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 the peptide's termini.

2. How Does the Calculator Work?

The calculator uses the Henderson-Hasselbalch equation:

Where:

• \( pH \) — The pH of the solution
• \( pK_a(i) \) — Acid dissociation constants for positive charges
• \( pK_a(j) \) — Acid dissociation constants for negative charges

Explanation: The equation calculates the fraction of each ionizable group that is protonated or deprotonated at the given pH.

3. Importance of Net Charge Calculation

Details: Peptide net charge affects solubility, binding interactions, electrophoretic mobility, and is crucial for understanding peptide behavior in different pH environments.

4. Using the Calculator

Tips: Enter the peptide sequence using one-letter amino acid codes and specify the pH (0-14). The calculator will determine the net charge at that pH.

5. Frequently Asked Questions (FAQ)

Q1: What pKa values are used in the calculation?
A: Standard pKa values for amino acid side chains and termini are used (Asp:3.9, Glu:4.3, His:6.0, Cys:8.3, Tyr:10.1, Lys:10.5, Arg:12.0, N-term:8.0, C-term:3.1).

Q2: How accurate is this calculation?
A: It provides a good estimate but actual pKa values can vary depending on the peptide sequence and environment.

Q3: What does a net charge of zero mean?
A: This is the isoelectric point (pI) where the peptide has equal positive and negative charges.

Q4: Can I use modified amino acids?
A: This calculator only handles standard amino acids. Modified residues require specialized calculations.

Q5: Why is net charge important in electrophoresis?
A: The net charge determines the direction and speed of peptide migration in an electric field.