i was wondering if it is to do with the phi and psi angles of tryptophan that doesn't make it favorable to be found in proteins or is it to with its high metabolic expense that it's not so common in proteins. Any suggestions?
There must surely be important evolutionary and functional reasons for the relative scarcity of tryptophan in proteins, and this is reflected in the fact that there is only one codon for tryptophan. Looked at the other way around (and I mean this humorously), you could say that the reason Trp appears in proteins so infrequently is that there is only one codon out of 61 for it (UGG).
Tryptophan is solicited for plethora of metabolic pathways involving secondary metabolites. That might explain why it's rare to find in proteins.
- Tryptophan has a polar side chain but its side chain conformation is not energetically favored (i.e its not staggered). It has to do with the substituents on the on side chain c atom ie. C-Beta.
- Another reason is the bulky group; because of the ring structure, it causes steric hindrances when it comes in contact with another bulky group in an alpha helix.
- Overall it depends on the the protein motif ie. all alpha, all beta, alpha/beta or apha-beta whether an aminoacids can be present in a protein or not. You might like to know that apha is stabalized by local interaction while beta is stabilized by interstrand interaction. Therefore, the presence of any amino acid can't just be decided by its structure alone, it is also decided by the other amino acids around it, which may stabilize or destabilize the over all polypeptide.
- I suggest you to also go through the first 3 chapters of Branden and tooze. very nice and simple explanations for similar kind of doubts.
There must surely be important evolutionary and functional reasons for the relative scarcity of tryptophan in proteins, and this is reflected in the fact that there is only one codon for tryptophan. Looked at the other way around (and I mean this humorously), you could say that the reason Trp appears in proteins so infrequently is that there is only one codon out of 61 for it (UGG).
also note that tryptophan is bioenergetically the most "expensive" amino acid. it does make sense then to use it only when really needed for function.
If I recall correctly you need about 70 ATP molecules to synthesize one L-Trp molecule. Others like serine only need about 10. Apparently the energy demand relates directly to codon usage: http://www.nig.ac.jp/labs/EvoGen/research/metabolic.html
Another possible reason is that tryptophan is not only strongly hydrophobic, but it is also the amino acid with the highest volume. This destines it within a protein in the apolar core but, particularly as a result of mutations, finding space in a system already organized in a compact way, is energetically costly and structurally disruptive.
Tryptophan is often found in transmembrane proteins at the hydrophobic/hydrophilic interface, where it seems to have an important functional role.
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