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Labeling and Protecting Groups used in Peptide Synthesis

 Labeling and Protecting Groups used in Peptide Synthesis

In a peptide, each monomer unit in the sequence chain is known as an amino acid residue. The term residue refers to the fact that each amino acid in a peptide or protein sequence has lost one molecule of water during polymerization or synthesis. In peptides and proteins, the number of water molecules lost is one less than the number of residues. The peptide Ala-Val-Met, or AVM, or more precise L-alanyl-L-valyl-L-methionine has the following structure:

Figure 1: Structure and model of AVM. The model of the structure is displayed as a stick model with dots showing the Van Der Waals spheres.

Solid phase peptide synthesis is now commonly used for the formation of peptide bonds. To successfully link amino acids together to form a multitude of peptides protection strategies are needed. For peptide synthesis, protecting strategies have been developed utilizing a variety of temporary protecting groups that can be selectively removed either during or after synthesis. The Fmoc (9-fluorenyl-methoxycarbonyl)-group has become the most widely used N-terminal protection group in Fmoc-peptide synthesis strategies.

Figure 2: Structure and model of Fmoc-Cl.

Figure 3: Structural  models of Fmoc-Amino Acid and Fmoc-Dipeptide.

Since amino acid side chains represent a broad range of organic functional groups, a collection of different specific protecting groups has been developed over the years. Most of these are now commercially available. The following tables contain a list of protecting groups.

        Delta Mass and Masses of some
        Protecting Groups and Adducts

Δm and m

Group

14.027

Methylation, Me: Adding CH2

15       

Methyl, CH3

22

Sodium, Na

28.104

Formyl, CHO

28.054, 29

Ethyl, CH3CH2

38

Potassium, K

42.037

Acetyl, Ac

56.108, 57.1

tBu; tert-Butyl, C4H9

90.126

Anisyl

90.1, 91.1

Bzl; Benzyl, C7H7

96.009

TFA, trifluoroacetyl

100.117

Boc, t-Butyloxycarbonyl

104.108

Bz, Benzoyl

106.191

Thioanizyl, thiocresyl

222.243

Fmoc

243.3

Trt, Trityl; C17H15

252.3. 253.3

Pbf

266.361, 267.4

Pmc

 See also ABRF Delta Mass: https://abrf.org/delta-mass

Protecting groups most often used in organic synthesis and solid phase peptide synthesis (SPPS)

Protecting Group

Groups protected

Introduction

Cleavage

tert-Butyl

 

C4H9;  RW:  57.1

-CO2H

-OH

-SH

 

or

 

Moderately strong acid (e.g. 

95%  CF3CO2H

or

HCl in dioxane)

 Benzyl (Bzl)

 

C7H7;  RW:  91.1

-CO2H

-OH

-SH

 

Hydrogenolysis

(e.g. H2 / Pd)

or Strong acid

(e.g. HF or

HBr in CF3CO2H)

(or for SH protection Na/NH3)

Trityl (Trt)

C17H15; RW:  243.3

-CONH2

-SH

(His imidazole

)

(-NH2)



 

Mild acid

(e.g. CH3CO2H

or

5% CF3CO2H in organic solvent)

Methyl, ethyl


CH3, CH3CH3

RW:  15; 29

- CO2H

CH3OH or C2H5OH with acid catalyst (HCl or

Basic saponification

(e.g.

CH3OH/NaOH)

2,2,5,7,8-pentamethyl-chroman-6-sulphonyl (Pmc)

C14H19O3S; RW:  267.4

-NHC(NH2)=NH

(Arg)

 

Moderately strong acid

(e.g. CF3CO2H)

2,2,4,6,7-pentamethyl-dihydro-benzofuran-5-sulfonyl (Pbf)

C13H17O3S;  RW:  253.3

-NHC(NH2)=NH

(Arg)




 

Moderately strong acid

(e.g. CF3CO2H)

-.-