Chemical Abbreviation List Related to Peptides

1-Nal

β-(1-Naphthyl)-L-alanine

3-(1-Naphthyl)-L-alanine

A non-natural amino acid shown to be a useful building block in the synthesis of peptides withenhanced binding affinity and half-lives.

2-Nal

β-(2-Naphthyl)-L-alanine

An unnatural bicyclic aromatic amino acid that has been used in the synthesis of peptides (including cholecystokinin, vasoactive intestinal peptide and neurotensin analogues) with enhanced binding affinity.

4MbNA

4-Methoxy-β-naphthylamide

5FAM

5-Carboxyfluorescein

Fluorophor with an excitation at 492 nm and emission of 517 nm. Donors like FAM and 5FAM are often paired together with acceptors (CPQ2) for FRET experiments.

5TAMRA

Single isomer 5-Carboxytetramethyl rhodamine

5TAMRA and mixed-isomer 5/6-TAMRA are fluorophors with excitations at ~543 nm and emissions of ~572 nm.

Abu

L-α-Aminobutyric acid

A non-proteinogenic alpha amino acid. Abu is a homolog of alanine that contains an additional methylene (-CH2-) group.

Abz

2-Aminobenzoyl, or Anthraniloyl

A fluorophor with an excitation at 320 nm and emission of 420 nm.

Ac

Acetyl group. N-terminal acetylation

A common modifcation often used to resemble a peptide fragment within a protein. The side chain of a lysine (K) residue may also be acetylated to form Lys(Ac).

ACC

7-amino-4-carbamoylmethylcoumarin

A fluorophor with an excitation at 365 nm and emission of 440 nm.

Acm

Acetamidomethyl

A thiol protection group for cysteine orginally introduced in 1972 by Ralph Hirschmann. Acm groups are stable to acids and bases normally associated with peptide synthesis, but is removed by iodine (I2).

Ada

Adamantyl

AEPA

[4-(2-aminoethyl)phenyl]-acetic acid

AFC

7-Amino-4-trifluoromethyl-coumarin

Fluorophor with an excitation at 376 nm and emission of 480 nm.

Aha

7-Aminoheptanoic acid

A hydrophobic spacer that contains seven carbons.

Ahx

6-Aminohexanoic acid

C6

A hydrophobic spacer typically incorporated into sequences to separate the peptide from tags and dye.

Aib

α-Aminoisobutyric acid

α-Methyl-alanine

Non-proteinogenic amino acid that promotes helical conformations in peptides.

Aloc

Allyloxycarbonyl

A protection group used to protect an amino group (or carboxylic acid or alcohol group). In an orthogonal deprotection scheme, Aloc can be removed using tetrakis(triphenylphosphine)palladium(0).

AMC

7-Amino-4-methyl-coumaride

Amc

Fluorophor with an excitation at 350 nm and emission of 450 nm.

Aph

Aminophenylalanine

A non-proteinogenic amino acid bearing an aminophenylmethylene side chain.

Arg(Me2)

N,N-dimethyl-L-arginine (asymmetrical)

Asu

L-α-Aminosuberic acid

L-2-Aminooctanoic acid

A hydrophobic spacer that contains 8 carbons.

Aza

A group used specifically for instances where nitrogen replaces carbon in a compound, either as the divalent group NH for the group CH2, or a single trivalent nitrogen atom for the group CH.

Benzoyl

Benzoyl

Bz, C6H5CO-

A aroyl protection group for alcohols and can be easily removed by hydrolysis in dilute basic solution.

beta-Ala

beta-alanine

Boc

tert-butoxycarbonyl or tert-butyloxycarbonyl

A protection group for amines. Boc groups can be removed with strong acids such as trifluoroacetic acid in dichloromethane, or with HCl in methanol.

Bom

Benzyloxymethyl

A protection group for alcohols (hydroxyl groups) and can be removed with H2 Pd/C, Na/NH3/EtOH, and other conditions.

Bpa

4-Benzoyl-L-phenylalanine

Bz

Benzoyl

C6H5CO-

A aroyl protection group for alcohols and can be easily removed by hydrolysis in dilute basic solution.

