Question

Why can the Edman degradation not be used effectively with very long peptides? Hint: Think about the stoichiometry of the peptides and the Edman reagent and the percent yield of the organic reactions involving them.

Short answer

Edman degradation is ineffective for very long peptides because the cumulative loss in yield over multiple cycles reduces accuracy.

Step-by-step solution

- Understand Edman Degradation

Edman degradation is a method used to sequence amino acids in a peptide. It involves the cleavage of the N-terminal amino acid, which is then identified.

- Consider the Yield of Each Cycle

Each cycle of Edman degradation does not have a 100% yield. This means that not every peptide bond is cleaved and identified correctly.

- Calculate the Effect of Yield Over Multiple Cycles

If the yield of each cycle is less than 100%, the yield decreases exponentially with each additional cycle. For example, with a 98% yield per cycle, after 10 cycles the overall yield would be 98%^10.

- Apply the Concept to Long Peptides

For long peptides, the exponential decrease in yield due to the repeated cycles results in a significantly lower overall yield. This means that accurate sequencing becomes progressively more difficult.

- Conclusion

The effectiveness of Edman degradation decreases with peptide length due to cumulative losses in yield, making it impractical for very long peptides.

Key concepts

peptide sequencing

Peptide sequencing is the process of determining the order of amino acids in a peptide or protein.
One of the most common methods for sequencing peptides is Edman degradation.
This method sequentially removes amino acids from the N-terminal end of the peptide.
Each removed amino acid can then be identified.
This provides the amino acid sequence step-by-step.
However, this process can become less efficient with longer peptides due to cumulative errors.

yield calculation

Yield calculation is critical for understanding the efficiency of Edman degradation.
In this context, yield refers to the percentage of peptide bonds successfully cleaved and identified in each cycle of the degradation process.
For instance, if each cycle has a yield of 98%, not all peptide bonds are cleaved accurately.
Therefore, after one cycle, 98% of the original peptides are correctly identified.
However, after multiple cycles, the effective yield decreases exponentially, making the overall process less reliable.

N-terminal amino acid

The N-terminal amino acid of a peptide is crucial for Edman degradation.
This method targets the N-terminal amino acid, cleaving it one at a time.
Identifying the N-terminal amino acid allows for the stepwise sequencing of the peptide.
However, if the yield of each cycle is not 100%, some N-terminal amino acids might not be identified correctly, which can cause errors that accumulate with each subsequent cycle.

organic reactions

Edman degradation involves several organic reactions to cleave and identify amino acids.
The efficiency of these reactions determines the yield and accuracy of the sequencing.
In an ideal scenario, each organic reaction in the cycle should proceed with a high yield.
However, in practice, the yield is often less than 100%, leading to errors.
As a result, the longer the peptide, the more cycles are required, and the more the cumulative yield decreases.

long peptide inefficiency

The inefficiency of Edman degradation increases with the length of the peptide.
As each cycle does not yield a 100% success rate, the overall yield decreases exponentially with each additional cycle.
This makes sequencing very long peptides impractical with Edman degradation.
The combined losses in yield across multiple cycles result in significantly lower accuracy and reliability of the sequencing for long peptides.
Thus, alternative methods like mass spectrometry might be preferred for sequencing longer peptides.