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Prion protein 2 aptamer
Description
In 2006, R. Mercey and colleagues used in vitro selection to isolate RNA aptamers that bind to sheep recombinant prion protein. The minimal sequence that they found necessary for binding of RM312 to PrP presents a striking similarity with one previously described PrP aptamer of comparable affinity. In addition, we here identify the two lysine clusters contained in the N-terminal part of PrP as its main nucleic-acid binding sites[1].SELEX
In 2006, R. Mercey et al. isolated specific sequences which bind specifically to PrP23-234 (recPrP) by 4 cycles of iterative selection and amplification[1].
Detailed information are accessible on SELEX page.
Structure
The RNA aptamers bound in vitro to sheep recombinant prion protein. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-AAGACGUCGGGGAUUGGCAAACCCCGUUUCCUUGAGCGACCCCCUGU-3'
Ligand information
SELEX ligand
Prion protein (PrP-c) is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Prion protein | P04273 | IPR000817 | 16.25 kDa | GQGGGTHNQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYYDGRRS | 1B10 | XM_005068660.4 |
The binding affinities between aptamers and PrP weredetermined by nitrocellulose filter-binding assays.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| RM312 | 5'-AAGACGUCGGGGAUUGGCAAACCCCGUUUCCUUGAGCGACCCCCUGU-3' | The ovine PrP | 20 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 |
|---|---|---|---|
| 2KUN-A | 10.7 | 3.1 | Major prion ptotein |
| 1I17-A | 6.8 | 3.2 | Prion-like ptotein |
| 8HM3-B | 4.9 | 2.6 | Putative ubiquitin |
| 1CQX-A | 4.5 | 3.7 | Flavohemoprotein |
| 8H17-A | 4.4 | 4.7 | Tlr1989 protein |
| 8BF9-G | 4.4 | 2.9 | RNA(1766) |
| 6THH-C | 4.3 | 3.0 | Sirv2 acrid1 (gp02) anti-crispr protein |
| 5ZIQ-A | 4.3 | 2.7 | Globin protein |
| 6Z5S-W | 4.2 | 2.9 | Light harvesting complex 1 protein w |
| 4CEJ-B | 4.2 | 3.4 | Atp-dependent helicase/nuclease subunit a |
References
[1] Fast, reversible interaction of prion protein with RNA aptamers containing specific sequence patterns.Mercey, R., Lantier, I., Maurel, M. C., Grosclaude, J., Lantier, F., & Marc, D.
Archives of virology, 151(11), 2197–2214. (2006)