What is use of Edman degradation?
A. Determination of amino acid sequence from the N-terminus of a protein
B. Nucleotide sequence of DNA
C. Determination of amino acid sequence form the C-terminus of a protein
D. Determination of RNA structure

Understanding Edman Degradation in Protein Sequencing

Edman degradation is a widely used method for determining the amino acid sequence of proteins. It allows researchers to identify the order of amino acids starting from the N-terminus (the amino end) of a protein or peptide. This technique has been instrumental in protein biochemistry and molecular biology, enabling researchers to decode protein structures and functions.

Correct Answer:

👉 The correct answer is A. Determination of amino acid sequence from the N-terminus of a protein

What is Edman Degradation?

Edman degradation is a chemical reaction that sequentially removes one amino acid at a time from the N-terminal end of a peptide or protein. The released amino acid is identified using chromatography or electrophoresis, allowing researchers to determine the sequence of the protein.

This technique was developed by Pehr Edman in 1950, revolutionizing the field of protein chemistry by providing a systematic and precise method for protein sequencing.

How Does Edman Degradation Work?

Step-by-Step Process:

1. Reaction with Phenyl Isothiocyanate (PITC):

   • The protein or peptide is treated with phenyl isothiocyanate (PITC) under alkaline conditions.
   • PITC reacts with the free amine group of the N-terminal amino acid to form a phenylthiocarbamoyl derivative.

2. Cyclization:

   • The phenylthiocarbamoyl derivative undergoes cyclization under acidic conditions, releasing the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative.

3. Identification:

   • The PTH-amino acid is identified using high-performance liquid chromatography (HPLC) or thin-layer chromatography (TLC).
   • The remaining peptide is intact and ready for the next round of degradation.

4. Repeat Process:

   • The process is repeated to identify the next amino acid, continuing until the desired sequence is determined.

Reaction Summary:

1. PITC + N-terminal amino acid → Phenylthiocarbamoyl derivative
2. Phenylthiocarbamoyl derivative → PTH-amino acid + Shortened peptide
3. PTH-amino acid → Identified by HPLC

Key Features of Edman Degradation

 Highly specific for the N-terminal end of proteins
 Capable of sequencing up to 50 amino acids accurately
 Preserves the integrity of the remaining peptide for further analysis
 Used for sequencing small peptides and polypeptides

Why Edman Degradation is Useful

• Allows identification of post-translational modifications
• Provides insight into protein folding and function
• Used to study enzyme-substrate interactions
• Facilitates protein engineering and drug design

Limitations of Edman Degradation

 Inefficient for proteins longer than 50 amino acids due to signal loss
 Cannot sequence proteins with a blocked N-terminus
 Post-translational modifications at the N-terminus may interfere with the reaction

Explanation of Other Options

B. Nucleotide sequence of DNA

• Edman degradation is not used for DNA sequencing.
• DNA sequencing is typically performed using methods such as Sanger sequencing or Next-Generation Sequencing (NGS).

C. Determination of amino acid sequence from the C-terminus of a protein

• Edman degradation only targets the N-terminus of a protein.
• Sequencing from the C-terminus requires other methods such as carboxypeptidase digestion.

D. Determination of RNA structure

• RNA structure is determined using techniques like X-ray crystallography, NMR, and RNA sequencing.
• Edman degradation is specific to proteins, not nucleic acids.

Applications of Edman Degradation

Protein Identification: Helps in identifying unknown proteins.
Enzyme Function: Determines the active site and functional residues in enzymes.
Comparative Analysis: Used to compare homologous proteins from different species.
Antibody Research: Helps in mapping the epitope-binding sites of antibodies.

Edman Degradation vs. Mass Spectrometry

Challenges in Edman Degradation

• Proteins with blocked N-terminus (e.g., acetylation) cannot be sequenced directly.
• High background noise from complex protein mixtures.
• Low yield for proteins longer than 50 amino acids due to incomplete reaction.

Conclusion

Edman degradation remains one of the most precise and reliable methods for determining the amino acid sequence of proteins from the N-terminal end. While it is limited by the size and modification state of the protein, it is highly effective for small peptides and proteins with accessible N-termini. Understanding how Edman degradation works helps in protein engineering, drug development, and biochemical research.