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Chemokine CCL17-aptamer
Description
In 2018, Lorenz Fülle and colleagues used SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique to isolate high affinity RNA aptamers that bind to the CCL17 protein[1].SELEX
In 2018, Lorenz Fülle and Nancy Steiner et al. isolated 2 specific sequences for targeting Chemokine CCL17 in 10 rounds of selection[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGGUCGUCGCGGGUUGGCUCGUAGAUCGGGCCGGUACAGACGACCCAGACGACUCGCUGAGGAUCCGAGA-3'
Ligand information
SELEX ligand
CCL17 is a powerful chemokine produced in the thymus and by antigen-presenting cells like dendritic cells, macrophages, and monocytes.CCL17 plays a complex role in cancer. It attracts T-regulatory cells allowing for some cancers to evade an immune response.| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Chemokine CCL17 | Q9WUZ6 | PF00048 | 10.467 kDa | MRSLQMLLLAALLLGTFLQHARAARATNVGRECCLDYFKGAIPIRKLVSWYKTSVECSRDAIVFLTVQGKLICADPKDKHVKKAIRLVKNPRP | 1NR2 | 20295 |
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| MF11.46 | 5'-GGGUCGUCGCGGGUUGGCUCGUAGAUCGGGCCGGUACAGACGACCCAGACGACUCGCUGAGGAUCCGAGA-3' | Chemokine CCL17 | 0.9 ± 0.1 nM |
| MF11 | 5'-AAUAGAGUCGUCGCGGGUUGGCUCGUAGAUCGGGCCGGUACAGACGACUCGCUGAGGAUCCGAGA-3' | Chemokine CCL17 | NA |
| MF35 | 5'-GAGCAGCAUUUGUGGUUUCCCGAUCGCUUCCCCUAAACAGCAGACGACUCGCUGAGGAUCCGAGA-3' | Chemokine CCL17 | NA |
| MF35.47 | 5'-GAGCAGCAUUUGUGGUUUCCCGAUCGCUUCCC-3' | Chemokine CCL17 | 7.5 ± 1.5 nM |
Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-socre | RMSD | Description |
|---|---|---|---|
| 1NR4-E | 12.3 | 0.8 | Thymus and activation-regulated chemokine |
| 2VXW-A | 11.5 | 0.9 | C-C motif chemokine 5 |
| 7SO0-B | 11.3 | 1.1 | Evasin p974 |
| 5EKI-E | 10.1 | 1.5 | C-C motif chemokine 21 |
| 2JYO-A | 9.5 | 2.0 | C-C motif chemokine 20 (small-inducible cytokine |
| 1B2T-A | 9.0 | 1.6 | Protein (fractalkine) |
| 2MP1-A | 8.3 | 1.9 | C-C motif chemokine 19 |
| 4HED-A | 7.6 | 1.8 | Uncharacterized protein |
| 1F9P-A | 7.5 | 2.1 | Connective tissue activating peptide-iii |
| 1O80-A | 7.4 | 2.5 | Small inducible cytokine b10 |
References
[1] RNA aptamers recognizing murine CCL17 inhibit T cell chemotaxis and reduce contact hypersensitivity in vivo.Fülle, L., Steiner, N., Funke, M., Gondorf, F., Pfeiffer, F., Siegl, J., ... & Förster, I.
Molecular Therapy, 26(1), 95-104. (2018)