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What is the higher order meaning of ribbon diagrams like this one? I know the first order meaning is a graphical representation of α-helices and β-sheets, but what else does it mean? Is the protein's function or behavior encoded in there? Do the α-helices helices and β-sheets form a kind of protein alphabet so that a particular arrangement (a "protein word") always has the same function?

An analogy might help: take the word ox. The zeroth order meaning is a circle followed by a cross; the first order meaning is the graphical representation of the sound oks; and the second order meaning is a castrated male bovine.

An English speaker who sees ox reads it as oks and understands it as castrated male bovine. A non-English speaker just sees a circle followed by a cross.

I'm at the non-English speaker level with ribbon diagrams and would like to get to the English speaker level. What does the protein researcher see and understand where I only see spirals and squiggles? Googling hasn't been helpful.

Protein diagram

Source

zencraft
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  • What is the source of the image? – MattDMo Aug 10 '21 at 21:15
  • Added source in edit – zencraft Aug 10 '21 at 21:20
  • @zencraft Nice analogy! – acvill Aug 10 '21 at 21:25
  • Do some research on "protein secondary structure". The figure you include is just trying to show where probably-relevant amino acid mutations are located in the S protein's 3D structure. For example, since an antibody would normally only have physical access to the outside of the S protein, a neutralizing-antibody-evading amino acid mutation buried inside the interior of the S protein is probably changing the overall 3D protein structure rather than just "disguising" a bit of the outside of the S protein by changing a bit of the surface. – Armand Aug 10 '21 at 21:29
  • I have, and it's not been much help. Another analogy might help: the stuff I've found by googling is like the quadratic formula, I'm looking for higher order understanding, like Galois groups. – zencraft Aug 10 '21 at 21:56

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There is no higher order meaning.

Ribbon diagrams are a cartoon representation of portions of a polypeptide chain that are engaged in what is termed the secondary structure of proteins — the regular areas of protein structure formed by hydrogen bonding of peptide bonds. These are either individual helices (α-helices) or adjacent flat pasta strips (β-sheets).

An experienced scientist in the field of protein structure can look at the combination of such features and perhaps recognize combinations that recur in proteins of similar function, but there is no — heaven preserve us — code. Ribbon diagrams are just one device for simplifying a complex object.

There are other types of representation that allow appreciation of surface charge, hydrophobicity or individual side chains. An author representing proteins in a paper will choose one (or a combination) that best allows the reader to understand the information he is trying to convey.

Ironically, in the diagram presented in the question they are merely serve as references to indicate the positions in the protein where mutations have occurred.

David
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