Bzl

Benzyl

A protection group for alcohols and amines. Bzl groups can be removed under reductive conditions (e.g., H2/Pd), oxidative conditions (e.g., CrO3/acetic acid) and the use of Lewis Acids.

C6

6-Aminohexanoic acid

Ahx

A hydrophobic spacer typically incorporated into sequences to separate the peptide from tags and dye.

Cbz

Benzyloxycarbonyl

Z

Cha

Cyclohexylalanine

A non-proteinogenic amino acid shown to be a useful building block in the synthesis of peptides.

Chg

L-Cyclohexylglycine

A non-proteinogenic amino acid shown to be a useful building block in the synthesis of peptides.

CHO

Aldehyde group, also known as the formyl group.

Cit

L-Citrulline

An α-amino acid that is contained in some proteins as a result of a post-translational modification. Systemic citrulline is a biomarker of intestinal functionality.

CMK

Chloromethylketone

CPQ2

CPQ2

Chromophor used as a quencher often paired with fluorescein (FAM).

CPQ-2

CPQ-2

Chromophor used as a quencher often paired with fluorescein (FAM).

Cy3

Cy3

A fluorophor with an excitation at 550 nm and emission of 570 nm.

Cy5

Cy5

A fluorophor with an excitation at 650 nm and emission of 670 nm.

Cy7

Cy7

A fluorophor with an excitation at 750 nm and emission of 773 nm.

Dab

L-α,γ-Diaminobutyric acid

Non-proteinogenic amino acid sometimes used as a linker for nucleic acds and other biomolecules.

Dabcyl

4-(4-Dimethylaminophenylazo)benzoyl

A chromophor often used as a quencher in conjunction with a fluorophore (e.g., EDANS). Dabcyl/EDANS FRET pair have a Forster radius of 3.3 nm.

Dansyl

5-(Dimethylamino) naphthalene-1-sulfonyl

Fluorophor with an excitation at 342 nm and emission of 562 nm.

Dap

Diaminopimelic acid

DAP

An amino acid and is an epsilon-carboxy derivative of lysine. Dab is found as peptidoglycans in the cell wall of gram-negative bacteria.

DCHA

Dicyclohexylammonium salt

Dde

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

Decy

decanoyl, CH3(CH2)8CO-

DL-Asp

DL-Aspartic acid

A racemic mixture of the proteinogenic amino acid L-aspartate and the non-proteinogenic amino acid D-aspartate.

DMF

N,N-Dimethylformamide

A high-boiling point solvent for peptide synthesis

DNP

2,4-Dinitrophenyl

A chromophor often used as a quenchor in FRET experiments

DOTA

1,4,7,10-tetraazacyclododecane-N,N,N,N-tetraacetic acid

A common metal chelator used as a complexing agent for lanthanide ions and other metal ions. Its complexes have applications as contrast agents and cancer treatments.

Dpr

2,3-Diaminopropionic acid

A non-proteinogenic amino acid found in some secondary metabolites, such as zwittermicin A[1] and tuberactinomycin.

EDANS

5-[(2-Aminoethyl)amino]naphthalene-1-sulfonyl

Fluorophore with an excitation at 340 nm and emission of 490 nm. EDANS are often paired together with acceptors like dabcyl for FRET experiments.

FAM

Carboxyfluorescein

Fluorophor with an excitation at 492 nm and emission of 517 nm. Donors like FAM and 5FAM are often paired together with acceptors (CPQ2) for FRET experiments.

FITC

Fluorescein isothiocyanate

A fluorophor with an excitation at 490 nm and emission of 520 nm.

Fm

Fluorenylmethyl

A protection group used to protect thiols, including cysteine residues in which thioethers are formed. Rremoval can be accomplished with strong bases such as piperidine.

FMK

Fluoromethylketone

Fmoc

9-Fluorenylmethyloxycarbonyl

A protection group for primary and secondary amines. It is a common main-chain protection for amino acids in solid-phase peptide synthesis (SPPS) because it can be easily removed with piperidine without disturbing the acid labile linker between the resin and peptide.

