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Bovine thrombin aptamer
Description
In 2003，Liu and Zhang used the SELEX methodology to select RNA aptamers against bovine thrombin. These aptamers, T705 and T710, specifically recognize bovine thrombin and inhibit bovine thrombin-catalyzed fibrin clot formation[1].SELEX
In 2003, Liu and colleagues used SELEX. Starting from a pool of DNA templates, after transcription, aptamers that bind specifically to bovine thrombin were selected after 7 rounds of selection and amplification[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'-GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA-3'
Ligand information
SELEX ligand
Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.-----from Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Bovine thrombin | P00735 | PIRSF001149 | 70.506 kDA | MARVRGPRLPGCLALAALFSLVHSQHVFLAHQQASSLLQRARRANKGFLEEVRKGNLERECLEEPCSREEAFEALESLSATDAFWAKYTACESARNPREKLNECLEGNCAEGVGMNYRGNVSVTRSGIECQLWRSRYPHKPEINSTTHPGADLRENFCRNPDGSITGPWCYTTSPTLRREECSVPVCGQDRVTVEVIPRSGGSTTSQSPLLETCVPDRGREYRGRLAVTTSGSRCLAWSSEQAKALSKDQDFNPAVPLAENFCRNPDGDEEGAWCYVADQPGDFEYCDLNYCEEPVDGDLGDRLGEDPDPDAAIEGRTSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGRIVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS | 1A0H | 280685 |
The aptamer bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| T705 aptamer | 5'-GCAAUGGUACGGUACUUCCUUUGGAAGAUAGCUGGAGAACUAACCAAAAGUGCACGCUACUUUGCUAA-3' | bovine thrombin | 164 nM |
| T710 aptamer | 5'-GCAAUGGUACGGUACUUCCAAGUGCGGGGGGGAGGUGGUGGUUCCAAAAGUGCACGCUACUUUGCUAA-3' | bovine thrombin | 240 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 |
|---|---|---|---|
| 5TO3-B | 42.9 | 0.8 | Prothrombin |
| 1Z8G-A | 34.2 | 1.4 | Serine Protease Hepsin |
| 7WQX-A | 32.1 | 1.6 | Enteropeptidase |
| 4KKD-B | 29.3 | 2.4 | Mannan-Binding Lectin Serine Protease 1 |
| 3H7T-A | 29.1 | 1.8 | Group 3 Allergen Smipp-S Yvt004A06 |
| 5I25-A | 27.7 | 2.1 | Coagulation Factor Xi |
| 4A5T-S | 27.0 | 2.4 | Plasminogen |
| 2XXL-B | 24.7 | 2.3 | Gram-Positive Specific Serine Protease, Isoform B |
| 2XWB-F | 24.3 | 2.4 | Complement C3B Beta Chain |
| 6BQM-A | 24.1 | 1.9 | Serine Protease Vesc |
References
[1] RNA aptamers specific for bovine thrombin.Liu X, Zhang D, Cao G, Yang G, Ding H, Liu G, Fan M, Shen B, Shao N.
J Mol Recognit. 16(1):23-7. (2003)