Extinction Coefficient Calculator Protein

Extinction Coefficient Equation:

\[ \varepsilon = (n_{Trp} \times 5690) + (n_{Tyr} \times 1280) + (n_{Cys} \times 120) \]

Tryptophan Residues (n_Trp):

count

Tyrosine Residues (n_Tyr):

count

Cysteine Residues (n_Cys):

count

Extinction Coefficient (ε):

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1. What is Protein Extinction Coefficient?

The extinction coefficient (ε) is a measure of how strongly a protein absorbs light at a specific wavelength, typically 280 nm. It depends on the number of aromatic amino acids (tryptophan, tyrosine) and cysteine residues in the protein structure.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient equation:

\[ \varepsilon = (n_{Trp} \times 5690) + (n_{Tyr} \times 1280) + (n_{Cys} \times 120) \]

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

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

3. Importance of Extinction Coefficient

Details: The extinction coefficient is essential for protein quantification using UV spectrophotometry, determining protein concentration, and monitoring protein purification processes.

4. Using the Calculator

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

5. Frequently Asked Questions (FAQ)

Q1: Why is extinction coefficient important?
A: It allows accurate protein concentration determination using UV absorbance at 280 nm without the need for standard curves.

Q2: What wavelength is used for protein extinction coefficient?
A: 280 nm is standard because aromatic amino acids (tryptophan and tyrosine) absorb strongly at this wavelength.

Q3: How accurate is this calculation?
A: This provides a theoretical estimate. Actual values may vary due to protein folding, solvent environment, and post-translational modifications.

Q4: Can I use this for modified proteins?
A: For proteins with significant modifications or non-standard chromophores, experimental determination is recommended.

Q5: What if my protein has no aromatic residues?
A: Proteins without tryptophan or tyrosine will have very low extinction coefficients and alternative quantification methods should be used.