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NOMENCLATURE

Frequently Asked Questions on Nomenclature

What is an amino acid?

Generally spoken, an amino acid is a carboxylic acid containing an amino substituent.
In most cases, the term “amino acid” refers to an α-amino acid. Amino and carboxyl moiety are linked to the same carbon atom, the α-carbon. Glycine, α-aminoacetic acid, is the simplest amino acid, the parent compound of this class of substances.
β-alanine is the parent compound of the β-amino acids.

How do you denote amino acids?

The proteinogenic amino acids are designated by their standard three-letter code abbreviation. Additionally, the one-letter code is used for denoting the sequences of peptides. Common three-letter abbreviations are used as well for common “unusual” amino acids, e.g. H-Hyp-OH - L-cis-hydroxyproline, H-Nle-OH - L-norleucine.

Pyroglutamyl is abbreviated as Pyr (quite a number of abbreviations is in use for this most important peptide modification, IUPAC/IUB: Glp).

For designations of other amino acids please see the glossary. Some abbreviations differ from literature use and IUPAC/IUB recommendations.

How do you abbreviate pyroglutamic acid ?

Pyroglutamic acid is abbreviated as Pyr or pE (in peptides).

What do you mean by unusual amino acids?

Only the 20 proteinogenic amino acids, i.e. amino acids corresponding to DNA/RNA codons, can be incorporated into proteins during translational synthesis. The proteins consisting of these amino acids are subjected to various post-translational modifications of their building blocks as hydroxylation, methylation, or phosphorylation. These modified amino acids matter for the biological activity of proteins and peptides excised from them. Other modifications of amino acids result from the "aging" of proteins and pathological processes.
As the number of amino acids discovered in nature is ever increasing, we prefer to avoid the term “unnatural amino acid” and thus designate all non-proteinogenic amino acids as “unusual amino acids”.
This category also includes the “non-α-amino acids”, as β-amino acids (e.g. isoserine), γ-amino acids (e.g. statine),…,ω-amino acids (e.g. ε-aminocaproic acid, 11-aminoundecaoic acid).

What do H on N-terminus and OH on C-terminus signify?

H- stands for an N-terminal free amino moiety, -OH for the unmodified C-terminal carboxyl group.

How do you denote the enantiomeric forms of the amino acids?

With few exceptions, natural peptides and proteins consist of L-amino acids. Hence we refrain from denoting the L-enantiomer when using the three-letter code, whereas the D-enantiomer and the racemate are designated by -D- and -DL-, respectively. In the one-letter code, capital letters are used for L-amino acids, lowercase for D-amino acids, racemates cannot be designated (e.g. H-Ala-Gly-OH or AG stands for L-alanyl-glycine, H-D-Ala-Gly-OH or aG for D-alanyl-glycine, and H-DL-Ala-Gly-OH signifies the racemic alanyl-glycine).

What do L- and D-enantiomer mean?

With the exception of glycine, all α-amino acids are asymmetric molecules. They can be obtained in two forms called enantiomers. The D-enantiomer (D: dexter) represents the mirror image of the L-enantiomer (L: laevus); image and mirror image cannot be super-imposed, which is possible when mirroring symmetric structures.

D- and L-enantiomer do not differ in their physical properties, but they rotate the plane of linearly polarized light. Most L-amino acids rotate the light counterclockwise. The rotation angle [α] for a given concentration, solvent, temperature, wavelength, and light path (length of the measuring cell) is specific for an amino acid derivative.

e.g. [α] determined for batches of both enantiomers of Fmoc-phenylalanine

measured at 589 nm (NaD line), 24°C, 0.1% in DMF

Fmoc-Phe-OH [α]D24 -39.1°

Fmoc-D-Phe-OH [α]D24 + 39.0°

Enantiomers differ considerably in their biological activity.

What does DL signify?

DL stands for a racemate, i.e. a 1:1 mixture of L-form and D-form.

H-DL-Ala-OH is a 1:1 mixture of L-alanine and D-alanine.

How do you denote amino acid derivatives?

N- and C-terminus are explicitely designated:

H-Ala-OH (and NOT Ala) stands for unmodified L-alanine, H-Ala-NH2 for L-alaninamide, H-Ala-OMe for the methyl ester.

