Keywords: Aptamer, Thrombin, Ambiguity, Article, Binding Affinity, Cell Polarity, Controlled Study, Crystal Structure, Crystallography, Molecular Recognition, Priority Journal, Protein Binding, Protein Dna Interaction, Protein Function, Protein Stability, Protein Structure, Structure Analysis, Nucleotide, X-Ray, Dna-Binding Proteins, Humans, Models,
Affiliations: *** IBB - CNR ***
Dip. di Chimica 'Paolo Corradini', Università di Napoli Federico II, Via Cintia, I-80126 Napoli, Italy
Ist. di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
Dip. di Chimica Delle Sostanze Naturali, Università di Napoli Federico II, Via D. Montesano 49, I-8013 Napoli, Italy
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Thrombin-aptamer recognition: a revealed ambiguity
Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, the key enzyme of coagulation cascade. TBA folds as a G-quadruplex structure, as proved by its NMR structure. The X-ray structure of the complex between TBA and human alpha-thrombin was solved at 2.9-A resolution, but did not provide details of the aptamer conformation and the interactions with the protein molecule. TBA is rapidly processed by nucleases. To improve the properties of TBA, a number of modified analogs have been produced. In particular, a modified TBA containing a 5'-5' polarity inversion site, mTBA, has higher stability and higher affinity toward thrombin with respect to TBA, although it has a lower inhibitory activity. We present the crystal structure of the thrombin-mTBA complex at 2.15-A resolution; the resulting model eventually provides a clear picture of thrombin-aptamers interaction, and also highlights the structural bases of the different properties of TBA and mTBA. Our findings open the way for a rational design of modified aptamers with improved potency as anticoagulant drugs.
Thrombin-aptamer recognition: a revealed ambiguity
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