Truncation Panels: What They Are and How to Design Them
What Is a Truncation Panel?
A truncation panel is a set of peptides derived from a longer parent peptide or identified reactive region. Each peptide is systematically shortened from the N-terminus, C-terminus, or both.
Truncation panels are commonly used after an overlapping peptide library has identified a reactive region. The goal is to determine the minimal binding motif or smallest sequence required for activity.
Why Are Truncation Panels Important?
Once a reactive region has been located, the exact boundaries of the binding site are often unknown. Truncation panels help refine this region with higher precision.
- Define minimal epitope length
- Identify critical boundary residues
- Improve assay specificity
- Reduce peptide size for downstream studies
This refinement step improves experimental clarity and may reduce synthesis cost for future work by eliminating unnecessary residues.
How to Design a Truncation Panel
Truncation panels are typically designed from a previously identified active peptide (for example, a 15-mer from an overlapping library).
There are three common approaches:
- N-terminal truncation: progressively remove amino acids from the beginning
- C-terminal truncation: progressively remove amino acids from the end
- Bidirectional truncation: shorten from both ends to narrow the minimal core
Example: If a 15-mer peptide is reactive, you may generate:
- 14-mer (remove 1 residue)
- 13-mer
- 12-mer
- Continue until activity is lost
The shortest peptide that retains activity defines the minimal motif.
When Should You Use Truncation Panels?
- After identifying a reactive peptide from an overlapping library
- When optimizing peptides for assay development
- When preparing minimal epitope peptides for mechanistic studies
- When refining sequences for downstream synthesis or scale-up
Use Our Peptide Design Software
To generate truncation panels quickly and accurately, use our Peptide Screening Tools:
https://www.biosyn.com/peptidescreeningtools.aspx
The tool allows you to:
- Input a parent peptide sequence
- Automatically generate N- and C-terminal truncations
- Export a formatted peptide list
- Prepare the design for synthesis or screening
If you provide the exported file along with your experimental goal, we can review the panel and recommend an efficient synthesis format.