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Title
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The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.
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Authors
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K.Padmanabhan,
K.P.Padmanabhan,
J.D.Ferrara,
J.E.Sadler,
A.Tulinsky.
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Ref.
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J Biol Chem, 1993,
268,
17651-17654.
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PubMed id
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Abstract
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The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG
15-nucleotide consensus sequence has been solved by x-ray crystallography and
refined at 2.9-A 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 different positively charged regions of two
symmetry-related thrombin molecules in the crystal structure making ionic and
hydrophobic interactions. One region is the fibrinogen recognition exosite and
the other, the putative heparin binding site. The lack of inhibition of
fibrinogen clotting and platelet activation by the DNA 15-mer with the
Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of
the DNA in the fibrinogen exosite. The association of DNA with the heparin site
of a neighboring molecule appears to simply compensate residual charge.
Differences in the 15-mer loop conformations between the complex and NMR
solution structures can be attributed to conformational changes upon thrombin
binding. Although G-quadruplexes are favored in the presence of monovalent
cations, there is no evidence of the latter in the thrombin complex.
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