Protein Extinction Coefficient Calculator Expasy

Protein Extinction Coefficient Equation:

\[ \varepsilon = \sum (n \times \varepsilon_{AA}) \]

Extinction Coefficient (ε):

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1. What Is The Protein Extinction Coefficient?

The protein extinction coefficient (ε) quantifies how strongly a protein absorbs light at a specific wavelength. It's essential for determining protein concentration using UV spectrophotometry and is calculated based on the number of specific amino acids in the protein sequence.

2. How Does The Calculator Work?

The calculator uses the standard Expasy equation:

\[ \varepsilon = n_{Trp} \times 5500 + n_{Tyr} \times 1490 + n_{Cys} \times 125 \]

Where:

\( n_{Trp} \) — Number of tryptophan residues
\( n_{Tyr} \) — Number of tyrosine residues
\( n_{Cys} \) — Number of cysteine residues (reduced form)

Explanation: The equation accounts for the three amino acids that contribute significantly to UV absorption at 280 nm, with tryptophan having the strongest absorption.

3. Importance Of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining protein concentration, which is essential for biochemical experiments, drug development, and quality control in biopharmaceutical production.

4. Using The Calculator

Tips: Enter the count of tryptophan (W), tyrosine (Y), and cysteine (C) residues from your protein sequence. All values must be non-negative integers.

5. Frequently Asked Questions (FAQ)

Q1: Why are only three amino acids considered?
A: Tryptophan, tyrosine, and cysteine are the primary contributors to UV absorption at 280 nm, with tryptophan having the strongest absorption coefficient.

Q2: What if my protein has disulfide bonds?
A: This calculator assumes reduced cysteine residues. For oxidized cysteines (disulfide bonds), the extinction coefficient contribution is negligible.

Q3: How accurate is this calculation?
A: The calculation provides a theoretical estimate. Actual measurements may vary slightly due to protein folding and local environment effects.

Q4: Can I use this for modified amino acids?
A: No, this calculator is designed for standard amino acids only. Modified residues may have different absorption properties.

Q5: What units is the result in?
A: The extinction coefficient is calculated in M⁻¹cm⁻¹ (molar extinction coefficient), which is standard for protein concentration measurements.