Primary Citation PubMed: 22669903
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High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
(2012) Nucleic Acids Res 40
PubMed: 22669903 | PubMedCentral: PMC3439905 | DOI: 10.1093/nar/gks512
ACCESSION NUMBERS PDB CODES: 4DIH and 4DII.
The coordinates of the structures have been deposited in the Protein Data Bank (Codes 4DIH and 4DII, for thrombin–TBA–Na and thrombin–TBA–K, respectively).
Interactions between thrombin and aptamers Thrombin–TBA–K (4DII) Thrombin–TBA–Na (4DIH) Thrombin–TBA (1HAO) Thrombin–mTBA (3QLP) Aptamer residue Protein residue Aptamer residue Protein residue Aptamer residue Protein residue Aptamer residue Protein residue Polar Thy3 (O4) His71 (ND1) Thy3 (N3) Glu77 (OE2) – – Thy12 (N3) Glu77 (OE2) Polar Thy4 (O4) Arg75 (NH2) Thy4 (O4) Arg75 (NH1, NH2) – – Thy13 (O4) Arg75 (NH1, NH2) Polar Thy4 (O2) Arg77A (NH1) Thy4 (O2) Arg77A (NH1) – – Thy13 (O3′) Asn78 (ND2) Polar Thy4 (N1) Arg77A (O) Thy4 (N1, N3) Arg77A (O) – – – – Polar Gua5 (O4′) Arg77A (NH2) Gua5 (O4′) Arg77A (NH2) – – Gua2 (O2P) Arg77A (NH1, NH2) Polar Thy13 (O2) Arg75 (NE, NH2) Thy13 (O2) Arg75 (NH2) – – Thy4 (O2) Arg75 (NH2) Polar Thy13 (O4′) Tyr76 (N) Thy13 (O4′) Tyr76 (N) – – Thy4 (O4′) Tyr76 (N) Polar Thy13 (N3) Tyr76 (O) Thy13 (N3) Tyr76 (O) – – Thy4 (O4) Arg77A (NH1) Hydrophobic Thy3 His71, Ile79, Tyr117 Thy3 Ile24, Ile79, Tyr117 Thy12 Ile24, His71, Ile79, Tyr117 Thy12 Ile79 Hydrophobic Thy4 Asn78, Ile79 Thy4 Ile79 – – Thy13 Asn78, Ile79 Hydrophobic Thy12 – Thy12 Tyr76 Thy3 Tyr76, Ile82 Thy3 Tyr76, Leu65, Ile82 Hydrophobic Thy13 Tyr76 Thy13 Tyr76 – – Thy4 Tyr76 Focusing the attention on the thrombin/TBA interactions in the Na + and K + complexes, it emerges that the Na + complex is characterized by a slightly larger buried surface area (502 versus 445 Å 2 ), higher surface complementarity index Sc (0.76 vs. 0.72), higher number of interface residues and intermolecular interactions ( Table 1 ), which are the result of correlated small re-arrangements at the exosite I of thrombin and at the TT loops of TBA.
Publication Year: 2012
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