Protein Molecular Weight Calculator

Category: Biology
- March 11, 2025
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The molecular weight of a protein is calculated using the sum of the average isotopic masses of its amino acid residues:

\[ MW = \sum (n_i \times MW_i) - (n_{peptide} \times MW_{H_2O}) \]

Where:

  • \(n_i\) = Number of each amino acid in the sequence
  • \(MW_i\) = Molecular weight of each amino acid
  • \(n_{peptide}\) = Total number of peptide bonds
  • \(MW_{H_2O}\) = Molecular weight of a water molecule (18.02 Da)

What is the Protein Molecular Weight Calculator?

The Protein Molecular Weight Calculator helps determine the molecular weight of a protein based on its amino acid sequence or composition. It also calculates additional properties such as theoretical isoelectric point (pI), extinction coefficient, hydrophobicity (GRAVY score), and net charge at pH 7.

How to Use the Calculator

The calculator offers multiple ways to input protein data:

  • Sequence Method: Enter the protein sequence using one-letter amino acid codes.
  • Composition Method: Manually input the count of each amino acid.
  • Advanced Options: Apply modifications such as acetylation, disulfide bonds, or terminal modifications.

Key Features

  • Calculates molecular weight in both Dalton (Da) and kilodalton (kDa).
  • Determines theoretical pI based on amino acid pKa values.
  • Calculates extinction coefficient for UV absorbance at 280 nm.
  • Estimates hydrophobicity using the GRAVY score.
  • Accounts for custom modifications such as phosphorylation, methylation, and amidation.

Why is Protein Molecular Weight Important?

Knowing the molecular weight of a protein is crucial for:

  • Electrophoresis analysis (SDS-PAGE, Western blotting).
  • Mass spectrometry identification.
  • Protein purification and chromatography.
  • Structural and functional studies.

Frequently Asked Questions

How is the theoretical pI calculated?

The isoelectric point (pI) is the pH at which the protein has no net charge. It is calculated using the Henderson-Hasselbalch equation:

\[ pI = \frac{pKa_{pos} + pKa_{neg}}{2} \]

What is the extinction coefficient?

The extinction coefficient is calculated using the number of tryptophan (W), tyrosine (Y), and cystine (C) residues:

\[ \varepsilon = (n_W \times 5500) + (n_Y \times 1490) + (n_C \times 125) \]

How does the calculator handle modifications?

The calculator allows you to apply various post-translational modifications, which are added to or subtracted from the protein's molecular weight.

What is the GRAVY score?

The Grand Average of Hydropathy (GRAVY) score is a measure of protein hydrophobicity. It is calculated as:

\[ GRAVY = \frac{\sum (Hydropathy_{AA} \times n_{AA})}{Total\ Amino\ Acids} \]

Why is the water molecule included in the calculation?

Each peptide bond formation results in the loss of one water molecule, so the total mass is adjusted accordingly.

Conclusion

The Protein Molecular Weight Calculator is a valuable tool for researchers and students in biochemistry and molecular biology. Whether analyzing protein structure, running experiments, or interpreting results, this tool provides essential molecular properties quickly and accurately.