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Integrin beta chain-2 (CD18) aptamer
Description
Famulok, M. et al. reported aptamers with affinity for CD18 in their article published in 1998. The TR-D28 aptamer was named by Famulok, M. et al. in the article[1].
SELEX
In their work published in 1999, Famulok, M. et al. used SELEX to isolate RNA aptamer sequences with affinity for CD18 from a nucleic acid library containing about 5×1014 sequences after 11 rounds of selection process. Proteins was pre-linked with agarose beads before co-incubation with nucleic acid libraries[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. This aptamer contains only one stem loop with multiple bulge. The 5' and 3' ends of aptamer each has an overhang[1].
5'-GGGCGCUAAGUCCUCGCUCAUACAACGAGGGGUCGUGUAGGGAUGUAUGGGCUUGGACACACGCGCGACUCGGAUCCUAC-3'
Ligand information
SELEX ligand
In molecular biology, CD18 (Integrin beta chain-2) is an integrin beta chain protein that is encoded by the ITGB2 gene in humans. Upon binding with one of a number of alpha chains, CD18 is capable of forming multiple heterodimers, which play significant roles in cellular adhesion and cell surface signaling, as well as important roles in immune responses. CD18 also exists in soluble, ligand binding forms. Deficiencies in CD18 expression can lead to adhesion defects in circulating white blood cells in humans, reducing the immune system's ability to fight off foreign invaders.-----From Wikipedia
UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.
Pfam: a widely recognised database of protein families and domains.
GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.
Mass: an intrinsic property of a body.
| Name | Uniprot ID | Pfam | Mass | Protein sequence | PDB ID | GenBank |
|---|---|---|---|---|---|---|
| CD18 | CD18 | PF00362 | 84.791 kDa |
......
MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPCGKYISCAECLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGMDRYLIYVDESRECVAGPNIAAIVGGTVAGIVLIGILLLVIWKALIHLSDLREYRRFEKEKLKSQWNNDNPLFKSATTTVMNPKFAES
|
1YUK 2P26 3K6S |
3689 |
Some isolated sequences bind to the affinity of the protein[1].
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| TR-D28 aptamer | 5'-GGGCGCUAAGUCCUCGCUCAUACAACGAGGGGUCGUGUAGGGAUGUAUGGGCUUGGACACACGCGCGACUCGGAUCCUAC-3' | CD18 | NA |
Similar compound(s)
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.
Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).
Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.
PDB: PDB ID+ chain name.
| PDB | Z-socre | RMSD (Å) | Description |
|---|---|---|---|
| 2P26-A | 37.8 | 0 | Original chain |
| 5E6W-A | 24.0 | 6.1 | Integrin beta-2 |
| 1JV2-B | 15.0 | 2.3 | Integrin, alpha V |
| 8T2V-B | 14.2 | 4.7 | Integrin alpha-IIB |
| 8JMW-A | 9.5 | 11.3 | S8 family serine peptidase |
| 6FVI-A | 9.0 | 2.1 | Centrosomal protein of 192 kDa |
| 8K2G-A | 8.4 | 3.1 | Oligosaccharide-releasing beta-N-acetylgalactosam |
| 7PTB-A | 8.3 | 8.5 | Centrosomal protein of 192 kDa |
| 2E6J-A | 8.3 | 2.1 | Hydin protein |
| 6LP4-A | 8.3 | 2.5 | Vesicle-associated membrane protein-associated PR |
| 4UJ6-A | 8.1 | 12.4 | Surface layer protein |
References
[1] Cytoplasmic RNA modulators of an inside-out signal-transduction cascade.Blind, M., Kolanus, W., & Famulok, M.
Proceedings of the National Academy of Sciences of the United States of America, 96(7), 3606–3610. (1999)