A short guide to abbreviations and their use in peptide science

Abbreviations, acronyms and symbolic representations are very much part of the language of peptide science – in conversational communication as much as in its literature. They are not only a convenience, either – they enable the necessary but distracting complexities of long chemical names and technical terms to be pushed into the background so the wood can be seen among the trees. Many of the abbreviations in use are so much in currency that they need no explanation. The main purpose of this editorial is to identify them and free authors from the hitherto tiresome requirement to define them in every paper. Those in the tables that follow – which will be updated from time to time – may in future be used in this Journal without explanation.

All other abbreviations should be defined. Previously published usage should be followed unless it is manifestly clumsy or inappropriate. Where it is necessary to devise new abbreviations and symbols, the general principles behind established examples should be followed. Thus, new amino-acid symbols should be of form Abc, with due thought for possible ambiguities (Dap might be obvious for diaminoproprionic acid, for example, but what about diaminopimelic acid?).

Where alternatives are indicated below, the first is preferred.

Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd. Reproduced with permission from J. Peptide Sci., 1999, 5, 465–471.

Aad

α-Aminoadipic acid

βAad

β-Aminoadipic acid

Abu

α-Aminobutyric acid

Aib

α-Aminoisobutyric acid; α-methylalanine

βAla

β-Alanine; 3-aminopropionic acid (avoid Bal)

Asu

α-Aminosuberic acid

Aze

Azetidine-2-carboxylic acid

Cha

β-Cyclohexylalanine

Cit

Citrulline; 2-amino-5-ureidovaleric acid

Dha

Dehydroalanine (also ΔAla)

Gla

γ-Carboxyglutamic acid

Glp

Pyroglutamic acid; 5-oxoproline (also pGlu)

Hph

Homophenylalanine (Hse=homoserine, and so on). Caution is necessary over the use of the prefix homo in relation to α-amino-acid names and the symbols for homo-analogues. When the term first became current, it was applied to analogues in which a side-chain CH₂ extension had been introduced. Thus homoserine has a side-chain CH₂CH₂OH, homoarginine CH₂CH₂CH₂NHC(═NH)NH₂, and so on. In such cases, the convention is that a new three-letter symbol for the analogue is derived from the parent, by taking H for homo and combining it with the first two characters of the parental symbol – hence, Hse, Har and so on. Now, however, there is a considerable literature on β-amino acids which are analogues of α-amino acids in which a CH₂ group has been inserted between the α-carbon and carboxyl group. These analogues have also been called homo-analogues, and there are instances for example not only of ‘homophenylalanine', NH₂CH(CH₂CH₂Ph)CO₂H, abbreviated Hph, but also ‘homophenylalanine', NH₂CH(CH₂Ph)CH₂CO₂H abbreviated Hph.Further, members of the analogue class with CH₂ interpolated between the α-carbon and the carboxyl group of the parent α-amino acid structure have been called both ‘α-homo'- and ‘β-homo’. Clearly great care is essential, and abbreviations for ‘homo’ analogues ought to be fully defined on every occasion. The term ‘β-homo’ seems preferable for backbone extension (emphasizing as it does that the residue has become a β-amino acid residue), with abbreviated symbolism as illustrated by βHph for NH₂CH(CH₂Ph)CH₂CO₂H.

Hyl

δ-Hydroxylysine

Hyp

4-Hydroxyproline

αIle

allo-Isoleucine; 2S, 3R in the l-series

Lan

Lanthionine; S-(2-amino-2-carboxyethyl)cysteine

MeAla

N-Methylalanine (MeVal=N-methylvaline, and so on). This style should not be used for α-methyl residues, for which either a separate unique symbol (such as Aib for α-methylalanine) should be used, or the position of the methyl group should be made explicit as in αMeTyr for α-methyltyrosine.

Nle

Norleucine; α-aminocaproic acid

Orn

Ornithine; 2,5-diaminopentanoic acid

Phg

Phenylglycine; 2-aminophenylacetic acid

Pip

Pipecolic acid; piperidine-s-carboxylic acid

Sar

Sarcosine; N-methylglycine

Sta

Statine; (3S, 4S)-4-amino-3-hydroxy-6-methyl-heptanoic acid

Thi

β-Thienylalanine

Tic

1,2,3,4-Tetrahydroisoquinoline-3-carboxylic acid

αThr

allo-Threonine; 2S, 3S in the l-series

Thz

Thiazolidine-4-carboxylic acid, thiaproline

Xaa

Unknown or unspecified (also Aaa)

The three-letter symbols should be used in accord with the IUPAC-IUB conventions, which have been published in many places (e.g. European J. Biochem. 1984; 138: 9–37), and which are (May 1999) also available with other relevant documents at: http://www.chem.qnw.ac.uk/iubmb/iubmb.html#03

