I've been wondering about this for a while.

I understand the representation of molecules with "sticks" where sticks represent a binding between atoms.
But when I look at the graphics of Rosetta, I also see these curls (I hope I user the right word, I don't speak English natively). What are these a representation of?
If it would be a bunch of sticks curled up, no problem, but they are shown with a surface, like a ribbon of some sort.

(They look related to the Helix from DNA, but I don't know either in DNA why it is represented like that. In other words, if you see such a curl representation, can one be sure of the exact combination of molecules inside? For example, for DNA, it can be either of the 4 acids (A,T,G,C) about anywhere, so this representation does not reveal all, just a possibility. Is this the same?)

Please release my brain, someone.. ;-)
Thanks

---

If sticks represent the bindings between atoms in a model you are familiar with, the curls (atcually, I believe the scientists would refer to them as ribbons) are just showing you the general shape of the atoms themselves.

The colors just go from red to blue in this representation. So the color in the default view of the display does not tell you which atoms.

You are correct that it is similar to DNA. But, as you point out, with DNA there are only 4 possibilities at any given location along the chain. With proteins there are closer to 20! So rather then the predictable shape of a double helix, a protein takes on a much more complex shape.

The shape that a given sequence assembles into is unique. So for a given amino acid sequence, only one shape will result. It is Rosetta's goal to predict the correct shape for a given amino acid sequence. Being able to make an accurate prediction, from only the amino acid sequence will allow accelerated drug development for many human diseases that have their basis in proteins within the body.

---

Rosetta Moderator: Mod.Sense

I've been wondering about this for a while.

I understand the representation of molecules with "sticks" where sticks represent a binding between atoms.
But when I look at the graphics of Rosetta, I also see these curls (I hope I user the right word, I don't speak English natively). What are these a representation of?
If it would be a bunch of sticks curled up, no problem, but they are shown with a surface, like a ribbon of some sort.

(They look related to the Helix from DNA, but I don't know either in DNA why it is represented like that. In other words, if you see such a curl representation, can one be sure of the exact combination of molecules inside? For example, for DNA, it can be either of the 4 acids (A,T,G,C) about anywhere, so this representation does not reveal all, just a possibility. Is this the same?)

Please release my brain, someone.. ;-)
Thanks

Mod.Sense is absolutely right, and I'm going to elaborate on his answer a bit.

I think that the curls you refer to are alpha helices, which are a type of secondary structure element found in proteins. The coils that you see in the BOINC graphics are termed alpha helices, and the arrow like structures you see are called beta strands. Each individual arrow is a beta strand, and a series of the arrows bonded together is called a beta sheet. Nearly any amino acid can be a part of any of the secondary structure elements, because the secondary structure elements involve atoms common to all amino acids (called backbone atoms).

The basic idea is that atoms within the backbone of the polypeptide chain can form hydrogen bonds to other backbone atoms, and these can give rise to alpha helices and beta strands, which are called secondary structure elements. These elements are often found within the final native structure of proteins. The ribbons and sheets aren't any wider or larger than other regions of the polypeptide chain, but they are usually important in understanding the final structure of a protein, which is why we highlight them within Rosetta's graphics. They also look very pretty to my eye.

Hopefully this answers your question. Cheers!

---

Ruben, I hope that translated better in to French, then it seems to in to English! :)

James, does this mean that the "coils" are basically a helix structure similar to DNA in the sense that the pattern is symmetric and the possible next item must be one of a small number of possibles, otherwise we twist out of the helix pattern? And so by looking at the AA sequence, when you see the next AA is not one of those possibles, the coil in the graphic is ended?

When we do work on "jumping" tasks, are these alpha helices the basic sub-components that we presume the shape of, and then look for how they might be connected together to find the full structure?

---

Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

Thanks y'all, for claring this up. Your teaching has lowered the unbearable lightness of being of this chap! ;-)

Just some other links for possible other people interested:
Alpha helix
β sheet


Feet1st, I think, if I understood everything correctly, I can answer your first question (paragraph): No, it can be any AA, and it's the hydrogen bonds that determine the helix shape. Furthermore while in DNA it's rather less variable it also consists of bases (the "inverse" of acids).

You last question: I have the impression it is like that indeed. Especially if you know that there are atoms that are invisible nextto the alpha's and beta's, it is much more acceptable how determined this is. (At least that is what I understood)

---