I have come across the following word end capping in pentapeptides. Does it mean fixing the Ramachandran angles of end amino acids?
This is difficult to answer without more context. It could simply mean that the N and C termini are blocked (often done to improve resistance to peptidases). Alternatively, it could be a reference to the method of synthesis with end capping to prevent deletion sequences and improve purity.
Hi Dr Vigneshwaran Kannan . If unreacted amine is still present after the second coupling, acetic anhydride should be used to cap it. Capping prevents deletion peptide impurities from forming by blocking any further reactions at the unreacted sites. Capping can also make purification of the crude peptide product easier. See the link: https://www.peptide.com/resources/solid-phase-peptide-synthesis/monitoring-of-peptide-coupling-and-capping/
Thanks Aref Wazwaz Nick Gee I have come across this word in the following MD simulation paper.
https://www.pnas.org/content/pnas/105/34/12259.full.pdf
Page number 2 under the section GGAGG: Sampling behavior..
The exact line is "For an end-capped pentapeptide, we assume that each (phi, psi) pair for the three internal residues can exist in four possible conformations".
I couldn't get what he means.
Okay thanks. Yes, it does mean capping (or 'blocking') of the N and C termini by acetylation and amidation, respectively. In the context of this paper which is about conformation, the capping has nothing to do with peptidase resistance (which is one reason for capping, as I mentioned earlier), here it is done to reflect more closely the structure in proteins. For example, for any stretch of 5 amino acids in a large protein, not one stretch will have both an amine and a carboxylic acid terminus. Only one will have a terminal amine (if not blocked naturally). And only one will have a terminal carboxyl. The overwhelming majority of 5 aa stretches in a protein are flanked by peptide bonds, which the capped synthetic peptides more closely reflect than the uncapped forms.
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