The effects of exosite occupancy on the substrate specificity of thrombin

Thrombin (EC 3.4.4.13) has two exosites that mediate interactions between the enzyme and its substrates and cofactors. The binding of ligands to the exosites alters the functions of the protease, for example, when the cofactor thrombomodulin binds to both exosites I and II, it converts the enzyme fr...

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Bibliographic Details
Published in:Archives of biochemistry and biophysics 2009-09, Vol.489 (1), p.48-54
Main Authors: Ng, Natasha May-Yoke, Quinsey, Noelene Sheila, Matthews, Antony Yaron, Kaiserman, Dion, Wijeyewickrema, Lakshmi Carmel, Bird, Phillip Ian, Thompson, Philip Evan, Pike, Robert Neil
Format: Article
Language:English
Subjects:
Catalytic Domain - physiology
Exosite
Heparin
Heparin - chemistry
Heparin - metabolism
Hirudins - chemistry
Hirudins - genetics
Hirudins - metabolism
Hirugen
Humans
Ligands
Peptide Fragments - chemistry
Peptide Fragments - genetics
Peptide Fragments - metabolism
Peptide Library
Protein Binding - physiology
Substrate specificity
Substrate Specificity - physiology
Thrombin
Thrombin - chemistry
Thrombin - genetics
Thrombin - metabolism
Thrombomodulin
Thrombomodulin - chemistry
Thrombomodulin - genetics
Thrombomodulin - metabolism
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Summary:Thrombin (EC 3.4.4.13) has two exosites that mediate interactions between the enzyme and its substrates and cofactors. The binding of ligands to the exosites alters the functions of the protease, for example, when the cofactor thrombomodulin binds to both exosites I and II, it converts the enzyme from a procoagulant to an anticoagulant factor. It is unknown whether ligand binding to a thrombin exosite will alter the substrate specificity of the enzyme and thus contribute to the changed substrate repertoire of the enzyme upon engagement with cofactors. We first examined whether binding of ligands to exosites I and II altered the activity of the enzyme against fluorogenic peptide substrates. The efficiency of cleavage of substrates by thrombin did change when thrombomodulin or hirugen was present, indicating that exosite I occupancy changed the active site of the protease. The presence of heparin did not change the activity of the enzyme, indicating that exosite II occupancy had little effect on active site function. Investigation of the effects of exosite I occupancy by hirugen on thrombin specificity using phage display substrate libraries revealed that the ligand only changed the specificity of the enzyme to a small degree. Occupancy of both exosites by thrombomodulin induced greater changes to the specificity of the enzyme, with the prime side showing broader changes in amino acid frequencies. Thus, exosite I ligands do affect the activity and specificity of thrombin, but not greatly enough to explain the altered substrate profile of the enzyme when complexed with thrombomodulin.
ISSN:0003-9861
1096-0384
DOI:10.1016/j.abb.2009.07.012