Ribosomal protein S8-aptamer

Apr 10, 2024 • Qiaozhen Liu, Zhaoji Qiu

Timeline

Description

In 1997, Moine Herve et al. conducted in vitro iterative selection of RNA aptamers capable of binding to S8. These aptamers revealed features in the S8 binding site that had been concealed during previous characterizations by the high base conservation throughout evolution. In 2014, Milya Davlieva et al. investigated the structural adaptation of an RNA aptamer binding to bacterial ribosomal protein S8^[1,2].

SELEX

In 2014, Milya Davlieva et al. identified RNA sequences that lacked the conserved features of helix 21 but could bind the S8 protein with high affinity and specificity. The starting library had molecules with 16 randomized nucleotides in an RNA hairpin stem. After 10 rounds of selection, the RNA pool was cloned and 40 inserts sequenced. Alignment showed native-like and non-natural binding sites^[2].

Detailed information are accessible on SELEX page.

Structure

2D representation

The structure of aptamer RNA-2 is clearly defined, having a global fold of a hairpin that is terminated on one end by the UUCG tetraloop. The RNA-2 aptamer was named by Milya Davlieva et al. in the article. The RNA-2 aptamer was the main aptamer sequence studied in the Structure article. Here, we utilized Ribodraw to complete the figure based on the 3D structure information<^[2,5].

5'-GGGAUGCUCAGUGAUCCUUCGGGAUAUCAGGGCAUCCC-3'

3D visualisation

Milya Davlieva et al. sovled the crystal structure, at 2.69 Å resolution, of an RNA aptamer bound to Bacillus ribosomal S8 protein has been determined. In the free state, the internal loop of the ribosomal protein S8 aptamer hairpin stem encompasses G-A, U-U and A-A mismatches, adopting an overall helical A-form geometry. For the purpose of binding Ribosomal protein S8, the internal loop undergoes a significant rearrangement of its secondary structure, giving rise to the formation of a base triple and a base quartet. The PDB ID of this structure is 4PDB^[2].

Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 4PDB at 2.69 Å resolution. ribosomal S8 protein (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with ribosomal S8 protein.

Ligand information

SELEX ligand

Milya Davlieva et al. investigated the affinity of the RNA aptamer via EMSA (electrophoretic mobility shift assay) and ITC (isothermal titration calorimetry) experiments^[2].

Structure ligand

40S ribosomal protein S8 is a protein that in humans is encoded by the RPS8 gene. Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S8E family of ribosomal proteins.-----From Wiki

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.

Uniprot ID	Pfam	Mass	Protein sequence	PDB ID	GenBank
Q81VR6	IPR035987	29.24 kDa	GGPYLQ ...... VMTDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLKYGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVIVMTDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLKYGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVI	1SEI	947802

Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and selected the previous information with high 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-score	RMSD	Description
1SEI-A	28	0	Original chain
3RF2-A	18.5	1.9	30s ribosomal protein s8
8D8J-H	18.2	1.8	probable s-adenosyl-l-methioni
7QIX-T	17.2	2.2	18s rrna body
1I6U-A	17.1	2.2	16s rrna fragment
6ZUO-W	16.6	2.4	pre-18s ribosomal rna
7PWF-W	16.4	2.3	ribosomal protein s29a
6WDR-W	15.8	2.4	40s ribosomal protein a0-a
7PKU-h	13	2.9	ms35
4OCH-A	6.8	2.4	endonuclease muts2

References

[1] The RNA binding site of S8 ribosomal protein of Escherichia coli: Selex and hydroxyl radical probing studies.
Moine, H., Cachia, C., Westhof, E., Ehresmann, B., & Ehresmann, C.
RNA (New York, N.Y.), 3(3), 255–268. (1997)
[2] Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.
Davlieva, M., Donarski, J., Wang, J., Shamoo, Y., & Nikonowicz, E. P.
Nucleic acids research, 42(16), 10795–10808. (2014)
[3] The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition.
Autiero, I., Ruvo, M., Improta, R., & Vitagliano, L.
Biochimica et Biophysica Acta (BBA)-General Subjects, 1862(4), 1006-1016. (2018)
[4] Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking.
Oliveira, R., Pinho, E., Sousa, A. L., Dias, Ó., Azevedo, N. F., & Almeida, C.
PloS one, 17(3), e0264701. (2022)
[5] Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.
Pavan, M., Bassani, D., Sturlese, M., & Moro, S.
NAR genomics and bioinformatics, 4(4), lqac088. (2022)