two Greek key, key motifs.
They're colored red and green
and so let's look at the topology diagram
and let's look at
what's adjacent to one another in space.
We can see that strand 3 is actually adjacent to strand 8
as it forms this circular, um, part of the, of the barrel.
So the drawing out the topology diagram,
we would put strand 3 antiparallel to strand 8,
that's the adjacency,
and then if we just go what's next to 3,
well it's 2 followed by 1 followed by 4.
So if we start, ah, from the other direction,
we see that strand 8 is next to 5
which is next to 6 and they're all antiparallel.
That's the adjacency and that comes by examining
what's next to what in this three-dimensional diagram.
What about connectivity?
Well, there you just start at the N terminus,
that's going to be strand 1
and we- now we see that this is a Greek key motif;
1 is connected to 2 is connected to 3
and then 3 is what loops back all the way over to strand 4
and makes that antiparallel to strand #1.
We can see that strand 4 is what joins together
the two different Greek key motifs.
There's the connectivity.
We've got a connect to strand 4 to strand 5
and so the C terminus of strand 4
must connect to the N terminus of strand 5,
and so there's the long loop that comes over there;
5 is connected to 6 is connected to 7
and that loops over to 8.
That's our second Greek key motif.
The last of the β structures
is known as the jelly roll barrel.
And the reason for this is you can kind of see
how it looks like we've kneaded the dough
that would be formed,
that would be used to form a, a jelly roll,
how it's kneaded and woven back and forth.
And, you should be able to, I won't go through it in detail
- starting from this three-dimensional structure
of the jelly roll motif with the N terminus position here,
go through and find that the adjacency and connectivity
looks like this kneaded bread dough
of a, of a jelly roll pay, pastry.