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For DNA one can distinguish between

  • protein-coding DNA sequences, i.e. nucleic acid sequences inside DNA (vs. non-coding sequences)

  • DNA sequences that do not code for proteins but are transcribed into functional RNA

  • non-transcribed DNA sequences that have other (e.g. regulatory or structural) functions

  • non-transcribed and non-functional DNA sequences (‘junk DNA’)

The relative proportions of these seem to depend heavily on the organism and are only roughly known.

What I wonder is whether there are protein sequences (i.e. amino acid sequences inside a protein) that have no functional purpose.

A non-functional protein sequence might be a sequence that is neither effective to the outside (e.g. as a site for post-translational modification) nor to the inside (e.g. in folding). But even those parts of the protein might contribute structurally by their sheer presence and mass which is important when considering proteins not only as chemical but also as somehow mechanical devices. This might be called its structural purpose.

Assuming that each part of a protein has either a functional or only a structural purpose the question arises what the relative proportions of functional vs. only structural parts are.

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  • $\begingroup$ Could your title be : "Do non-functional protein sequences actually exist?" (possibly without the "actually")? It seems like you are saying that surely all sequences have some function. $\endgroup$ – gilleain Dec 20 '17 at 16:34
  • $\begingroup$ I have removed the word sequence as a qualifier for protein wherever what you are talking about is the physical entity — the product of translation of a mRNA — a protein. Further, the terminology you use is unfortunate because the term ‘functional’ is often used in contrast to structural. I have therefore added “junk” as an alternative. Finally, your question is unanswerable. If a protein exists, it is impossible to prove that has no function. I have added this as an answer, but I think your question should be withdrawn on that basis. $\endgroup$ – David Dec 20 '17 at 16:48
  • $\begingroup$ I'm afraid you distorted the spirit of my question which was intended to be explicitely about amino-acid sequences inside a protein, not about the protein as a whole. $\endgroup$ – Hans-Peter Stricker Dec 20 '17 at 17:12
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    $\begingroup$ I suggest a question with the title: "Are there functionless stretches of amino acids in proteins?" And the question follows in the next comment. If it fits the bill (perhaps with changes) you could mount it and we could modify this question and cross reference them. $\endgroup$ – David Dec 21 '17 at 17:46
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    $\begingroup$ Suggestion for Question: The variation in amino acid sequence of the same protein in different species indicates that at certain positions different shapes or even polarity are possible. Nevertheless an amino acids at such positions may be necessary for the overall structure of the protein. In contrast I am interested to know about stretches of several (perhaps six or more) successive amino acids — tails or loops, perhaps — that evidence suggests to be unnecessary for the protein. Do these exist and, if so, what proportion of the proteome do they constitute? $\endgroup$ – David Dec 21 '17 at 17:48
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This question is unanswerable as, if a protein exists as a physical entity in a cell it is possible to demonstrate it has a functional or structural role, but it is logically impossible to demonstrate it has no such role. The best one can say is that “it has no known function (role)”.

That said, in the course of evolution following gene duplication and divergence it is theoretically possible that on the way to acquiring a new functional role there is a stage at which a protein has no such role. One might be able to identify such proteins in a gene family like the globins by examining a range of species, as has been done for the globin genes. I am not aware of any such studies.

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