Furoyl

Furan-2-carbonyl

GABA

Gamma-aminobutyric acid

gamma-Glu

γ-L-Glutamyl-

Gla

γ-Carboxy-L-glutamic acid

α-amino acid found occasionally in proteins by way of a post-translational carboxylation of glutamic acid residues. This modification enables calcium ion chelation and is mainly found in clotting factors and other proteins associated with coagulation cascade.

Glp

Pyroglutamic Acid

pGlu, Pyr

A proteogenic amino acid found on the N-terminal position of proteins. It results from the cyclization of an N-terminal glutamic acid residue to form a lactam.

Homoarg

L-Homoarginine

L-α-Amino-ε-guanidinohexanoic acid

Non-proteogenic amino acid and homolog of arginine that contains an additional methylene group on the side chain. Replacing argnine with homoarginine renders peptides and proteins resistant to proteolysis by trypsin

Homocit

L-Homocitrulline

L-α-Amino-ε-ureidohexanoic acid

An amino acid homolog of citrulline (Cit). Homocit is one methylene longer side chain than Cit and is a metabolite that results when lysine reacts with cyanate. During renal failure, the urea concentration increases and carbamylation of many proteins can occur, which can be detected as a biomarker.

Hse

Homoserine

Non-proteogenic α-amino acid that differs from serine by the insertion of an additional methylene group on the sidechain.

Hyp

trans-4-Hydroxy-L-proline

A hydroxylated variant of proline. While not natually encoded, Hyp is found in variety of mamailian (e.g., collagen, elastin, and argonaute 2) and plant proteins such as glycoproteins (HRGPs) found in plant cell walls.

iPr

iso-propyl

i-Pr

A hydrophobic alkyl group equivlent to a valine sidechain.

Lys(Me)

N-methyl lysine

Lys(Me1)

N-methyl lysine

Lys(Me2)

N-dimethyl lysine

Lys(Me3)

N-trimethyl lysine

MBHA

4-Methylbenzhydrylamine

A type linker used in solid-phase peptide synthesis that is often loaded onto polystyrene resin.

Mbs

4-Methoxybenzenesulfonyl

An arylsulfonyl protection group used to protect amines and guanidino function of arginine residues. Mbs is stable to hydrogenation and is removed with TFA/(CH3)2S or methansulfonic acid.

Mbzl

4-Methylbenzyl

A protection group mainly for sulfides of cysteine residues and is compatible with Boc/Bzl strategy of peptide synthesis.

Mca

(7-Methoxycoumarin-4-yl)acetyl

Fluorophor with an excitation at 325 nm and emission of 392 nm.

Me

Methyl (e.g., R-CH3) may be used in a variety of ways for peptide synthesis. The methylation of amide groups is a common method for adding steric constraints in peptides.

MeAla

N-methyl alanine

MeNle

N-methyl-L-norleucine

MeOSuc

Methoxysuccinyl

Met(O)

L-Methionine sulfoxide

Met(O)2

L-Methionine sulfone

Mmt

4-Methoxytrityl

Protection group mainly used for cysteine and Lysine sidechains. Mmt can be removed under mild acid conditions (e.g., 1% TFA, AcOH).

Mob

4-Methoxybenzyl

A protection group mainly used for sulfide groups of cysteine residues. Mob may be removed with TFMSA or HF.

Mpr

3-Mercaptopropionyl

Mtt

4-Methyltrityl

Myr

Myristyl group (Myristic acid)

CH3(CH2)12-

N3

Azide group (+N≡-N–N–R) reacts with an alkyne to afford a triazole (i.e., Click Chemistry)

Nal

β-(1-Naphthyl)-L-alanine

3-(1-Naphthyl)-L-alanine

As non-natural amino acid shown to be a useful buildingbock in the synthesis of peptides with enhanced bindingaffinity and half-lives.

NHEt

Ethylamide

NHMe

N-Methylamide

NHNH2

Hydrazide

NHOH

Hydroxamate

Nic

Nicotinyl

Nle

Norleucine

NMe2

N,N-Dimethylamide

NMP

N-Methyl-2-pyrrolidone

Highly a polar solvent used in SPPS that efficiently solvates the resin and may improve the coupling yield.

