title: [Investigation of interaction of thrombin-binding aptamer with thrombin and prethrombin-2 by simulation of molecular dynamics].
abstract: Thrombin is a major component of blood clotting and involved in the formation of a fibrin clot. One of the precursors during thrombin maturation is prethrombin-2, with the presence of Arg363-Ile364 bond between the light and heavy chain of protein, the only distinction from thrombin. Prethrombin-2 is able to interact with less efficiency with a 15-mer thrombin-binding aptamer (TBA). We investigate the interaction of both known conformers of TBA with thrombin and prethrombin-2 by simulation of molecular dynamics. It was shown that TBA could interact with thrombin in both conformations with similar efficiency, although a stable complex of prethrombin-2 with TBA was found only in conformation identical with the aptamer structure, pdb 1HAO. Analysis of molecular dynamics of complexes offered an assumption that the motion of the exosite-1 forming loop Lys428-Ile438 determined the difference in affinity of the complexes of TBA with thrombin and prethrombin-2.
authors.forename: D S
authors.initials: DS
authors.lastname: Shcherbinin
authors.forename: A V
authors.initials: AV
authors.lastname: Veselovsliĭ
mesh_terms: D052158:Aptamers, Peptide / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011516:Prothrombin / Q000737:chemistry* / Q000378:metabolism; D013917:Thrombin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D052158:Aptamers, Peptide; D011516:Prothrombin; C012007:prethrombins; D013917:Thrombin