 Before I introduce you to keratin, which is the last fibrous protein, we should revisit the helices. Remember when I talked about the alpha helix backbone and how we could turn that backbone into a surface and then start to look at the ridges and valleys here. I'm going to rehash that in slightly more detail. Now, I told you that there are hydrogen bonds from amino acid I to I plus 4, but that of course means that amino acid I and amino acid I plus 4 are going to be somewhat close to each other. And that also means that their side chains are going to be somewhat close to each other. And if we look here, this is I mean side chain I and then you're just going to need to trust me that that is side chain I plus 4 and then I drawn a line to line up those side chains. These are still small side chains. I'm just alanine here. So in terms even alanine as small as it is creates a small of ridge or dots on the surface. If I were to pick isoleucine or leucine or something, they would be significantly larger. If I line those up in with I and I plus 4, these dotted lines make roughly a 25 degree angle compared to the direction of the helix here. And we just choose to say that this is a positive direction. So it's plus 25 degrees. Sorry minus 25 degrees minus 25. I could also take the preceding amino acid. So rather than I to I plus 4, I could do I to I plus 3. That would be in the opposite direction. And this creates a an angle that is roughly 45 degrees in the other direction. Don't worry so much about the sign. As you see, I have to think about this every time too. This is just an alternative way of thinking on the ridges because those ridges aren't really contingent, right? They kind of dots where the amino acids are going so that there's space between them either in this direction or that direction. There were two more things about amino acids that I think you should know. In a helix there is 3.6 residues per turn. So one turn is exactly one lap in the helix. That means that there is 100 degrees between two amino acids. Nice and even number. It's almost exact. But just almost. This creates nice space-filling effect and in particular it means that I could take one of these amino acids, sorry, one of these helices, pair it up with another helix and try to pack them. Like this. Remember, one helix here, one helix here, turn one of them around because the surfaces should be facing each other and then we just rotate them until we get the ridges to fit the valleys in the other helices. And then you get this combination that you'd heat roughly minus 20 degrees tilt between the two helices. That is fine, but what if I tried a little bit harder to, on the one hand, get them to line up a little bit more and try to find some sort of regular pattern here. So one challenge is that 3.6 is complicated. It's going to take a very long time before I get back. It would be much easier if this was 3 or 4. But I can't push the helix as much to get exactly 3 or 4. But in some cases I can get very nice repeating units looking like this. This is a concept called coiled coiled. So if I stretch the helices just a little bit and instead of having 3.6 residues per turn, I go down to 3.5 residues per turn. That means that each turn is a little bit tighter now, right? But that means that after two turns, I'm back where I started. So if I start on the inside here and then I take two turns, I'm back in the same position. This will create a very nice and regular structure where the two helices are embracing each other roughly like snakes. Unfortunately, I can't turn my arms that many turns. And this can go on for a very, very, very long period. Several turns. One common case where you're going to see this is myosin. So these are fibers. They're proteins involved in our muscles and you might have seen movies about this. They're kind of renderings, but the whole idea is that what happens when our muscles are moving, you're essentially having one of these fibers walking along another fiber and gradually graphing them. The exact mechanism about that I won't have time to go through today, but given time, I might let's see if I can do it later in the class. But the idea is for this to work, you need to have some sort of long fibers, right? And these long coiled, coiled helices, they create a structure exactly like this. So it's nothing like collagen. It's not a long, it's not a macroscopic fiber and it's not super rigid, but it's something that can be extended to maybe say a hundred amino acids in length or a bit longer. This also happens on occasion of the surface of proteins or so if you need receptors basically. If you need something sticking out a bit, but it should be slightly more rigid than individual helices. Coiled coils is a beautiful way to make it. There are some things one would have to think about here. You can't put two bulky amino acids in the area where they're going to face each other, right? Because if you were to put a tryptophan here, there would not be, well, there would be a large bump between the helices. Basically, it's not going to happen. And if these are going to be out in water, you might be able to put something hydrophobic here, but there should certainly be hydrophilic on the outside. We occasionally illustrate this way with so-called helical wheels. This is not quite strictly a helical wheel. I'll show you a better soon. But if I'm looking down the helix here and then I just draw the residues here, one, two, three, four, five, et cetera, then you can see from the side here that what residues should be hydrophobic and what residues should be hydrophilic. Otherwise, it might not be obvious if you put like every three or four residues in a particular pattern. This is a theme on the topic I mentioned briefly at last lecture, at least during the seminar. It's called super secondary structure. So it's not the secondary structure. It's not one helix. It is two helices, but on the other end, it's not really a tertiary structure. Well, maybe it is a tertiary structure, but it's a very common pattern that we see in many different proteins. And then it makes sense for us to classify this again, just to make sense of it, then realize we've seen that before. So this is a super secondary structure element or motif called coiled coiled helices. So it's a super secondary structure. Coiled coils or helix is a coil. But this 3.5 thing, it's not always exactly 3.5, but it's going to prove very advantageous to have these at 3.5 turns per helix instead of 3.6. I mentioned this thing about the hydrophobic part here. What if you put something specific there and make sure that every seventh residue is hydrophobic? Well, I'll show you what we can do with that.