NO2

Nitro

NOTA

2,2′,2”-(1,4,7-triazacyclononane-1,4,7-triyl)triacetic acid

A metal chelator used as a complexing agent for metal ions. Its complexes have applications as contrast agents and cancer treatments.

Nps

2-Nitrophenylsulfenyl

NPys

3-Nitro-2-pyridinesulfenyl

Nva

L-Norvalyl (L-2-Aminovaleryl)

L-Norvaline

A non-polar aliphatic amino acid and homolog of Abu.

OBzl

Benzyl ester

OcHex

Cyclohexyl ester

OEt

Ethyl ester

OFm

Fluorenylmethyl ester

OHex

Hexyl ester

Oic

L-Octahydroindole-2-carboxylic acid

OMe

Methyl ester

ONp

p-Nitrophenyl ester

OPcp

Pentachlorophenyl ester

OPfp

Pentafluorophenyl ester

OPh

Phenyl ester

Orn

Ornithine

OSu

Succinimide ester

OtBu

t-Butyl ester

Pal

2-Pyridylalanine

Palmitic acid (PAL), hexadecanoic acid

Palmitoyl

Palmitic acid group

Pbf

2,2,4,6,7-Pentamethyldihydrobenzofuran-5-sulfonyl

PEG

Polyethylene glycol

PEG2

Polyethylene glycol linker (--CH2-CH2-O-CH2-CH2-O-CH2-CH2--)

PEG4

Polyethylene glycol linker (--CH2-CH2-O-CH2-CH2-O-CH2-CH2-O-CH2-CH2-O-CH2-CH2--)

Pen

L-Penicillamine

β,β-Dimethyl-L-cysteine

pGlu

Pyroglutamic Acid

Glp, Pyr

A proteogenic amino acid found on the N-terminal position of proteins. It results from the cyclization of an N-terminal glutamic acid residue to form a lactam.

Phaa

Phenylacetic acid

Phg

L-Phenylglycine

Pmp

β-Mercapto-β,β-cyclopentamethylene propionic acid

pNA

p-Nitroanilide

p-nitro-Phe

para-nitro-phenylalanine

pSer

Phospho-L-serine

pThr

Phospho-L-threonine

pTyr

Phospho-L-tyrosine

Pyr

Pyroglutamic Acid

Glp, pGlu

A proteogenic amino acid found on the N-terminal position of proteins. It results from the cyclization of an N-terminal glutamic acid residue to form a lactam.

QSY21

QSY21TM

A non-fluorescent amine-quenching chromophore with a broad and intense absorption at 661nm used as a quencher in FRET applications.

R110

Rhodamine 110

A fluorophore with an excitation wavelength fo 485 nm and emission wavelength fo 535 nm.

Sar

Sarcosine

N-Methylglycine

Sta

Statyl-((3S,4S)-4-amino-3-hydroxy-6-methylheptanoyl)

Suc

Succinyl

TAMRA

mixed-isomer 5/6-TAMRA

Single isomer 5-Carboxytetramethyl rhodamine (5TAMRA) and mixed-isomer 5/6-TAMRA are fluorophors with excitations at ~543 nm and emissions of ~572 nm.

tBu

t-Butyl ether protection groups

Are commonly used in Fmoc-SPPS to protect hydroxyl bearing side chains of serine, threonine, tyrosine, and hydroxyproline and can removed with strong acids such as trifluroroacetic acid (TFA).

Tfa

Trifluoroacetyl

Trifluoroacetic Acid, TFA

The most common salt and counter ion for synthetic peptides.

Thi

β-2-Thienylalanine

An unnatural amino acid containing a thiophene side chain

Tic

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

Tle

tert-butyl-leucine

Tos

Tosyl

4-Toluenesulfonyl

Trt

Trityl

triphenylmethyl, Tr

A protection group for amines – removed by acid and hydrogenolysis.

Tyr(Me)

Methyltyrosine

Xan

Xanthyl

β-Ala

β-Alanine

Naturally occurring β amino acid

βNA

β-Naphthylamide

β-NA

A non-natural amino acid shown to be a useful building block in the synthesis of peptides with enhanced binding affinity and half-lives.