Extinction Coefficient Calculator Peptide

Peptide Extinction Coefficient Equation:

\[ \varepsilon = n_{\text{peptide}} \times 5690 \text{ (at 214 nm approx)} \]

Extinction Coefficient (ε):

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1. What is Peptide Extinction Coefficient?

The peptide extinction coefficient estimates the absorbance of peptide bonds at 214 nm wavelength. This calculation is essential for quantifying protein concentration using UV spectrophotometry, particularly when aromatic amino acids are absent or minimal.

2. How Does the Calculator Work?

The calculator uses the peptide extinction coefficient equation:

\[ \varepsilon = n_{\text{peptide}} \times 5690 \text{ (at 214 nm approx)} \]

Where:

\( \varepsilon \) — Extinction coefficient (M⁻¹ cm⁻¹)
\( n_{\text{peptide}} \) — Number of peptide bonds in the protein/peptide
5690 — Molar extinction coefficient per peptide bond at 214 nm

Explanation: The equation calculates the theoretical extinction coefficient based on the number of peptide bonds, which absorb UV light at 214 nm due to the n→π* transition of the amide group.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining protein concentration, monitoring protein purification, and ensuring proper experimental conditions in biochemical and biophysical studies.

4. Using the Calculator

Tips: Enter the number of peptide bonds in your protein/peptide. For a protein with N amino acids, the number of peptide bonds is typically N-1. All values must be valid (n_peptide > 0).

5. Frequently Asked Questions (FAQ)

Q1: Why use 214 nm instead of 280 nm?
A: 214 nm detects peptide bonds, making it suitable for proteins lacking aromatic amino acids (Trp, Tyr), while 280 nm specifically detects these aromatic residues.

Q2: How accurate is this calculation?
A: This provides a theoretical estimate. Actual values may vary due to protein structure, solvent conditions, and specific amino acid composition.

Q3: When should I use this method?
A: Use for proteins with minimal aromatic amino acids, or when 280 nm absorbance is unreliable. Also useful for peptides and small proteins.

Q4: What are typical extinction coefficient values?
A: Values range from thousands to hundreds of thousands M⁻¹ cm⁻¹ depending on protein size and composition. Larger proteins with more peptide bonds have higher coefficients.

Q5: Can this be used for concentration determination?
A: Yes, using Beer-Lambert law: Concentration = Absorbance / (ε × path length). Ensure measurements are within the linear range of your spectrophotometer.