How to calculate a protein’s molecular weight (Da and kDa)

A protein’s weight is just the sum of its amino-acid residues plus one water molecule for the free ends. It is the number you compare against a gel ladder, and it falls straight out of the sequence.

The formula

When amino acids join, each peptide bond releases a water molecule, so the mass of a chain is the sum of the residue masses (each amino acid minus that lost water) plus one whole water (18.015 Da) added back for the free N- and C-termini:

MW = Σ(residue masses) + 18.015 Da

Residue masses are standard average isotopic values — glycine is 57.05 Da, alanine 71.08 Da, tryptophan (the heaviest) 186.21 Da. Averaging over typical proteins, a residue is roughly 110 Da, which is where the rule of thumb “number of residues × 110 ≈ molecular weight” comes from.

A worked example you can check

The dipeptide glycylglycine (GG) is two glycines: 2 × 57.0519 + 18.01524 = 132.12 Da, which matches the known mass of the molecule. Scale that up to a 10-residue peptide likeMAKFGPTDEF and you get 1,142.3 Da (≈ 1.14 kDa), an average of 114 Da per residue.

Reading it on a gel

Molecular weight is usually quoted in kilodaltons (kDa = 1,000 Da) because that is how protein ladders are marked. The predicted weight tells you roughly where a band should run — but migration is not perfectly linear in mass, and the real product can differ from the sequence prediction.

What this does not include

This is the average mass of the bare polypeptide. It assumes no modifications: disulfide bonds, glycosylation, phosphorylation, cleaved signal peptides and bound cofactors all shift the observed mass. It is also the average, not the monoisotopic, mass that mass spectrometry reports — the monoisotopic value is slightly lower.