Hemagglutinin aptamer

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Description

In 2005, Kumar, P. K et al. used Surface Plasma Resonance (SPR) technology, also known as Biocore technology, to select and analyze RNA aptamers with high affinity for human influenza virus hemagglutinin (HA). The Kd value of wild-type aptamer clone A for HA is approximately 200 pM, while the newly discovered sequence clone B has a Kd value of 115 ± 23 pM for HA[1].



SELEX

In 2005, Kumar, P. K et al. began with an RNA library of around 1013 sequences. After five rounds of screening, they obtained multiple high-affinity RNA aptamer clone sequences. Around 50% of these showed strong binding to the target protein. Of these, approximately 35% were wild-type and 16% were newly identified sequences[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. Clone B aptamer binds to Hemagglutinin influenza virus (HA influenza virus)[1].

5'-GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU-3'

drawing

Ligand information

SELEX ligand

Some isolated sequences bind to the affinity of the protein[1].

Name Sequence Ligand Affinity
clone A 5'-GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU-3' HA 200 pM
clone B 5'-GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU-3' HA 115 ± 23 pM

Structure ligand

Haemagglutinin (HA) is one of two main surface fusion glycoproteins embedded in the envelope of influenza viruses, the other being neuraminidase (NA). There are sixteen known HA subtypes (H1-H16) and nine NA subtypes (N1-N9), which together are used to classify influenza viruses (e.g. H5N1). The antigenic variations in HA and NA enable the virus to evade host antibodies made to previous influenza strains, accounting for recurrent influenza epidemics. The HA glycoprotein is present in the viral membrane as a single polypeptide (HA0), which must be cleaved by the host's trypsin-like proteases to produce two peptides (HA1 and HA2) in order for the virus to be infectious. Once HA0 is cleaved, the newly exposed N-terminal of the HA2 peptide then acts to fuse the viral envelope to the cellular membrane of the host cell, which allows the viral negative-stranded RNA to infect the host cell. The type of host protease can influence the infectivity and pathogenicity of the virus.-----From Pfam

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
Hemagglutinin (HA) A0A097PF13 IPR000149 63.635 kDa
...... MKTIIALSYILCLVFAQKLPGNDNSTATLCLGHHAVSNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILDGENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLNYKYPALNVTMPNNEKFDKLYIWGVLHPSTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQINGKLNRLIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI
NA AY832929.1


References

[1] Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance.
Misono, T. S., & Kumar, P. K.
Analytical biochemistry, 342(2), 312–317. (2005)