Protein Calculator Molecular Weight Extinction Coefficient

Extinction Coefficient Formula:

\[ \varepsilon \approx 5500 \times (W + Y) + 1490 \times (C) \text{ for } 280 \text{ nm} \]

Extinction Coefficient (ε):

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1. What is the Extinction Coefficient?

The extinction coefficient (ε) is a measure of how strongly a chemical species absorbs light at a particular wavelength. For proteins at 280 nm, it's primarily determined by the content of tryptophan, tyrosine, and cystine residues.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient formula:

\[ \varepsilon \approx 5500 \times (W + Y) + 1490 \times (C) \text{ for } 280 \text{ nm} \]

Where:

\( \varepsilon \) — Extinction coefficient (L/mol·cm)
\( W \) — Tryptophan count (unitless)
\( Y \) — Tyrosine count (unitless)
\( C \) — Cystine count (unitless)

Explanation: The formula approximates the molar extinction coefficient at 280 nm based on the number of specific amino acid residues that contribute to UV absorption.

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 number of tryptophan (W), tyrosine (Y), and cystine (C) 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 UV light at 280 nm due to their aromatic structures.

Q2: How accurate is this approximation?
A: This provides a good estimate for most proteins, but the actual extinction coefficient can vary depending on the protein's environment and structure.

Q3: What if my protein has no tryptophan residues?
A: The calculation still works - the tryptophan contribution will be zero, and the extinction coefficient will be based on tyrosine and cystine content.

Q4: Can this be used for other wavelengths?
A: This specific formula is designed for 280 nm measurements. Other wavelengths require different coefficients and calculations.

Q5: How is this related to protein concentration?
A: Protein concentration can be calculated using Beer-Lambert law: Concentration = Absorbance / (ε × path length)