Side chain modifications are put in brackets -Xaa(Y)-:

Fmoc-Lys(Boc)-OH designates an Nα-fmocylated, side-chain (Nε)-bocylated L-lysine.

How do you denote peptides? (by amino acid sequence)

By three-letter code and one-letter code.
Three-letter code:
N- and C-terminus are specified, H- signifies a free amino terminus, -OH an unmodified C-terminus, -NH2 a peptide amide, e.g. H-Ala-Ala-Ala-OH, H-Ala-D-Ala-Ala-OH, H-Ala-Ala-Ala-NH2.
One-Letter code:
Only modified termini are specified, e.g. AAA, Ac-AAA, AAA-NH2.
In case of peptides containing unusual amino acids, the three-letter code abbreviation can be inserted and marked as such by hyphens: Ac-SYS-Nle-EHfRWGKPV-NH2.

How do you denote peptides? (by name)

Most bioactive peptides carry names (often more than one name) derived from their origin or their activity. Abbreviations of these names are also common use. Their sequences tend to be species-specific, hence a choice of species can be attached to the name:

Endothelin-1 (human, bovine, dog, mouse, porcine, rat) (ET-1)

Bachem also offers partial sequences of such peptides:

Amyloid β-Protein (25-35)

and N-terminally labeled peptides:

Biotinyl-BNP-32 (human) (Biotinyl-Brain Natriuretic Peptide-32 (human))

Amino acid replacements or modifications are designated by mentioning the newly introduced or modified amino acid(s) and the position of exchange:

(Gly28,Cys30)-Amyloid β-Protein (1-30); (Lys(biotinyl)29)-Cortistatin-29 (human)

Omissions are marked by "Des"

(Des-Gly77,Des-His78)-Myelin Basic Protein (68-84) (bovine)

How do you designate peptide modifications, e.g. a C-terminal amide?

Peptides can be modified
- at the N-terminus
e.g. N-acetylation: H-Ala-Gly-… -> Ac-Ala-Gly-… (Ac-AG…)
- at the C-terminus
e.g. amidation: …-Gly-Ala-OH -> …-Gly-Ala-NH2 (…GA-NH2)
Both modifications are widespread in nature.
- at the side-chains of amino acids
e.g. acetylation of lysine..-Lys-.. -> ..-Lys(Ac)-..  (…K(Ac)…)
       NOTE: -Cys- stands for a cysteine residue containing a free thiol group, unless disulfide formation is
       mentioned explicitly
- at the backbone of the peptide
e.g. by incorporation of D-amino acids …-Ala-Leu-D-Phe-Tyr-… (…ALfY…)
Abbreviations have been defined for most modifications, others are written out in full
e.g. H-Phe-pyrrolidide, H-Lys(isopropyl)-OH
Our notation does not distinguish between temporary -protecting groups- and permanent modifications of peptides.

Not all modifications can be transformed unambiguously into one-letter code, but terminal modifications such as Ac or NH2 or D-amino acids (lowercase letters) or simple side-chain modifications (put in brackets) do not cause difficulties.

How do you designate disulfide bridges?

The sequence extension (disulfide bond) indicates an intra- or intermolecular disulfide bridge formed by two cysteines. Positions of the cysteines involved in the disulfide bond are only mentioned if the peptide contains two or more bridges.
One-letter code sequences lack designations of disulfide bridges.
e.g.
H-Asn-Arg-Cys-Ser-Gln-Gly-Ser-Cys-Trp-Asn-OH
(Disulfide bond)
NRCSQGSCWN
H-Arg-Asp-Cys-Cys-Thr-Hyp-Hyp-Lys-Lys-Cys-Lys-Asp-Arg-Gln-Cys-Lys-Hyp-Gln-Arg-Cys-Cys-Ala-NH2
(Disulfide bonds between Cys3 and Cys15/Cys4 and Cys20/Cys10 and Cys21)
RDCCT-Hyp-Hyp- KKCKDRQCK-Hyp-QRCCA-NH2

 

Sequences (three-letter code) of Cys-containing peptides lacking “disulfide bond” (or a similar extension) contain free thiol moieties!