It would be superfluous to attempt to repeat all the detail which can be found at the above address, and the ramifications are extensive, but a few remarks focussing on common misuses and confusions may assist. The three-letter symbol standing alone represents the unmodified intact amino acid, of the l-configuration unless otherwise stated (but the l-configuration may be indicated if desired for emphasis: e.g. l-Ala). The same three-letter symbol, however, also stands for the corresponding amino acid residue. The symbols can thus be used to represent peptides (e.g. AlaAla or Ala-Ala=alanylalanine). When nothing is shown attached to either side of the three-letter symbol it is meant to be understood that the amino group (always understood to be on the left) or carboxyl group is unmodified, but this can be emphasized, so AlaAla=H-AlaAla-OH. Note however that indicating free termini by presenting the terminal group in full is wrong; NH₂AlaAlaCO₂H implies a hydrazino group at one end and an α-keto acid derivative at the other. Representation of a free terminal carboxyl group by writing H on the right is also wrong because that implies a terminal aldehyde.

Side chains are understood to be unsubstituted if nothing is shown, but a substituent can be indicated by use of brackets or attachment by a vertical bond up or down. Thus an O-methylserine residue could be shown as 1, 2, or 3.

Note that the oxygen atom is not shown: it is contained in the three-letter symbol – showing it, as in Ser(OMe), would imply that a peroxy group was present. Bonds up or down should be used only for indicating side-chain substitution. Confusions may creep in if the three-letter symbols are used thoughtlessly in representations of cyclic peptides. Consider by way of example the hypothetical cyclopeptide threonylalanylalanylglutamic acid. It might be thought that this compound could be economically represented 4.

But this is wrong because the left hand vertical bond implies an ester link between the two side chains, and strictly speaking if the right hand vertical bond means anything it means that the two Ala α-carbons are linked by a CH₂CH₂ bridge. This objection could be circumvented by writing the structure as in 5.

But this is now ambiguous because the convention that the symbols are to be read as having the amino nitrogen to the left cannot be imposed on both lines. The direction of the peptide bond needs to be shown with an arrow pointing from CO to N, as in 6.

Actually the simplest representation is on one line, as in 7.

Ac

Acetyl

Acm

Acetamidomethyl

Adoc

1-Adamantyloxycarbonyl

Alloc

Allyloxycarbonyl

Boc

t-Butoxycarbonyl

Bom

π-Benzyloxymethyl

Bpoc

2-(4-Biphenylyl)isopropoxycarbonyl

Btm

Benzylthiomethyl

Bum

π-t-Butoxymethyl

Buⁱ

i-Butyl

Buⁿ

n-Butyl

Bu^t

t-Butyl

Bz

Benzoyl

Bzl

Benzyl (also Bn); Bzl(OMe)=4-methoxybenzyl and so on

Cha

Cyclohexylammonium salt

Clt

2-Chlorotrityl

Dcha

Dicyclohexylammonium salt

Dde

1-(4,4-Dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl

Ddz

2-(3,5-Dimethoxyphenyl)-isopropoxycarbonyl

Dnp

2,4-Dinitrophenyl

Dpp

Diphenylphosphinyl

Et

Ethyl

Fmoc

9-Fluorenylmethoxycarbonyl

For

Formyl

Mbh

4,4′-Dimethoxydiphenylmethyl, 4,4′-Dimethoxybenzhydryl

Mbs

4-Methoxybenzenesulphonyl

Me

Methyl

Mob

4-Methoxybenzyl

Mtr

2,3,6-Trimethyl,4-methoxybenzenesulphonyl

Nps

2-Nitrophenylsulphenyl

OA11

Allyl ester

OBt

1-Benzotriazolyl ester

OcHx

Cyclohexyl ester

ONp

4-Nitrophenyl ester

OPcp

Pentachlorophenyl ester

OPfp

Pentafluorophenyl ester

OSu

Succinimido ester

OTce

2,2,2-Trichloroethyl ester

OTcp

2,4,5-Trichlorophenyl ester

Tmob

2,4,5-Trimethoxybenzyl

Mtt

4-Methyltrityl

Pac

Phenacyl, PhCOCH₂ (care! Pac also=PhCH₂CO)

Ph

Phenyl

Pht

Phthaloyl

Scm

Methoxycarbonylsulphenyl

Pmc

2,2,5,7,8-Pentamethylchroman-6-sulphonyl

Prⁱ

i-Propyl

Prⁿ

n-Propyl

Tfa

Trifluoroacetyl

Tos

4-Toluenesulphonyl (also Ts)

