N-terminus in protein

n-terminus

Introduction

N-terminus is a residue in a peptide that has an amino group (-NH₂). Amino acid is the essential component of protein. Each amino acid contains at least one amino group (-NH₂) and one carboxyl group (-COOH). The polymers of amino acids are peptides.

A peptide is linked by Peptide bonds between the amino group of each amino acid and the carboxyl group of the neighboring amino acid. This peptide bond has two ends. The end with a free amino group of a peptide chain is known as the N-terminus.

Many peptides combine together to form polypeptides or proteins. Each amino acid unit in the peptide is known as the residue. It is also a residue in the peptide. When a peptide chain starts, this terminal group comes first. It is a very important residue of peptides. They play a vital role in the peptide chain. Below is a discussion of the structure, function, and analysis of this terminal group in protein (1) & (3).

N-terminus

There are two residues present in a peptide bond. N-terminus and C- terminus. It is also known as amino-terminal residue or N-terminal or amino-terminus. In a peptide chain, the amino group of an amino acid is attached to the Carboxyl group of other amino acids. This chain has two end parts. It is the first part. This terminal group represents the end of a protein with a free amino group (2).

Definition

N-terminus is a starting part of the polypeptide chain which has a free amino group. It is located at the end of the polypeptide chain. The amino group in the peptide is bound to form a chain with another carboxyl group. But the last amino acid of the protein is only attached to the end of the carboxyl. So the residue of the free amino group is present as N-terminus (1).

Features

1. They describe the start of polypeptide or protein and suggest the free amino group of amino acids.

2. N-terminus carried out by labeling the free alpha-amino groups.

3. It is a negatively charged residue.

4. This terminus directly delivers the protein to the right cell organelles.

5. Its color is blue in the protein.

6. According to the convention, when drawing a protein structure this terminal group is present on the left side of the polypeptide chain.

7. There are two ends of the peptide chain. It is the first part of a peptide chain.

8. This terminal group is the primary part of a protein that comes out of a ribosome during protein synthesis.

9. It has a free amino group that is bound to the α-carbon atom.

10. When the protein is translated from messenger RNA, this terminal group is first translated (2) & (3).

Structure

In a polypeptide chain, a peptide has two residues. This terminal group is the first residue. Amino acids have two functional groups, such as an amino group and a carboxyl group. When an amino group of amino acids is attached to the alpha-carbon, then this residue is formed.

One amino group of amino acid is attached with the Carboxyl group (-COOH) of another amino acid. This link is formed through a dehydration reaction. Then the end amino group of a Protein is only attached with the end Carboxyl group (-COOH). And the residue of the free amino group is present in the form of the N-terminus.

When a protein molecule is observed in a graphics program, the amino group that is visible with the lowest residue is N-terminus (1).

Analysis of N-terminus

The following three methods are generally used for sequencing peptides from the N-terminus.

1. DNP method or Sanger method

The DNP method was coined by F. Sanger. In this method, the peptide chain is reacted with 2, 4-dinitrofluorobenzene (DNFB), which brings about substitution of DNFB by a free amino group to yield an N-Dinitrophenyl (DNP) derivative.  The hydrolysis of the peptide chain gives rise to the separation of labeled N-terminus amino acid (DNP-amino acid) and a mixture of other amino acids. Hence, DNP-amino acid so separated has been identified to determine this amino group.

2. Dansyl method

In this method, the reaction of the peptide chain with 5-dimethylaminonaphthalene-1-sulfonylchloride takes place at the N-terminus. The hydrolysis of the peptide chain gives rise to the formation of Dansyl amino acid.

This Dansyl amino acid on irradiation with UV light shows fluorescence. Thus the N-terminus is identified.

3. Edman degradation

This is the most important and frequently used method for determining the N-terminus amino acid residue. The peptide is reacted with phenyl isothiocynate to yield a phenylthiourea in this method. When this derivative is treated with anhydrous HCL in an organic solvent, the N-terminus amino acid is cleaved as a thiazolinone derivative from the remainder of the peptide.

This derivative is unstable under the conditions of its formation and rearranges to a pehylthiohydantoin (PTH), which is isolated and identified by comparing it with standard samples of PTH derivatives of known amino acids. The great advantage of this method is that it leaves the rest of the peptide chain intact so that the analysis can be repeated and the new N-terminus of the shortened peptide identified (1) & (4).

Function

1. N-terminus is an important determinant of the protein.

2. It supplies many of the structural elements of a cell and bound cells together.

3. This terminus is the first part of the polypeptide chain. So it plays an important role for the formation of protein.

4. It is involved in the direct delivery of proteins to the right cell organelles.

5. They often contain the signal peptide sequence (3) & (4).

Q&A

1. How to determine n and c terminus?

The N-terminus is determined by reacting the protein with dansyl chloride. Dansyl chloride reacts with an amino group in the protein. And C-terminus is determined by the addition of carboxypeptidase enzymes. This enzyme divides amino acids from C-terminal (1).

2. What is the n terminus?

N-terminus is a residue of a peptide. The terminal group of amino acids with a free amino group is known as N-terminus (1).

3. What is n terminus?

The end of the peptide with the free amino group is known as N-terminus (1).

4. How to identify n terminus?

There are several methods by which this terminal group is identified. These are

1. 1-fluoro-2, 4-dinitrobenzene reacts with a free amino group. This reaction takes place with the amino group or the N-terminus of the polypeptide chain.

2. The N-terminus is identified by reacting the protein with dansyl chloride. Dansyl chloride reacts with an amino group in the protein.

3. A reaction occurs between an amino group of the N-terminus and the reagent phenyl isothiocyanate.

These are the three methods that enable the identification of the N-terminus (4).

5. What are the n terminus and c terminus of a protein?

N-terminus

The first part of the polypeptide chain with the free amino group is called the N-terminus of a protein.

C-terminus

The end part of the polypeptide chain with the free carboxyl group is called the C-terminus of a protein (2).

Reference

1. Nimai Tewari. Advance Organic Chemistry. Books and Allied (P) Ltd. Chapter: Amino acids, peptides, proteins enzymes, and nucleic acids. Page No: 716 to 718.

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