1. What is the Extinction Coefficient?

The extinction coefficient (ε) is a measure of how strongly a chemical species absorbs light at a particular wavelength. For proteins, it's typically calculated at 280 nm and depends on the content of aromatic amino acids (tryptophan, tyrosine) and cysteine.

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
• 5690 — Molar extinction coefficient for tryptophan (M⁻¹cm⁻¹)
• 1280 — Molar extinction coefficient for tyrosine (M⁻¹cm⁻¹)
• 120 — Molar extinction coefficient for cysteine (M⁻¹cm⁻¹)

Explanation: The equation calculates the theoretical extinction coefficient at 280 nm based on the amino acid composition of a protein.

3. Importance of Extinction Coefficient Calculation

Details: The extinction coefficient is crucial for determining protein concentration using UV absorbance measurements. Accurate concentration determination is essential for various biochemical and biophysical experiments.

4. Using the Calculator

Tips: Enter the number of tryptophan, tyrosine, and cysteine residues in your protein sequence. All values must be non-negative integers.

5. Frequently Asked Questions (FAQ)

Q1: Why are only Trp, Tyr, and Cys considered?
A: These three amino acids are the primary contributors to UV absorbance at 280 nm due to their aromatic side chains.

Q2: What units is the extinction coefficient in?
A: The extinction coefficient is typically expressed in M⁻¹cm⁻¹ (molar extinction coefficient).

Q3: How accurate is this calculation?
A: This provides a theoretical estimate. The actual extinction coefficient may vary slightly due to protein folding and environmental factors affecting the chromophores.

Q4: Can I use this for peptides and small proteins?
A: Yes, this equation works for proteins and peptides of any size, as long as you know the amino acid composition.

Q5: What if my protein has no aromatic amino acids?
A: Proteins without Trp, Tyr, or Cys will have very low extinction coefficients at 280 nm, making UV concentration determination difficult.