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I'm going through an Amber Molecular Dynamics tutorial here and am a bit confused about why in step 8, we create a sequence as:

foo = seq { ACE ALA NME }

and this is called a dipeptide. I think there's only one amino acid, alanine, isn't there?

enter image description here

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closed as off-topic by Mithoron, A.K., Karsten Theis, Todd Minehardt, Soumik Das Apr 6 at 8:29

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    $\begingroup$ I would consider this a monopeptide, but there is a non-zero probability that I am missing some other salient point about why this particular system was chosen for modelling. $\endgroup$ – orthocresol Apr 2 at 22:46
  • $\begingroup$ I miss seeing why this was closed, even if the posed question does not reveal a remarkable amount of effort. Basically the poster says: the peptide contains one aminoacid, so why is it called a dipeptide? Not sure what else the critics were looking for. $\endgroup$ – Buck Thorn Apr 20 at 8:23
  • $\begingroup$ I agree, there’s really no need for closure. $\endgroup$ – orthocresol Apr 21 at 11:24
  • $\begingroup$ Plus, more factually, it wasn't a homework question but one that I asked after discussing with other computational folks in the lab I work in. Given the responses denote some ambiguity in the interpretation of counting peptides, this seems like a helpful reference to keep around. $\endgroup$ – MarteriaGirl Apr 21 at 13:45
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The nomenclature here is based on counting the number of backbone peptide bonds rather than the number of aminoacids. This does not apply the usual naming convention.

If you look at the wikipedia page on "peptide (amide) bond", it states

A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another along a peptide or protein chain.

It can also be called an eupeptide bond to separate it from an isopeptide bond, a different type of amide bond between two amino acids.

Furthermore,

When two amino acids form a dipeptide through a peptide bond it is type of condensation reaction. [...] The two joined amino acids are called a dipeptide.

Note that you can have aminoacids connected through their side chains. Glutathione (GSH) comes to mind as a good example of this:

enter image description here

It contains three aminoacids (Gly, Cys and Glu). Would you call this a "tripeptide"?

The wikipedia does:

It is a tripeptide with a gamma peptide linkage between the carboxyl group of the glutamate side chain and the amine group of cysteine, and the carboxyl group of cysteine is attached by normal peptide linkage to a glycine.

What about the bonds in GSH? The wikipedia goes on:

[...] the tripeptide glutathione is synthesized in two steps from free amino acids, by two enzymes: glutamate–cysteine ligase (forms an isopeptide bond [emphasis mine], which is not a peptide bond) and glutathione synthetase (forms a peptide bond).

So, here they call GSH a tripeptide based on the number of aminoacids, not the number or even type of "peptide bond".

Hmm, pretty confusing. Perhaps then it is best to go to the original literature on the subject, linked in the wikipedia:

  1. "Nomenclature and Symbolism for Amino Acids and Peptides. Recommendations 1983". European Journal of Biochemistry. 138 (1): 9–37. 1984.

  2. "Glossary of terms used in physical organic chemistry (IUPAC Recommendations 1994)". Pure and Applied Chemistry. 66 (5): 1077–1184.

According to reference 1:

Part 1, Section C : PEPTIDE NOMENCLATURE

3AA-11. DEFINITION OF PEPTIDES

A peptide is any compound produced by amide formation between a carboxyl group of one amino acid and an amino group of another. The amide bonds in peptides may be called peptide bonds. The word peptide usually applies to compounds whose amide bonds are formed between C-1 of one amino acid and N-2 of another (sometimes called eupeptide bonds), but it includes compounds with residues linked by other amide bonds (sometimes called isopeptide bonds). Peptides with fewer than about 10- 20 residues may also be called oligopeptides ; those with more, polypeptides. Polypeptides of specific sequence of more than about 50 residues are usually known as proteins, but authors differ greatly on where they start using this term.

There is some degree of ambiguity regarding the numerical prefixes to the term "peptide", which are not discussed explicitly. But the above article provides a solid guideline about what you should call a peptide, namely two or more aminoacids linked through amide bonds.

So what about AcAlaNHMe (the capped alanine peptide in question)? One reason it is called a dipeptide (and not a peptide or tripeptide) is to emphasize that it contains two peptide (or amide) plains with intervening $\phi$ and $\psi$ dihedral angles which confer the potential conformational flexibility of a regular tripeptide. This is discussed for instance in this article.

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  • $\begingroup$ In your last sentence, do you mean it confers the conformational flexibility of a regular dipeptide? $\endgroup$ – MarteriaGirl Apr 3 at 15:46
  • $\begingroup$ @MarteriaGirl I actually meant a tripeptide, a regular linear peptide consisting of three aminoacids linked by two peptide bonds, with the central aminoacid and the peptide planes defining psi and phi dihedral angles. The phi/psi conformational space available to the Ala dipeptide you show can be argued to approximate that available to a tripeptide. $\endgroup$ – Buck Thorn Apr 3 at 18:09
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If the peptide were made exclusively out of amino acids, you would simply count the amino acids to get the name. One amino acid is an amino acid, two amino acids connected by a single peptide bond is a dipeptide, three amino acids connected by two peptide bonds is a tripeptide and so on.

For this case, you have two peptide bonds, so you might call it a tripeptide. Or you argue that there is one amino acid only, and you call it an amino acid with two protecting groups. Or, and this is a strange way of thinking about it in my mind, you say that there are two amino groups and two carboxylic acid groups upon hydrolysis so it is - a dipeptide.

I would not dare say this if I hadn't found this way of counting elsewhere, in a tutorial of another software.

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