1. What is Peptide Extinction Coefficient?

The peptide extinction coefficient (ε) quantifies how strongly a peptide absorbs light at a specific wavelength. It's calculated as the sum of individual residue coefficients and is expressed in M⁻¹ cm⁻¹ units.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient equation:

Where:

• \( \varepsilon \) — Extinction coefficient (M⁻¹ cm⁻¹)
• Residue Coefficients — Individual amino acid absorption contributions

Explanation: The equation sums the extinction coefficients of all aromatic amino acids (Trp, Tyr, Cys) in the peptide sequence, as these are the primary contributors to UV absorption at 280 nm.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining protein concentration using UV spectrophotometry, which is essential for various biochemical and biophysical studies.

4. Using the Calculator

Tips: Enter the peptide sequence using single-letter amino acid codes. The calculator will sum the extinction coefficients of all residues, with special emphasis on tryptophan (W), tyrosine (Y), and cysteine (C) residues.

5. Frequently Asked Questions (FAQ)

Q1: Which amino acids contribute to extinction coefficient?
A: Primarily tryptophan (W), tyrosine (Y), and cysteine (C) contribute significantly to UV absorption at 280 nm.

Q2: What are typical extinction coefficient values?
A: Values range from 0 for peptides without aromatic residues to over 50,000 M⁻¹ cm⁻¹ for peptides rich in tryptophan residues.

Q3: How is extinction coefficient used experimentally?
A: It's used to calculate protein concentration using the Beer-Lambert law: Concentration = Absorbance / (ε × path length).

Q4: Are there limitations to this calculation?
A: The calculation assumes additive contributions and may not account for environmental factors or tertiary structure effects on absorption.

Q5: Can this be used for modified amino acids?
A: Standard calculations only consider natural amino acids. Modified residues may require experimental determination or specialized coefficients.