1. What is Peptide Net Charge?

The net charge of a peptide is the sum of all positive and negative charges on the molecule at a given pH. It's determined by the ionization states of amino acid side chains and terminal groups.

2. How Does the Calculator Work?

The calculator uses the Henderson-Hasselbalch equation to determine the charge state of each ionizable group:

Where:

• \( pH \) — The pH of interest
• \( pKa \) — Acid dissociation constant for each ionizable group

Explanation: The calculator sums charges from N-terminus, C-terminus, and all ionizable side chains (Asp, Glu, Arg, Lys, His, Cys, Tyr).

3. Importance of Net Charge Calculation

Details: Net charge affects peptide solubility, binding interactions, and electrophoretic mobility. It's crucial for purification (ion exchange chromatography) and predicting behavior in biological systems.

4. Using the Calculator

Tips: Enter peptide sequence (1-letter or 3-letter code) and desired pH. The calculator automatically recognizes standard amino acids and ignores non-amino acid characters.

5. Frequently Asked Questions (FAQ)

Q1: What pH range is valid?
A: The calculator works for pH 0-14, though most biological applications use pH 2-12.

Q2: Are modified amino acids supported?
A: This calculator handles standard amino acids only. For modifications (phosphorylation, acetylation), use specialized tools.

Q3: Why is my peptide's charge pH-dependent?
A: As pH changes, protonation states of ionizable groups change, affecting overall charge.

Q4: What's the isoelectric point (pI)?
A: pI is the pH where net charge is zero. This calculator helps estimate pI by testing different pH values.

Q5: How accurate are these calculations?
A: Calculations are theoretical. Actual charges may vary due to local environment, peptide structure, and neighboring group effects.