Expasy Extinction Coefficient Calculator

Extinction Coefficient Equation:

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

Number of Tryptophan Residues (n_Trp):

count

Number of Tyrosine Residues (n_Tyr):

count

Number of Cystine Pairs (n_Cys):

count

Extinction Coefficient (ε):

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1. What is the Expasy Extinction Coefficient Calculator?

The Expasy Extinction Coefficient Calculator estimates the molar extinction coefficient at 280 nm for a protein sequence using the Edelhoch method. This calculation is based on the ProtParam tool from Expasy and provides essential information for protein quantification and characterization.

2. How Does the Calculator Work?

The calculator uses the Edelhoch 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 cystine pairs (disulfide bonds)
5500 — Molar extinction coefficient for tryptophan at 280 nm
1490 — Molar extinction coefficient for tyrosine at 280 nm
125 — Molar extinction coefficient for cystine at 280 nm

Explanation: The equation calculates the theoretical extinction coefficient based on the aromatic amino acid content of the protein, with tryptophan contributing most significantly due to its high extinction coefficient.

3. Importance of Extinction Coefficient Calculation

Details: The extinction coefficient is crucial for determining protein concentration using UV spectrophotometry, monitoring protein purification, and ensuring accurate protein quantification in biochemical and biophysical studies.

4. Using the Calculator

Tips: Enter the number of tryptophan residues, tyrosine residues, and cystine pairs from your protein sequence. All values must be non-negative integers. The calculator will provide the extinction coefficient in M⁻¹ cm⁻¹.

5. Frequently Asked Questions (FAQ)

Q1: Why is the extinction coefficient important?
A: It allows accurate determination of protein concentration using the Beer-Lambert law (A = εcl), which is essential for most protein biochemistry experiments.

Q2: What are typical extinction coefficient values?
A: Values typically range from 10,000 to 100,000 M⁻¹ cm⁻¹, depending on the protein's size and aromatic amino acid content.

Q3: Why are only Trp, Tyr, and Cys considered?
A: These three amino acids are the primary contributors to UV absorption at 280 nm due to their aromatic rings and disulfide bonds.

Q4: How accurate is this calculation?
A: The calculation provides a theoretical estimate. Actual values may vary due to protein folding, solvent environment, and local structural effects on chromophores.

Q5: Can this be used for modified proteins?
A: For proteins with chromophoric modifications (e.g., fluorescent tags, heme groups), additional contributions to extinction must be considered separately.