1. What is the Extinction Coefficient?

The molar extinction coefficient (ε) at 280 nm is a measure of how strongly a protein absorbs light at 280 nm wavelength. This value depends on the protein's aromatic amino acid content - specifically tryptophan, tyrosine, and cysteine disulfide bonds.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient equation:

Where:

• \( Trp \) — Number of tryptophan residues
• \( Tyr \) — Number of tyrosine residues
• \( Cys\ pairs \) — Number of disulfide bonds (cysteine pairs)
• \( 5,500 \) — Extinction coefficient for tryptophan (M⁻¹cm⁻¹)
• \( 1,490 \) — Extinction coefficient for tyrosine (M⁻¹cm⁻¹)
• \( 125 \) — Extinction coefficient for each disulfide bond (M⁻¹cm⁻¹)

Explanation: The equation calculates the theoretical extinction coefficient based on the protein's amino acid composition, with each aromatic residue contributing to the total absorbance at 280 nm.

3. Importance of Extinction Coefficient

Details: The extinction coefficient is essential for determining protein concentration using UV spectrophotometry. It allows researchers to quantify protein samples without the need for standard curves or colorimetric assays.

4. Using the Calculator

Tips: Enter the number of tryptophan residues, tyrosine residues, and disulfide bonds from your protein sequence. All values must be non-negative integers. The calculator will provide the theoretical molar extinction coefficient in M⁻¹cm⁻¹.

5. Frequently Asked Questions (FAQ)

Q1: Why is the extinction coefficient important?
A: It enables accurate protein concentration determination using the Beer-Lambert law: Concentration = Absorbance / (ε × path length).

Q2: What are typical extinction coefficient values?
A: Values range from ~10,000 to over 100,000 M⁻¹cm⁻¹ depending on the protein's size and aromatic amino acid content.

Q3: How accurate is this theoretical calculation?
A: Theoretical values are generally within 5-10% of experimentally determined values for most proteins under native conditions.

Q4: Does protein denaturation affect the extinction coefficient?
A: Yes, denaturation can change the extinction coefficient by 5-20% due to changes in the local environment of aromatic residues.

Q5: Can I use this for proteins with chromophores?
A: No, this calculator is for proteins without additional chromophores. Proteins with heme groups, flavins, or other chromophores require experimental determination.