Calculator Inputs
Example Data Table
| Example Input | Value | Purpose |
|---|---|---|
| Sequence Name | Tutorial Peptide | Labels the report and exports. |
| Sequence | ACDEHKRYY | Provides amino acid composition automatically. |
| Analysis pH | 7.00 | Shows net charge at a chosen condition. |
| Preset | Lehninger | Loads a common pKa reference set. |
| Curve Range | 0.00 to 14.00 | Builds the titration-style charge curve. |
| Curve Step | 0.25 | Controls graph smoothness and export detail. |
Formula Used
The calculator estimates protein charge with Henderson-Hasselbalch style fractional ionization. It sums positively charged groups and subtracts negatively charged groups across a selected pH range.
Basic groups: fraction protonated = 1 / (1 + 10^(pH - pKa))
Acidic groups: fraction deprotonated = 1 / (1 + 10^(pKa - pH))
Net charge: N-term + K + R + H - C-term - D - E - C - Y
The predicted isoelectric point is the pH where the net charge approaches zero. This file uses a numerical bisection search between pH 0 and 14.
How to Use This Calculator
- Choose Sequence Mode to paste an amino acid sequence, or choose Manual Counts Mode to enter ionizable residue counts directly.
- Select a pKa preset, or keep the preset and edit any pKa fields you want to customize.
- Enter the analysis pH and define the graph range and step size for the charge profile.
- Click Calculate pI. The result section appears above the form with pI, charge, tables, and a Plotly chart.
- Use the CSV and PDF buttons to export the calculated report for lab notes, coursework, or internal review.
FAQs
1. What is the protein isoelectric point?
It is the pH where the protein's average net charge is approximately zero. At that condition, mobility in an electric field is minimized.
2. Can I use this for short peptides?
Yes. The same charge-balance approach works for peptides, provided the ionizable groups and terminal groups are represented correctly.
3. Why are there multiple pKa presets?
Different references report slightly different pKa values. Presets let you compare assumptions and choose the reference style that fits your workflow.
4. Why might the estimate differ from experiment?
Real proteins have structural microenvironments, salt effects, solvent effects, and post-translational changes. Those factors shift effective pKa values away from simple textbook constants.
5. Which residues affect the calculation most?
Aspartate, glutamate, cysteine, tyrosine, histidine, lysine, arginine, and both termini drive the charge calculation in this model.
6. What does net charge at analysis pH mean?
It reports the predicted overall charge at the exact pH you choose. Positive values suggest net cationic behavior, while negative values suggest net anionic behavior.
7. Is manual counts mode useful without a sequence?
Yes. Manual mode is useful when you already know residue counts from another tool, a composition sheet, or a simplified teaching example.
8. What do the CSV and PDF exports contain?
They include the summary values, ionizable group table, and charge profile data. That makes the output easy to save, review, and share.