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 amino acid composition and disulfide bonds, providing crucial information for protein quantification and characterization.

2. How Does the Calculator Work?

The calculator uses the protein extinction coefficient formula:

Where:

• \( ε \) — Molar extinction coefficient (M⁻¹ cm⁻¹)
• \( Σ ε_{aa} \) — Sum of extinction coefficients from individual amino acids
• \( ε_{disulfide} \) — Contribution from disulfide bonds

Explanation: The total extinction coefficient is the sum of contributions from aromatic amino acids (mainly tryptophan and tyrosine) and cystine residues from disulfide bonds.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is essential for determining protein concentration using UV absorbance, monitoring protein purification, and studying protein-ligand interactions.

4. Using the Calculator

Tips: Enter the sum of amino acid contributions and disulfide bond contributions in M⁻¹ cm⁻¹. Both values must be non-negative. For accurate results, use established values for individual amino acid extinction coefficients.

5. Frequently Asked Questions (FAQ)

Q1: Which amino acids contribute most to extinction coefficient?
A: Tryptophan and tyrosine contribute most significantly, with tryptophan having the highest molar extinction coefficient at 280 nm.

Q2: How do disulfide bonds affect extinction coefficient?
A: Cystine residues from disulfide bonds contribute approximately 125 M⁻¹ cm⁻¹ per disulfide bond at 280 nm.

Q3: What is the typical range for protein extinction coefficients?
A: Protein extinction coefficients typically range from 10,000 to 100,000 M⁻¹ cm⁻¹, depending on the protein's size and aromatic amino acid content.

Q4: Can this calculator be used for modified proteins?
A: For proteins with chromophoric modifications or non-standard amino acids, additional contributions may need to be considered.

Q5: How accurate are calculated extinction coefficients?
A: Calculated values are generally within 5-10% of experimentally determined values for most native proteins under standard conditions.