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Type IVB Pili aptamer
Description
In 2005, Qin Pan and colleagues have applied a systematic evolution of ligands by exponential enrichment approach to select oligonucleotides (aptamers) as ligands that specifically bind to type IVB pili. The selected aptamer could significantly inhibit the entry of the piliated strain (but not that of the nonpiliated strain) into human THP-1 cells[1].SELEX
In 2005, Qin Pan et al. isolated RNA aptamers binding to type IVB pili of S. enterica serovar Typhi by 8 cycles of iterative selection[1].
Detailed information are accessible on SELEX page.
Structure
The aptamers could significantly inhibit the entry of the piliated strain (but not that of the nonpiliated strain) into humanTHP-1 cells. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-UCACUGUUAUCCGAUAGCAGCGCGGGAUGA-3'
Ligand information
SELEX ligand
Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. Proteins in this entry appear to be secretins for pilus formation, although they are quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Some proteins may be examples of bundle-forming pilus B (bfpB).-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Type IVB Pili | Q9ZIU9 | IPR013359 | 15.83 kDa | MWGKKDAGTELTNYQTLATNTIGMMKGVDGYAFTSGAKMTDTLIQAGAAKGMTVSGDPASGSATLWNSWGGQIVVAPDTAGGTGFNNGFTITTNKVPQSACVSISTGMSRSGGTSGIKINGNNHTDAKVTAEIASSECTADNGRTGTNTLVFNYNG | 1Q5F | CP046429.1 |
The binding affinities between aptamers and pre-PilS (structural protein of type IVB pili) were determined by nitrocellulose filter-binding assays.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| S-PS8.4 | 5'-UCACUGUUAUCCGAUAGCAGCGCGGGAUGA-3' | Type IVB pili of S. enterica serovar Typhi | 8.56 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 |
|---|---|---|---|
| 1Q5F-A | 31.5 | 0.0 | Plis |
| 3VOR-A | 7.4 | 4.6 | Cfa/iii pllin |
| 8UHF-B | 6.3 | 4.1 | Toxin co-regulated pilin |
| 4H5B-A | 4.6 | 4.6 | Dr_1245 protein |
| 1RY9-A | 4.6 | 4.0 | Surface presentation of antigens protein spak |
| 1XKP-B | 4.3 | 4.0 | Putative membrane-bound yop targeting protein yop |
| 4QS4-A | 4.0 | 4.4 | Cofb |
| 2IA7-A | 3.8 | 3.7 | Tail lysozyme, putative |
| 2FM8-A | 3.8 | 4.1 | Surface presentation of antigens protein spak |
| 5HC9-A | 3.2 | 4.3 | Trna nucleotidyl transferase-related protein |
References
[1] Aptamers that preferentially bind type IVB pili and inhibit human monocytic-cell invasion by Salmonella enterica serovar typhi.Pan, Q., Zhang, X. L., Wu, H. Y., He, P. W., Wang, F., Zhang, M. S., Hu, J. M., Xia, B., & Wu, J.
Antimicrobial agents and chemotherapy, 49(10), 4052–4060. (2005)