Protein Molecular Weight Calculator

What Is Protein Molecular Weight? The molecular weight (MW) of a protein is the sum of the masses of all its amino acids, minus water molecules lost during peptide bond formation. MW is measured in Daltons (Da) or kilodaltons (kDa). 1 kDa = 1,000 Da. A Dalton equals 1/12 the mass of one carbon-12 atom — approximately 1.66 × 10⁻²⁴ grams. Proteins range from ~50 Da (short peptides) to over 3,000 kDa (titin, the largest known protein at 3,816 kDa).

The 20 Standard Amino Acids and Their Masses Each amino acid residue has a specific average mass (in Daltons): Glycine (G): 57.05 — the smallest amino acid, no side chain. Alanine (A): 71.08 — small, non-polar. Valine (V): 99.13, Leucine (L): 113.16, Isoleucine (I): 113.16 — branched chain amino acids. Serine (S): 87.08, Threonine (T): 101.10 — polar hydroxyl-containing. Cysteine (C): 103.14 — forms disulfide bonds. Methionine (M): 131.20 — always the first amino acid in eukaryotic protein translation. Aspartate (D): 115.09, Glutamate (E): 129.12 — negatively charged at physiological pH. Asparagine (N): 114.10, Glutamine (Q): 128.13 — amide-containing, polar. Lysine (K): 128.17, Arginine (R): 156.19 — positively charged at physiological pH. Histidine (H): 137.14 — unique: can be positive or neutral depending on local pH. Phenylalanine (F): 147.18, Tyrosine (Y): 163.18, Tryptophan (W): 186.21 — aromatic. Proline (P): 97.12 — cyclic structure, introduces kinks in protein chains.

Calculating Molecular Weight from Sequence Add the residue masses of all amino acids. Subtract 18.02 Da for each peptide bond formed (n−1 bonds for n amino acids). Or equivalently: add all residue masses + 18.02 Da (one water molecule) for the complete protein.

Why Molecular Weight Matters SDS-PAGE: proteins migrate based on their size. MW ladders (protein markers) use proteins of known size to estimate unknown protein MW. Typical range: 10–250 kDa. Ultrafiltration: molecular weight cutoff (MWCO) filters select proteins by size. Mass spectrometry: directly measures protein MW with high precision. Modern instruments can measure to within 1 Da for proteins up to 100 kDa. Drug development: antibodies are ~150 kDa. Small molecule drugs are typically under 0.5 kDa.

Post-Translational Modifications The calculated MW from sequence alone does not include post-translational modifications (PTMs). Glycosylation can add 2–100 kDa depending on the extent and type. Phosphorylation adds 80 Da per phosphate group. Disulfide bonds do not change MW (they are intramolecular oxidation, releasing 2H but no mass change in standard conditions). His-tags commonly used in recombinant proteins add approximately 2.0–2.5 kDa for a 6×His tag.