1. What is Molar Extinction Coefficient?

The molar extinction coefficient (ε) is a measure of how strongly a chemical species absorbs light at a particular wavelength. For proteins, it's calculated from the amino acid composition, primarily considering tryptophan, tyrosine, and cysteine residues.

2. How Does the Calculator Work?

The calculator uses the following equation:

Where:

• \( \varepsilon_{\text{residue}} \) — Contribution from individual amino acids
• \( \varepsilon_{\text{disulfide}} \) — Contribution from disulfide bonds

Standard values:

• Tryptophan (W): 5500 M⁻¹ cm⁻¹
• Tyrosine (Y): 1490 M⁻¹ cm⁻¹
• Cysteine (C): 125 M⁻¹ cm⁻¹
• Disulfide bond: 125 M⁻¹ cm⁻¹ per bond

3. Importance of Extinction Coefficient

Details: The extinction coefficient is essential for protein quantification using UV spectrophotometry, determining protein concentration, and studying protein-ligand interactions.

4. Using the Calculator

Tips: Enter the protein sequence using single-letter amino acid codes. Specify the number of disulfide bonds in the protein. The sequence should contain only valid amino acid characters.

5. Frequently Asked Questions (FAQ)

Q1: Which amino acids contribute to extinction coefficient?
A: Primarily tryptophan, tyrosine, and cysteine. Other amino acids have negligible absorption at 280 nm.

Q2: Why are disulfide bonds included separately?
A: Cysteine in disulfide bonds contributes differently than reduced cysteine due to changes in electronic structure.

Q3: At what wavelength is this calculated?
A: Typically at 280 nm, where tryptophan and tyrosine absorb most strongly.

Q4: How accurate is this calculation?
A: It provides a good estimate, but actual values can vary due to protein folding and local environment effects.

Q5: Can this be used for modified proteins?
A: For proteins with chromophoric modifications, additional contributions may need to be considered.