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Figure 1.
FIG. 1. The induced-fit heparin binding mechanism of
antithrombin. a, antithrombin (ribbon diagram) interacts with
heparin (ball-and-stick) in an apparent three step, four state
mechanism. The native state is in the low activity and low
affinity conformation with its reactive center loop (yellow and
green) partially inserted into the main  -sheet A (red). The
specific heparin pentasaccharide interacts with antithrombin
primarily via helices A (green) and D (cyan). Although kinetic
data fit a model with only one weak-binding intermediate, I[1],
a recent crystallographic structure suggests that there may be
an additional intermediate that has undergone all conformational
changes save expulsion of the reactive center loop and helix D
elongation, I[2]. Full activation occurs only after expulsion of
the hinge region of the reactive center loop, and the closing of
-sheet A to the five
stranded form (Activated). b-e, stereo representations of the
main chain and selected side chains of hinge region and
surrounding residues reveal important interactions in several
crystal forms of antithrombin. b-e correspond to native (  -glycoform, 1e05 [PDB]
), pentasaccharide-activated (1e03 [PDB]
), S380C-fluorescein-derivatized (1dzh [PDB]
), and the heparin-bound intermediate I2 (1nq9 [PDB]
), respectively. In native AT (b) the P13 Glu (381) bridges
strands 3, 4, and 5A to helix F residues (Arg-197 and Glu-195)
through a series of salt-bridges and hydrogen bonds. In the
activated conformation (c) strands 3 and 5A have annealed with
P13 Glu interacting with strands 2 and 3A and helix F. A
fluorescein moiety at the P14 position (d) blocked the native
P13 interactions leading to an activated conformation in
solution. One of the major conformational responses to heparin
binding in the intermediate I[2] (e) is the repositioning of
Tyr-220 so that it no longer interacts with P13 Glu. Residue
numbers are given for some of the residues for clarity.
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