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Screening the molecular surface of human anticoagulant protein C: A search for interaction sites

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Abstract

Protein C (PC), a 62 kDa multi-modular zymogen, is activated to an anticoagulant serine protease (activated PC or APC) by thrombin bound to thrombomodulin on the surface of endothelial cells. PC/APC interacts with many proteins and the characterisation of these interactions is not trivial. However, molecular modelling methods help to study these complex biological processes and provide basis for rational experimental design and interpretation of the results. PC/APC consists of a Gla domain followed by two EGF modules and a serine protease domain. In this report, we present two structural models for full-length APC and two equivalent models for full-length PC, based on the X-ray structures of Gla-domainless APC and of known serine protease zymogens. The overall elongated shape of the models is further cross-validated using size exclusion chromatography which allows evaluation of the Stokes radius (rs for PC = 33.15 Å rs for APC = 34.19 Å), frictional ratio and axial ratio. We then propose potential binding sites at the surface of PC/APC using surface hydrophobicity as a determinant of the preferred sites of intermolecular recognition. Most of the predicted binding sites are consistent with previously reported experimental data, while some clusters highlight new regions that should be involved in protein-protein interactions.

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Authors and Affiliations

  1. School of Pharmacy, INSERM U428, 4 Ave. de l'Observatoire, F-75006, Paris, France

    Bruno O. Villoutreix

  2. Frederick Cancer Research and Development Center, National Cancer Institute, Science Applications International Corporation, