Protein Molecular Weight, Isoelectric Point (pI) & Composition Calculator
Welcome to the Bioinformatics Daily Protein Molecular Weight & Isoelectric Point Calculator. Designed for structural biologists, biochemists, and bioinformatics students, this client-side utility computes thermodynamic and physicochemical properties directly in your browser without transmitting sequence data over the network.
| 1-Letter | 3-Letter | Amino Acid | Class | Count | Molar % | Residue Mass (Da) |
|---|---|---|---|---|---|---|
| Paste amino acid sequence to generate breakdown. | ||||||
Theoretical & Biophysical Principles
1. Calculation of Polypeptide Molecular Weight
Proteins are linear polymers of amino acid residues joined by covalent peptide bonds (amide linkages). Formation of each peptide bond releases one molecule of water (H2O, 18.015 Da):
Molecular Weight (Da) = M(terminal H2O) + Sum of residue masseswhere M(terminal H2O) = 18.01524 Da accounts for the terminal free amino hydrogen (-H) at the N-terminus and the free carboxyl hydroxyl (-OH) at the C-terminus.
2. Isoelectric Point (pI) Determination
The isoelectric point is the specific pH at which a macromolecule carries no net electrical charge (Z = 0):
- Below the pI (pH < pI): The protein carries a net positive charge.
- Above the pI (pH > pI): The protein carries a net negative charge.
The net charge Z(pH) is formulated via the Henderson-Hasselbalch equation:
Z(pH) = Sum(Positively Charged Groups) - Sum(Negatively Charged Groups)where positively ionizable moieties include the N-terminal α-amino group and the basic side chains of Arg, Lys, and His; negatively ionizable groups comprise the C-terminal carboxyl and side chains of Asp, Glu, Cys, and Tyr. We employ an iterative binary search (bisection) to locate the precise root Z(pH) = 0.
3. Spectrophotometric Extinction Coefficient (ε280)
Ultraviolet light absorption of folded proteins at 280 nm is primarily dictated by aromatic residues (Tryptophan and Tyrosine) and cystine disulfide linkages:
ε280 (M⁻¹ cm⁻¹) = (N_Trp * 5500) + (N_Tyr * 1490) + (N_Cystine * 125)Using the Beer-Lambert Law (A = ε * c * l), the calculated coefficient allows determination of purified protein concentration via spectrophotometry (NanoDrop / UV-Vis).
Scholarly References
- Bjellqvist, B., Hughes, G. J., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J. C., Frutiger, S., & Hochstrasser, D. (1993). The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14(10), 1023–1031.
- Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., & Gray, T. (1995). How to measure and predict the molar absorption coefficient of a protein. Protein Science, 4(11), 2411–2423.
- Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In The Proteomics Protocols Handbook (pp. 571–607). Humana Press.