Protein Extinction Coefficient Calculator

The Protein Extinction Coefficient Calculator estimates the molar extinction coefficient based on your protein's tryptophan, tyrosine, and cystine residues. This tool helps biochemists and researchers quickly determine accurate protein concentration for spectrophotometric analysis. Whether you are monitoring purification, running assays, or quantifying samples, this tool saves time and ensures lab precision.

Count of tryptophan residues in the protein sequence
Count of tyrosine residues in the protein sequence
Count of cystine residues (disulfide bonds) in the protein
Molecular weight of the protein in kilodaltons (kDa)

How Molar Extinction Coefficient Is Calculated

The molar extinction coefficient measures how strongly a protein absorbs light at a specific wavelength. We calculate this using the Gill and von Hippel equation, which weighs the contribution of specific light-absorbing amino acids.

ε = (nW × 5500) + (nY × 1490) + (nC × 125)

Where:

  • ε = Molar extinction coefficient
  • nW = Number of tryptophan residues
  • nY = Number of tyrosine residues
  • nC = Number of cystine residues

First, count the number of tryptophan, tyrosine, and cystine residues in your sequence. This step matters because these are the only amino acids that absorb significantly at 280 nm. Next, multiply each count by its specific constant to find its individual contribution. Finally, add these values together to get the total coefficient. This method provides a reliable estimate that is typically accurate within 5-10% for most native proteins.

What Your Molar Extinction Coefficient Means

This number tells you how much light a 1 M solution of your protein absorbs. You use this value to find out exactly how much protein is in your test tube without destroying the sample.

High Coefficient (Over 40,000 M⁻¹cm⁻¹): Your protein is rich in tryptophan. This is beneficial because you can detect very small amounts of the protein easily with a spectrophotometer.

Low Coefficient (Under 10,000 M⁻¹cm⁻¹): Your protein has very few aromatic residues. You will need a higher concentration to get a reliable reading, or you might need a different detection method.

Important

This value assumes the protein is in its native, folded state. If the protein unfolds, the environment around the amino acids changes, which can slightly alter the absorbance.

This calculator is for informational purposes only and is not a substitute for laboratory validation. For critical experiments, always determine the coefficient experimentally using accurate standards.

Use this calculated value as a baseline for your experiments, but always verify it with a standard curve if you need extreme precision.

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