8BW5

X-ray structure of the complex between human alpha thrombin and the duplex/quadruplex aptamer M08s-1_41mer

Summary for 8BW5

• Entry DOI: 10.2210/pdb8bw5/pdb
• Descriptor: Thrombin light chain, Thrombin heavy chain, M08s-1_41mer, ... (7 entities in total)
• Functional Keywords: dna aptamer, g-quadruplex, duplex, duplex/quadruplex, thrombin binding aptamer, thrombin, coagulation factor, anticoagulant, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 48932.44

Authors

Troisi, R.,Napolitano, V.,Sica, F. (deposition date: 2022-12-06, release date: 2023-07-19, Last modification date: 2024-10-16)

Primary citation

Troisi, R.,Napolitano, V.,Rossitto, E.,Osman, W.,Nagano, M.,Wakui, K.,Popowicz, G.M.,Yoshimoto, K.,Sica, F.
Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.
Nucleic Acids Res., 51:8880-8890, 2023

PubMed Abstract: Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.

PubMed: 37503836
DOI: 10.1093/nar/gkad634

Experimental method

X-RAY DIFFRACTION (2.8 Å)