pI Calculator

What is isoelectric point?

The isoelectric point (pI) is the pH at which a protein carries no net electrical charge. At this pH, the positive and negative charges on ionizable amino acid side chains and termini are perfectly balanced, resulting in a neutral molecule.

The pI is a fundamental physicochemical property that determines protein behavior in solution. Proteins have minimal solubility at their pI because they lack electrostatic repulsion between molecules, making them prone to aggregation. This property is exploited in isoelectric focusing, a separation technique that concentrates proteins at their pI values.

For practical applications, the pI guides buffer selection for protein purification, predicts migration in electrophoresis, and informs formulation strategies for biopharmaceuticals.

For a comprehensive analysis including pI alongside molecular weight and extinction coefficient, use our Protein Parameters calculator.

How does pI calculation work?

Henderson-Hasselbalch framework

The calculation uses the Henderson-Hasselbalch equation to determine the net charge of a protein at any given pH. For each ionizable group, the fractional charge depends on the pH and the group's dissociation constant (pKa).

Positively charged groups (N-terminus, Lys, Arg, His):

The charge contribution is calculated as Q = 1 / (1 + 10^(pH - pKa)), where the group becomes increasingly deprotonated (uncharged) as pH rises above its pKa.

Negatively charged groups (C-terminus, Asp, Glu, Cys, Tyr):

The charge contribution is calculated as Q = -1 / (1 + 10^(pKa - pH)), where the group becomes increasingly deprotonated (charged) as pH rises above its pKa.

The total net charge is the sum of contributions from all ionizable groups in the protein. The isoelectric point is the pH where this sum equals zero.

Ionizable residues

Seven amino acids contribute charged side chains that determine protein pI:

• Positive contributors: Lysine (K, $\varepsilon$-amino), Arginine (R, guanidinium), Histidine (H, imidazole)
• Negative contributors: Aspartate (D, $\beta$-carboxyl), Glutamate (E, $\delta$-carboxyl), Cysteine (C, thiol), Tyrosine (Y, phenol)

Additionally, the N-terminus (amino group) and C-terminus (carboxyl group) contribute positive and negative charges, respectively. For short peptides, these terminal charges can dominate the overall pI.

pKa values

We use the Bjellqvist pKa set, which provides experimentally derived values optimized for protein pI prediction:

Bisection method

The pI is found using a bisection algorithm that iteratively narrows the pH range. Starting with pH bounds of 0 and 14, the algorithm calculates the net charge at the midpoint. If the charge is positive, the pI must be higher (protein needs more deprotonation); if negative, the pI must be lower. The search space is halved with each iteration until converging to 0.01 pH unit precision, typically within 10-12 iterations.

Understanding the results

The output provides three values for each protein:

• Protein ID: Identifier extracted from the FASTA header
• Number of Amino Acids: Total sequence length
• Isoelectric Point: Theoretical pI value (pH units)

Most proteins have pI values between 4 and 12, with the majority falling between 5 and 8. The distribution reflects amino acid composition: acidic proteins (rich in Asp/Glu) have low pI values, while basic proteins (rich in Lys/Arg) have high pI values.

Practical applications

Understanding protein pI is essential for several experimental workflows.

Chromatography buffer design: Ion exchange chromatography separates proteins based on charge. To bind a protein to a cation exchanger, use a pH above its pI (protein negatively charged); for anion exchange, use pH below the pI. The difference between buffer pH and pI determines binding strength.

Isoelectric focusing (IEF): This technique creates a pH gradient and drives proteins to their pI positions using an electric field. High-resolution IEF can resolve proteins differing by as little as 0.01 pH units, making accurate pI prediction valuable for method development.

Solubility and formulation: Proteins are least soluble at their pI and may precipitate. For storage buffers and formulations, select a pH at least 1-2 units away from the pI to maintain solubility. This is particularly important for antibody therapeutics and recombinant proteins.

Electrophoresis interpretation: In native PAGE, proteins migrate based on their charge-to-mass ratio. Knowing the pI helps predict migration direction and explains why some proteins fail to enter gels at certain pH values.

Limitations

The calculated pI is theoretical and assumes ideal conditions. Several factors can cause discrepancies with experimental values:

Post-translational modifications (PTMs): Phosphorylation adds negative charges, glycosylation masks charged residues, and acetylation neutralizes positive charges. Eukaryotic proteins often have extensive modifications that shift the observed pI from theoretical predictions.

Disulfide bonds: Cysteine residues involved in disulfide bonds do not contribute charged thiol groups. The calculation assumes all cysteines are reduced and charged, which overestimates the contribution of cysteine residues in proteins with disulfide bonds.

Environmental context: The pKa values used are derived from model compounds in aqueous solution. In folded proteins, local microenvironments can shift pKa values by 2-3 units. Buried charged residues, salt bridges, and nearby charged groups all affect ionization behavior.

Protein disorder: Intrinsically disordered regions have different ionization properties than folded domains. Predictions for disordered proteins or unfolded states may be less accurate than for globular proteins.

Despite these limitations, theoretical pI calculations provide a reliable starting point for experimental design and typically agree with measured values within 0.5-1.0 pH units for most globular proteins.

Related tools

For comprehensive protein analysis, explore these related calculators:

• Protein Parameters - Calculate pI alongside molecular weight, extinction coefficient, and other physicochemical properties in a single analysis
• Molecular Weight - Determine exact and average molecular weight from sequence
• Extinction Coefficient - Calculate molar absorptivity at 280 nm for concentration determination
• Amino Acid Composition - Analyze the frequency and distribution of amino acids that determine pI
• GRAVY - Assess overall hydrophobicity, which often correlates with charge distribution
• Instability Index - Predict protein stability in solution, complementing solubility predictions from pI