Ac-RTSKKR-pNA is a chromogenic hexapeptide substrate for dengue virus NS2B-NS3 protease. The Ac-Arg-Thr-Ser-Lys-Lys-Arg sequence represents the P6–P1 portion associated with the NS2A/NS2B viral polyprotein cleavage site and carries a C-terminal p-nitroaniline reporter.
The substrate provides a defined system for investigating cleavage-site recognition, viral serine protease kinetics and peptide-based inhibitor development.
Product Information
| Property | Specification |
|---|---|
| Product Name | Ac-RTSKKR-pNA |
| Catalog No. | AS2524 |
| CAS No. | 410532-55-7 |
| Sequence | Ac-Arg-Thr-Ser-Lys-Lys-Arg-pNA |
| Sequence Shortening | Ac-RTSKKR-pNA |
| Peptide Length | 6 amino-acid residues |
| Molecular Formula | C39H68N16O11 |
| Molecular Weight | Approximately 937.08 Da |
| Reporter Group | p-Nitroaniline (pNA) |
| Research Enzyme | Dengue virus NS2B-NS3 protease |
| Cleavage-Site Context | NS2A/NS2B |
Dibasic Cleavage-Site Architecture
The C-terminal portion of the recognition sequence contains Lys-Arg at P2–P1, matching the strong preference of dengue NS2B-NS3 protease for basic residues immediately upstream of many viral polyprotein cleavage sites.
The RTSK segment extends the substrate to P6 and provides additional contacts that contribute to the recognition profile of this defined hexapeptide.
This makes Ac-RTSKKR-pNA useful for studying how natural cleavage-site sequence influences protease binding and catalysis.
Published Kinetic Context
In a study using recombinant dengue virus type 2 NS2B-NS3 protease, Ac-RTSKKR-pNA showed a reported Km of approximately 98 µM, kcat of approximately 0.019 s−1, and catalytic efficiency of approximately 191 M−1s−1 under the study conditions.
These values place its measured catalytic efficiency in the same general range as the 3/4A substrate in that experiment, while the 2B/3 substrate showed substantially weaker apparent substrate affinity.
We recommend using published kinetic values as a benchmark for assay design rather than as acceptance criteria for a different recombinant protease construct or buffer system.
Colorimetric Protease Measurement
Cleavage at the peptide–pNA bond releases free p-nitroaniline. The resulting colorimetric signal can be monitored near 405 nm, supporting endpoint or kinetic measurements with standard absorbance plate readers.
For inhibitor screening, the substrate concentration relative to Km should be considered because inappropriate substrate loading can affect apparent inhibitor potency.
Quality and Procurement Considerations
For quantitative viral protease assays, peptide purity should be evaluated together with molecular identity and reporter-group integrity. Differences in substrate composition or incomplete reporter conjugation can directly affect apparent turnover.
Our Peptide Quality Control capabilities support analytical HPLC and mass spectrometry with batch-specific documentation according to the selected specification.
Researchers selecting material for sensitive kinetic studies can also review our Recommended Peptide Purity guidance.
Frequently Asked Questions
What dengue cleavage site does Ac-RTSKKR-pNA model?
The RTSKKR sequence represents the P6–P1 region associated with the NS2A/NS2B polyprotein junction.
Why are Lys and Arg important in this substrate?
Dengue NS2B-NS3 protease commonly recognizes basic residues at positions immediately upstream of the cleavage site. This substrate contains Lys-Arg at P2–P1.
Can substrate analogs be designed for inhibitor studies?
Sequence substitutions, non-natural residues and alternative reporter formats can be evaluated through Chemical Peptide Synthesis.