Troc

2,2,2-Trichloroethoxycarbonyl

Trt

Trityl, triphenylmethyl

Xan

9-Xanthydryl

Z

Benzyloxycarbonyl (also Cbz). Z(2C1)=2-chlorobenzyloxycarbonyl and so on

DKP

Diketopiperazine

NCA

N-Carboxyanhydride

PTH

Phenylthiohydantoin

UNCA

Urethane N-carboxyanhydride

BOP

1-Benzotriazolyloxy-tris-dimethylamino-phosphonium hexafluorophosphate

CDI

Carbonyldiimidazole

DBU

Diazabicyclo[5.4.0]-undec-7-ene

DCCI

Dicyclohexylcarbodiimide (also DCC)

DCHU

Dicyclohexylurea (also DCU)

DCM

Dichloromethane

DEAD

Diethyl azodicarboxylate (DMAD=the dimethyl analogue)

DIPCI

Diisopropylcarbodiimide (also DIC)

DIPEA

Diisopropylethylamine (also DIEA)

DMA

Dimethylacetamide

DMAP

4-Dimethylaminopyridine

DMF

Dimethylformamide

DMS

Dimethylsulphide

DMSO

Dimethylsulphoxide

DPAA

Diphenylphosphoryl azide

EEDQ

2-Ethoxy-1-ethoxycarbonyl-1,2-dihydroquinoline

HATU

This is the acronym for the ‘uronium’ coupling reagent derived from HOAt, which was originally thought to have the structure 8, the Hexafluorophosphate salt of the O-(7-Azabenzotriazol-lyl)-Tetramethyl Uronium cation.

In fact this reagent has the isomeric N-oxide structure 9 in the crystalline state, the unwieldy correct name of which does not conform logically with the acronym, but the acronym continues in use.

Similarly, the corresponding reagent derived from HOBt has the firmly attached label HBTU (the tetrafluoroborate salt is also used: TBTU), despite the fact that it is not actually a uronium salt.

HMP

Hexamethylphosphoric triamide (also HMPA, HMPTA)

HOAt

1-Hydroxy-7-azabenzotriazole

HOBt

1-Hydroxybenzotriazole

HOCt

1-Hydroxy-4-ethoxycarbonyl-1,2,3-triazole

NDMBA

N,N′-Dimethylbarbituric acid

NMM

N-Methylmorpholine

PAM

Phenylacetamidomethyl resin

PEG

Polyethylene glycol

PtBOP

1-Benzotriazolyloxy-tris-pyrrolidinophosphonium hexafluorophosphate

SDS

Sodium dodecyl sulphate

TBAF

Tetrabutylammonium fluoride

TBTU

See remarks under HATU above

TEA

Triethylamine

TFA

Trifluoroacetic acid

TFE

Trifluoroethanol

TFMSA

Trifluoromethanesulphonic acid

THF

Tetrahydrofuran

WSCI

Water soluble carbodiimide: 1-ethyl-3-(3′-dimethylaminopropyl)-carbodiimide hydrochloride (also EDC)

CD

Circular dichroism

COSY

Correlated spectroscopy

CZE

Capillary zone electrophoresis

ELISA

Enzyme-linked immunosorbent assay

ESI

Electrospray ionization

ESR

Electron spin resonance

FAB

Fast atom bombardment

FT

Fourier transform

GLC

Gas liquid chromatography

hplc

High performance liquid chromatography

IR

Infra red

MALDI

Matrix-assisted laser desorption ionization

MS

Mass spectrometry

NMR

Nuclear magnetic resonance

nOe

Nuclear Overhauser effect

NOESY

Nuclear Overhauser enhanced spectroscopy

ORD

Optical rotatory dispersion

PAGE

Polyacrylamide gel electrophoresis

RIA

Radioimmunoassay

ROESY

Rotating frame nuclear Overhauser enhanced spectroscopy

RP

Reversed phase

SPPS

Solid phase peptide synthesis

TLC

Thin layer chromatography

TOCSY

Total correlation spectroscopy

TOF

Time of flight

UV

Ultraviolet

Ab

Antibody

ACE

Angiotensin-converting enzyme

ACTH

Adrenocorticotropic hormone

Ag

Antigen

AIDS

Acquired immunodeficiency syndrome

ANP

Atrial natriuretic polypeptide

ATP

Adenosine triphosphate

BK

Bradykinin

BSA

Bovine serum albumin

CCK

Cholecystokinin

DNA

Deoxyribonucleic acid

FSH

Follicle stimulating hormone

GH

Growth hormone

HIV

Human immunodeficiency virus

LHRH

Luteinizing hormone releasing hormone

MAP

Multiple antigen peptide

NPY

Neuropeptide Y

OT

Oxytocin

PTH

Parathyroid hormone

QSAR

Quantitative structure–activity relationship

RNA

Ribonucleic acid

TASP

Template-assembled synthetic protein

TRH

Thyrotropin releasing hormone

VIP

Vasoactive intestinal peptide

VP

Vasopressin

J. H. Jones