1. What is the Peptide Extinction Coefficient?

The peptide extinction coefficient estimates the molar absorptivity of proteins and peptides at 280 nm based on their amino acid composition. This parameter is essential for quantifying protein concentration using UV spectrophotometry.

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 cysteine disulfide bonds
• 5500 — Extinction coefficient for tryptophan (M⁻¹·cm⁻¹)
• 1490 — Extinction coefficient for tyrosine (M⁻¹·cm⁻¹)
• 125 — Extinction coefficient for cysteine pairs (M⁻¹·cm⁻¹)

Explanation: The equation accounts for the primary chromophores in proteins that absorb light at 280 nm, with tryptophan contributing the most to the extinction coefficient.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining protein concentration, monitoring protein purification, and ensuring proper experimental conditions in biochemical and biophysical studies.

4. Using the Calculator

Tips: Enter the number of tryptophan residues, tyrosine residues, and cysteine disulfide bond pairs. All values must be non-negative integers. The result provides the estimated molar extinction coefficient at 280 nm.

5. Frequently Asked Questions (FAQ)

Q1: Why is extinction coefficient important for protein studies?
A: The extinction coefficient allows researchers to accurately determine protein concentration using UV spectrophotometry, which is essential for experimental reproducibility and data interpretation.

Q2: What are typical extinction coefficient values?
A: Extinction coefficients vary widely depending on protein size and composition, typically ranging from 10,000 to 100,000 M⁻¹·cm⁻¹ for most proteins.

Q3: When should this calculation be used?
A: Use this calculation when you know the amino acid sequence of your protein and need to determine concentration using absorbance at 280 nm.

Q4: Are there limitations to this equation?
A: This is an estimation method. Actual values may vary due to protein folding, solvent conditions, and the local environment of chromophores.

Q5: How accurate is this calculation?
A: For most standard proteins, this calculation provides a good estimate (±5-10%), but for precise work, experimental determination is recommended.