1. What is Peptide Net Charge?

The net charge of a peptide is the sum of all positive and negative charges on the peptide at a given pH. It depends on the ionization states of the N-terminus, C-terminus, and any ionizable side chains (Asp, Glu, His, Cys, Tyr, Lys, Arg).

2. How Does the Calculator Work?

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

Where:

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

Explanation: The equation calculates the fraction of each group that is protonated or deprotonated at the given pH, then sums all contributions.

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 (e.g., "YGGFL") and the desired pH (typically 1-14). The calculator will sum all charges at that pH.

5. Frequently Asked Questions (FAQ)

Q1: What pKa values are used in the calculation?
A: Standard pKa values are used for N-terminus (9.6), C-terminus (2.4), and side chains (Asp 3.9, Glu 4.3, His 6.0, Cys 8.3, Tyr 10.1, Lys 10.5, Arg 12.5).

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

Q3: What is the isoelectric point (pI)?
A: The pH at which the peptide has a net charge of zero. This calculator can help estimate pI by testing different pH values.

Q4: Do modifications affect the charge?
A: Yes, post-translational modifications like phosphorylation or acetylation can significantly alter the charge, but aren't accounted for in this basic calculator.

Q5: What's a typical net charge range?
A: Most peptides range from -10 to +10, depending on length and amino acid composition.