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tFKBP*3R-2G aptamer
Description
In 2005, Plummer KA and Carothers JM reported the identification of small RNA modules selected in vitro to bind a surface-engineered protein, but only when the two macromolecules are bound to a synthetic bifunctional small molecule[1].SELEX
In 2005, Plummer KA and colleagues used existing research to design the method required for the In vitro RNA selection. Starting from DNA containing a 60 nt region of random sequence, aptamers that bind specifically to TFKBP*3R-2G were selected after 7 rounds of selection and amplification. These aptamer, s23 and T1, can bind specifically to TFKBP*3R-2G were selected with high affinity[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the left figure is based on the article, and the right figure is based on the prediction results of the RNA fold website. We chose the minimum free energy (MFE) structure and used ribodraw tool to draw the figures[1].T1 aptamer: 5'-CGAAUGCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGCUUCG-3'
s23 aptamer: 5'-UCAUUUCAUUGUGGCGGUGCAGUCAAAUGUGAUGCUUCGUUCAGUGACGGGAGGGUUGUGAG-3'
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Ligand information
SELEX ligand
The FKBPs, or FK506 binding proteins, constitute a family of proteins that have prolyl isomerase activity and are related to the cyclophilins in function, though not in amino acid sequence. FKBPs have been identified in many eukaryotes, ranging from yeast to humans, and function as protein folding chaperones for proteins containing proline residues. Along with cyclophilin, FKBPs belong to the immunophilin family.-----From Wiki
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| TFKBP*3R-2G | P20081 | PF00254 | 12.158 kDa | MSEVIEGNVKIDRISPGDGATFPKTGDLVTIHYTGTLENGQKFDSSVDRGSPFQCNIGVGQVIKGWDVGIPKLSVGEKARLTIPGPYAYGPRGFPGLIPPNSTLVFDVELLKVN | 1YAT | 855587 |
The aptamer bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| s23 aptamer | 5'-GGGUUCGAAUGCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGCUUCGUAGUGUAAACUGACGUGGCGGUGUUACUUUACUGUUACGCUAGGUUACGGG-3' | TFKBP*3R-2G | 4.3 ± 0.5 nM |
| T1 s23 aptamer | 5'-CGAAUGCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGCUUCG-3' | TFKBP*3R-2G | 2.8 ± 0.2 nM |
| T2 s23 aptamer | 5'-GCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGC-3' | TFKBP*3R-2G | 16.1 ± 3.6 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 |
|---|---|---|---|
| 5KLX-D | 20.8 | 1.1 | Chimera Protein Of Ubiquitin-Like Protein Smt3 |
| 5NJX-A | 20.4 | 1.1 | Peptidyl-Prolyl Cis-Trans Isomerase Fkbp5 |
| 3JYM-B | 19.1 | 1.5 | Fk506-Binding Protein (Fkbp) From Wheat |
| 5MGX-G | 18.8 | 1.3 | Yeast Hsp90 C-Terminus |
| 5I7P-A | 18.7 | 1.5 | Peptidyl-Prolyl Cis-Trans Isomerase Fkbp1A, Fkbp-T |
| 4MSP-A | 18.0 | 1.2 | Peptidyl-Prolyl Cis-Trans Isomerase Fkbp14 |
| 1Q6U-A | 17.8 | 1.2 | Fkbp-Type Peptidyl-Prolyl Cis-Trans Isomerase Fkp |
| 2MPH-A | 17.3 | 1.6 | Peptidyl-Prolyl Cis-Trans Isomerase Fkbp3 |
| 7EU3-4 | 14.5 | 1.6 | Nad(P)H-Quinone Oxidoreductase Subunit 1, Chlorop |
| 2MF9-A | 13.6 | 2.0 | Peptidyl-Prolyl Cis-Trans Isomerase Fkbp8 |
References
[1] In vitro selection of RNA aptamers against a composite small molecule-protein surface.Plummer KA, Carothers JM, Yoshimura M, Szostak JW, Verdine GL.
Nucleic Acids Res. 33(17):5602-10. (2005)