1. What is the Extinction Coefficient?

The extinction coefficient (ε) is a measure of how strongly a chemical species absorbs light at a given wavelength. For proteins, it is calculated based on the number of aromatic amino acids (tryptophan, tyrosine) and cysteine residues that contribute to UV absorbance at 280 nm.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient equation:

Where:

• \( n_{Trp} \) — Number of tryptophan residues
• \( n_{Tyr} \) — Number of tyrosine residues
• \( n_{Cys} \) — Number of cysteine residues
• 5500 — Molar extinction coefficient for tryptophan (M⁻¹ cm⁻¹)
• 1490 — Molar extinction coefficient for tyrosine (M⁻¹ cm⁻¹)
• 125 — Molar extinction coefficient for cysteine (M⁻¹ cm⁻¹)

Explanation: The equation accounts for the contribution of each chromophoric amino acid to the total UV absorbance at 280 nm, with tryptophan having the strongest absorbance.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for protein quantification, concentration determination, spectrophotometric analysis, and various biochemical applications including protein purification and characterization.

4. Using the Calculator

Tips: Enter the count of each amino acid type (tryptophan, tyrosine, cysteine) from your protein sequence. All values must be non-negative integers. The calculator will compute the theoretical extinction coefficient at 280 nm.

5. Frequently Asked Questions (FAQ)

Q1: Why are only three amino acids considered?
A: Tryptophan, tyrosine, and cysteine are the primary contributors to UV absorbance at 280 nm due to their aromatic rings and disulfide bonds.

Q2: What is the typical range for protein extinction coefficients?
A: Extinction coefficients typically range from 10,000 to 100,000 M⁻¹ cm⁻¹, depending on the protein's size and amino acid composition.

Q3: Can this be used for protein concentration determination?
A: Yes, once you have the extinction coefficient, you can use Beer-Lambert law (A = εcl) to calculate protein concentration from absorbance measurements.

Q4: Are there limitations to this calculation?
A: This provides a theoretical value. Actual extinction may vary due to protein folding, solvent environment, and post-translational modifications.

Q5: What if my protein has no aromatic amino acids?
A: Proteins without tryptophan, tyrosine, or cysteine will have very low extinction coefficients and may require alternative quantification methods.