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Peptide Synthesis---2. Fundamentals of Peptide Synthesis

Author:N/A    | Post time:2012-05-26

2. Fundamentals of Peptide Synthesis
Top of page
1. Introduction
2. Fundamentals of Peptide Synthesis
3. Strategies for Peptide Synthesis
4. Chain-Growing and Side-Chain Protective Groups
5. Coupling Methods
6. Side Reactions
7. Summary and Outlook
The link between neighboring amino acids in a protein or peptide is called amide bond or peptide bond. It is formed by an endothermic condensation reaction that covalently links the carboxy group of one amino acid with the amino group of another one. This polymerization results into a uniform peptide backbone that, except for proline, is the same for all the different amino acids (Fig. 1).
Figure 1. Structure of the peptide backbone
The different properties of peptides are determined by the individual sequence of 20 different side chains (Table 2,   Amino Acids). For example, the inner core of a protein is quite often made of amino acids with hydrophobic side chains that stick together trying to minimize the contact with water molecules. Thereby, the hydrophobic core forms a framework that presents other exactly arranged hydrophilic amino acids to the aqueous phase where interaction with binding partners is possible. It is noteworthy that a peptide has an intrinsic direction of sequence: each amino acid within the polymer has its own N-terminal and its C-terminal end.
Table 2. Classification ofnatural amino acids
Acidic amino acids Structure
________________________________________ ________________________________________
Aspartic acid D Asp 

Glutamic acid E Glu 

Basic amino acids Structure
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Lysine K Lys 

Arginine R Arg 

Histidine H His 

Polar, uncharged amino acids Structure
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Glycine G Gly 

Cysteine C Cys 

Serine S Ser 

Threonine T Thr 

Asparagine N Asn 

Glutamine Q Gln 

Tyrosine Y Tyr 

Nonpolar (hydrophobic) amino acids Structure
________________________________________ ________________________________________
Alanine A Ala 

Valine V Val 

Leucine L Leu 

Isoleucine I Ile 

Methionine M Met 

Proline P Pro 

Phenylalanine F Phe 

Tryptophan W Trp 

When the protein synthesis is inside the cell, the procedure is as follows:
Special enzymes (aminoacyl tRNA synthetases) specifically recognize individual amino acids and load them onto “their” transfer RNA (tRNA) that recognizes a specific triplet of the messenger RNA (mRNA). This “loading reaction” consumes two energy-rich bonds from ATP, and, thereby, chemically activates the amino acids at their C-terminal end by the formation of a mixed anhydride.
On the ribosome, the amino acids are exactly positioned in subnanometer dimensions according to the sequence of neighboring anticodons on the mRNA that these tRNAs recognize. Thus, potentially reactive side chains of the growing peptide are kept away from reactive groups of the activated amino acid while the amino acid is being coupled to the growing peptide chain by the formation of a peptide bond. Thereby, ribosomes function as truly digitally programmed nanomachine tools synthesizing individual peptides or proteins [1]. The elucidation of this procedure was awarded with the Nobel prize in 2009.
When the peptide synthesis is performed chemically, an analogous activation step is needed in order to achieve endergonic condensation of two amino acids (Fig. 2). Usually, the C-terminal carboxy group is made more susceptible to a nucleophilic attack by the amino group of the reaction partner (asterisk in Fig 2).
Figure 2. Specific condensation of two amino acids

CO* = activated C-terminus; tp = transient protective group; pp = permanent protective group
However, in contrast to the ribosomal synthesis the activated molecules are not exactly positioned but diffuse freely. Thus, this procedure would lead to the attack of any free amino group, and also of reactive side chains, e.g., sulfhydryl groups from cysteine, if no protecting strategy was applied. Therefore, the following protecting procedures have to be considered:
All reactive side chains must be protected during the whole procedure of chemical peptide synthesis (permanent side-chain protection).
Also the N-terminal amino group of one reaction partner must be protected to avoid an uncontrolled polymerization of the different monomers.
The N-terminal protective group must be removable without deprotection of the side-chain protection groups (orthogonal strategy) in order to regenerate a reaction partner at the end of the growing peptide chain (transient protection).
Finally, once the assembly of the peptide has been completed, all side-chain protective groups must be removed, and the peptide is eventually cleaved from the support.

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