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 Amino acid reactions

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مُساهمةموضوع: Amino acid reactions   الجمعة ديسمبر 25, 2009 1:52 pm

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Introduction
Reactive groups in amino acids include -NH2
and -COOH groups and groups present on side chains. In peptides and
proteins only the side chain is available for reactions (besides amino
and carboxylic groups at the terminal ends).

Please note that in peptides and proteins:

Compounds reacting with amino groups can affect both the amino group at N-terminal end and the epsilon-amino group of Lysine.

Compounds
reacting with carboxyl groups can affect the C-terminal carboxyl group
and carboxylic groups of aspartic and glutamic acid side chains.




NH2 group

Ninhydrin. Ninhydrin
(triketohydrindene hydrate) is an oxidating agent which leads to the
oxidative deamination of alpha-amino groups. It is very important for
the detection and the quantitative analysis of amino acids. Ninhydrin
also reacts with primary amines however the formation of carbon dioxide
is quite diagnostic for amino acids. Alpha amino acids yield a purple
substance that absorbs maximally at 570 nm. Imino acids (proline) yield
a yellow product (absorption maximum 440 nm).



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Sanger Reagent (FDNB). The
arylation (dinitrophenylation, DNP) reaction of amino groups with FDNB
(1-Fluoro-2,4-dinitrobenzene) was used by Sanger et al. (1955) for the
determination of the primary structure of insulin. The DNP-derivatives
are stable to acid hydrolysis.

The
reaction of FDNB with peptides/proteins leads to the formation of the
DNP-derivative of the terminal alpha-amino group and the DNP-derivative
of other reactive groups (e.g., the epsilon amino group of lysine).
After acid hydrolysis only one amino acid will result modified at the
alpha-amino group, i.e., the N-terminal residue. The DNP derivatives
after acid hydrolysis can be extracted with organic solvents and
identified by cromathography.


Dansyl Chloride. 1-dimethylaminonaphtalene-5-sulphonyl
chloride (Dansyl chloride) is useful for the determination of the
N-terminal residue in peptides and proteins. The dansyl derivative is
highly fluorescent (much more sensitive than FDNB) and stable to acid
hydrolysis.



Cyanate




It is worth noting thatcyanate ion is formed when urea is dissolved in water:
NH2CONH2NH4+ + NCO-
thus proteins in urea solutions can be carbamylated.
Edman Degradation. Phenylisotiocyanate (Edman Reagent) is the must in protein and peptide sequencing ..........




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After treatment with anidrous trifluoroacetic acid (TFA, F3CCOOH)
the peptide bond involving the carboxyl of the N-terminal residue is
cleaved (cleavage reaction) with the formation of the thiazolinone
derivative. The treatment with TFA does not affect the other peptide
bonds leaving a peptide chain with n-1 amino acid residues.

The
treatment of the thiazolinone derivative with aqueous acid (conversion
reaction) leads to the formation of Phenylthiohydantoin (PTH)
derivative of N-terminal amino acid which can be identified by chromatography.





The residue peptide chain can be now submitted to a new coupling reaction and the next amino acid can be identified.

Phosgene and Carbon Disulfide. The
reaction of these compounds with alpha-amino acids yields N-carboxy
anhydrydes. These compounds react with nucleophilic reagents and have
been used as intermediates in the synthesis of peptides.




Maleic Anydride. Maleic
anydride is used to modify lysine residues in a protein. Trypsin does
not recognize these modified residues thus cleaving only at arginyl
bonds.




Experimental conditions. Add slowly a 4-5 fold excess of reactive at pH 8.5-9.5. This pH maximize the NH2 form of amino groups and minimize the hydrolysis of maleic anydride by H2O and OH-.
Keep pH to the initial value by adding dilute NaOH. The reaction can be
considered terminated when no further variations in pH occur. Do not
use buffer containing amino groups. Urea and guanidine hydrocloride are
allowed. Amino groups can be restored lowering the pH at 3.5.

Formaldehyde. Formaldehyde, the most simple aldehyde, is a colorless gas (boiling point -21 oC)
with a pungent odor. It is also known as formalin, embalming fluid, or
formol. The term formalin is referred to aqueous solutions.
Formaldehyde can also occur in solid state as a polymer
(paraformaldehyde and trioxymethylene, see figure below). The heating
of these polymers allows to obtain anydrous formaldehyde. At high
levels, formaldehyde is a probable human carcinogen.

It reacts with amino groups and it is used to fix protein by means of a methylenic bridge (see reaction below).
It
is also used in the so called formol titration, where the reaction of
formaldehyde with the unprotonated form of the amino acid leads to the
formation of methylol derivatives:


2HCHO + --NH2 = (HOCH2)2 - N ---
As a consequence of this reaction the equilibrium:


-NH3+ = -NH2 + H+
is
moved to the right with liberation of protons which can be titrated
with NaOH. During the digestion of protein by proteases there is the
liberation of amino groups thus the titration with formol can be used
to follow the extent of the reaction.




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