How do I see if a Cys in a peptide is free or oxidized ?

Sequences of Cys-containing peptides lacking “disulfide bond” (or a similar extension) contain free thiol moieties, they have to be protected from inadvertent oxidation.

e.g.

H-Tyr-Gly-Gln-Val-Pro-Met-Cys-Asp-Ala-Gly-Glu-Gln-Cys-Ala-Val-OH

 - free sulfhydryl groups

H-Tyr-Gly-Gln-Val-Pro-Met-Cys-Asp-Ala-Gly-Glu-Gln-Cys-Ala-Val-OH (disulfide bond)

- oxidized sulfhydryls

A protocol for the reversal of inadvertent oxidation of Cys peptides can be downloaded from our website.

How do you designate cyclic peptides?

Cyclic peptides obtained by amide bond formation (end-to-end, between the N-terminal amino group and the C-terminal carboxyl group) are designated by the preposition Cyclo (or c):
Cyclo(-Arg-Gly-Asp-D-Phe-Cys) or c(RGDfC).

How do you designate phosphorylated amino acids and peptides?

As it is a side-chain modification, phophorylation is denoted in brackets:
Phosphotyrosine H-Tyr(PO3H2)-OH
A phosphopeptide Ac-Tyr(PO3H2)-Tyr(PO3H2)-Tyr(PO3H2)-Ile-Glu-OH
Our derivatives of phosphorylated amino acids are assembled in subfamilies to be found in the families Serine, Threonine, and Tyrosine. The one-letter code equivalents of these phosphorylated amino acids are pS, pT, and pY.

What are β-Asp (isoaspartyl) and γ-Glu-peptides? How are they designated?

The "standard" peptide bond is formed between the α-carboxy group of an amino acid and the α-amino group of a second amino acid. The β-carboxyl of Asp and the γ-carboxyl of Glu can form amide bonds as well, then the α-carboxy function remains free:

α-peptide H-Asp-Ala-OH

β-peptide H-Asp(Ala-OH)-OH = H-β-Asp-Ala-OH

γ-peptide H-Glu(Ala-OH)-OH = H-γ-Glu-Ala-OH

Bachem offers a large choice of Asp and Glu derivatives suitable for synthesizing isoaspartyl and isoglutamyl peptides

e.g. Fmoc-Asp-OtBu, Boc-Glu-OBzl

How do isoasparagine and isoglutamine differ from Asn and Gln?

Asn and Gln can be considered as derivatives of Asp and Glu. The side-chain carboxy groups of these amino acids have been converted into carboxamides. Isoasparagine and isoglutamine result when amidating the α-carboxy moiety. The β-carboxyl of Isoasn and the γ-carboxy group of Isogln can participate in peptide bonds.

L-Isoasparagine: H-Asp-NH2

L-Isoglutamine: H-Glu-NH2

Isoasparagine derivatives are assembled in a subfamily filed under Aspartic Acid, isoglutamine derivatives can be found in the Glutamic Acid family.

How do you denote Nα- and Cα-alkylated amino acids?

Nα-alkylated amino acids and peptides are denoted in a slightly different manner:

e.g. N-Me-Ile-OH (not Me-Ile-OH nor H-MeIle-OH), Sar-OH (not H-Sar-OH),

      Boc-N-Me-Phe-N-Me-Phe-OH

Cα-methylated amino acids are designated likewise:

e.g. H-α-Me-Phe-OH

How do you denote His derivatives?

Two isomers can be formed when introducing a substituent at the imidazole nitrogen of histidine, the π- and the τ-isomer. Bachem explicitly designates the position of the substituent, if it is unambiguous, e.g. Fmoc-His(1-Trt)-OH (= Fmoc-His(τ-Trt)-OH, the bulkiness of the Trt moiety prevents the formation of the π-isomer), Boc-His(3-Bom)-OH (= Boc-His(π-Bom)-OH); H-His(Bzl)-OH on the other hand is obtained as a mixture of  π- and τ-isomer (Bachem: 3- and 1-isomer).

We recommend searching the appropriate subfamily of the Histidine family instead of entering the derivative.