Protein Molecular Weight Calculator Extinction Coefficient

Extinction Coefficient Formula:

\[ \varepsilon (M^{-1} cm^{-1}) = (N_{Trp} \times 5500) + (N_{Tyr} \times 1490) + (N_{Cys} \times 125) \]

Extinction Coefficient (ε):

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1. What is the Extinction Coefficient?

The extinction coefficient (ε) is a measure of how strongly a protein absorbs light at a specific wavelength. It is calculated based on the aromatic amino acid content (tryptophan, tyrosine, and cystine) and is expressed in units of M⁻¹ cm⁻¹.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient formula:

\[ \varepsilon (M^{-1} cm^{-1}) = (N_{Trp} \times 5500) + (N_{Tyr} \times 1490) + (N_{Cys} \times 125) \]

Where:

\( N_{Trp} \) — Number of tryptophan residues
\( N_{Tyr} \) — Number of tyrosine residues
\( N_{Cys} \) — Number of cystine residues
5500 — Extinction coefficient contribution per tryptophan
1490 — Extinction coefficient contribution per tyrosine
125 — Extinction coefficient contribution per cystine

Explanation: The equation accounts for the light-absorbing properties of aromatic amino acids in proteins at 280 nm wavelength.

3. Importance of Extinction Coefficient

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

4. Using the Calculator

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

5. Frequently Asked Questions (FAQ)

Q1: Why are these specific amino acids used?
A: Tryptophan, tyrosine, and cystine are the primary amino acids that absorb light at 280 nm due to their aromatic ring structures.

Q2: What is the typical range of extinction coefficients?
A: Extinction coefficients typically range from a few thousand to over 100,000 M⁻¹ cm⁻¹, depending on the protein's aromatic amino acid content.

Q3: How accurate is this calculation method?
A: This method provides a good estimate, but the actual extinction coefficient can vary slightly due to protein folding and local environment effects.

Q4: Can this be used for modified amino acids?
A: This calculation is for standard amino acids only. Modified amino acids may have different extinction properties.

Q5: What wavelength is this calculated for?
A: This extinction coefficient is calculated for measurements at 280 nm, which is the standard wavelength for protein quantification.