THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED-DNA APTAMER

The structure of a complex between human alpha-thrombin and a GGTTGGTG TGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crys tallography and refined at 2.9-angstrom resolution to an R value of 0. 159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two di fferent positively charged regions of two symmetry-related thrombin mo lecules in the crystal structure making ionic and hydrophobic interact ions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinoge n clotting and platelet activation by the DNA 15-mer with the Arg75 -- > Glu mutant of thrombin is consistent with the several salt bridges o f the DNA in the fibrinogen exosite. The association of DNA with the h eparin site of a neighboring molecule appears to simply compensate res idual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformation al changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the lat ter in the thrombin complex.