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The wealth of structural information now available for thrombin, its precursors,
its substrates, and its inhibitors allows a rationalization of its many roles.
alpha-thrombin is a rather rigid molecule, binding to its target molecules with
little conformational change. Comparison of alpha-thrombin with related
trypsin-like serine proteinases reveals an unusually deep and narrow active site
cleft, formed by loop insertions characteristic of thrombin. This canyon
structure is one of the prime causes for the narrow specificity of thrombin. The
observed modularity of thrombin allows a diversity in this specificity; its
"mix-and-match" nature is exemplified by its interactions with macromolecules
(Fig. 20). The apposition of the active site to a hydrophobic pocket (the apolar
binding site) on one side and a basic patch (the fibrinogen recognition exosite)
on the other allows for a fine tuning of enzymatic activity, as seen for
fibrinogen. Thrombin receptor appears to use the same sites, but in a different
way. Protein C seems only able to interact with thrombin if the recognition
exosite is occupied by thrombomodulin. These two sites are also optimally used
by hirudin, allowing the very tight binding observed; thrombin inhibition is
effected by blocking access to the active site. On the other hand, antithrombin
III makes little use of the recognition exosite; instead, its interactions are
tightened with the help of heparin, which binds to a second basic site (the
heparin binding site). Thrombin's modularity is a result of the conjunction of
amino acid residues of like properties, such as charge or hydrophobicity. The
charge distribution plays a role, not only in the binding of oppositely charged
moieties of interacting molecules, but also in selection and preorientation of
them. Nonproteolytic cellular properties are attributed to 1) the rigid
insertion loop at Tyr60A, and 2) a partially inaccessible RGD sequence. The
former can interact with cells in the native form; the latter would appear to be
presented only in an (at least partially) unfolded state. The membrane binding
properties of prothrombin can be understood from the ordered arrangement of
calcium ions on binding to the Gla domain. Kringle F2 binds to thrombin at the
heparin binding site through charge complementarity; a conformational change
appears to occur on binding. The observed rigidity of the thrombin molecule in
its complexes makes thrombin ideal for structure based drug design. Thrombin can
be inhibited either at the active site or at the fibrinogen recognition exosite,
or both.(ABSTRACT TRUNCATED AT 400 WORDS)
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