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R5 helix peptide-aptamer
Description
In 2000, Fukusho, S. et al. performed an in vitro selection of RNA aptamer on a 27 MHz quartz-crystal microbalance (QCM) for a simple R5 helix peptide as a model of N peptide from bacteriophade lambda. In 2014，In vitro selection of RNA (30 random-nucleotide region) was carried out with N-model-peptide immobilized on a 27 MHz quartz-crystal microbalance (QCM), and the RNA recognition specificity of the peptide was studied[1,3].SELEX
The R5-peptide was immobilized on Au electrode of a 27 MHz QCM plate through Au-S interaction having a long polyethylenoxide spacer. The R5-peptide-immobilized QCM was soaked into the buffer solution and the frequency decrease (mass increase) responding to the addition of random ssRNA was monitored in the aqueous solution. After monitoring selection process as frequency decrease (mass increase), the QCM was washed and the selected RNA was recovered. The ssRNA was reversed transcribed to DNA and amplified with PCR reaction. Then, the dsDNA was transcribed and used as the ssRNA for next selection. Selection processes were repeated 1-7 cycles. Random region sequences for selected clones after the seventh selection cycle with N-model-peptide[1,3].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figures is based on the article by ribodraw tool to draw[3].B-2 RNA aptamer: 5'-GGGAAACUGGAUGGAAUGGGCUCGAUGAAAAUCGACCGUGCGCUGAAAAGCACGCGAGGUCCUGCUGUAAGUGUGCCA-3'
B-6 RNA aptamer: 5'-GGGAAACUGGAUGGAAUGGGCUCGCAAGGCCCCCUGAGCUGCACAAGUUCAUGGCGAGGUCCUGCUGUAAGUGUGCCA-3'
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Ligand information
SELEX ligand
A simple R5 helix peptide as a model of N peptide from bacteriophade λ. Enterobacteria phage λ (lambda phage, coliphage λ, officially Escherichia virus Lambda) is a bacterial virus, or bacteriophage, that infects the bacterial species Escherichia coli (E. coli). It was discovered by Esther Lederberg in 1950. The virus particle consists of a head and a tail that can have tail fibers. The whole particle consists of 12–14 different proteins with more than 1000 protein molecules total and one DNA molecule located in the phage head. All characterized lambdoid phages possess an N protein-mediated transcription antitermination mechanism, with the exception of phage HK022.-----From WiKi
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Bacteriophage λ N-Peptide | P03045 | IPR020952 | 12.3 KDa | MDAQTRRRERRAEKQAQWKAANPLLVGVSAKPVNRPILSLNRKPKSRVESALNPIDLTVLAEYHKQIESNLQRIERKNQRTWYSKPGERGITCSGRQKIKGKSIPLI | 5LM7 | 2703540 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| B-2 RNA aptamer | 5'-GGGAAACUGGAUGGAAUGGGCUCGAUGAAAAUCGACCGUGCGCUGAAAAGCACGCGAGGUCCUGCUGUAAGUGUGCCA-3' | N-model-peptide | 24 ± 2 nM |
| B-6 RNA aptamer | 5'-GGGAAACUGGAUGGAAUGGGCUCGCAAGGCCCCCUGAGCUGCACAAGUUCAUGGCGAGGUCCUGCUGUAAGUGUGCCA-3' | N-model-peptide | 11 ± 0.1 nM |
| B-7 RNA aptamer | 5'-GGGAAACUGGAUGGAAUGGGCUCGCCAAAGUUGAAAAGCAGGAUACACGGCACUGCGAGGUCCUGCUGUAAGUGUGCCA-3' | N-model-peptide | 5.3 ± 0.5 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 |
|---|---|---|---|
| 5LM7-N | 7.2 | 0.0 | Transcription termination/antitermination protein |
| 6GOV-N | 4.4 | 2.5 | Transcription termination/antitermination protein |
| 5LM7-F | 4.3 | 2.6 | Transcription termination/antitermination protein |
| 6EXN-D | 2.1 | 7.2 | U2 snRNA |
| 6CP3-Z | 2.1 | 15.1 | ATP synthase subunit 9, mitochondrial |
| 4AUR-A | 2.0 | 39.6 | Leoa |
References
[1] In vitro selection and analysis of RNA aptamer recognize arginine-rich motif (ARM) model peptide on a QCM.Fukusho, S., Furusawa, H., & Okahata, Y.
Nucleic acids symposium series, (44), 187–188. (2000)
[2] In vitro selection and evaluation of RNA aptamers that recognize arginine-rich-motif model peptide on a quartz-crystal microbalance.
Fukusho, S., Furusawa, H., & Okahata, Y.
Chemical communications (Cambridge, England), (1), 88–89. (2002)
[3] Arginine arrangement of bacteriophage λ N-peptide plays a role as a core motif in GNRA tetraloop RNA binding.
Furusawa, H., Fukusho, S., & Okahata, Y.
Chembiochem : a European journal of chemical biology, 15(6), 865–871. (2014)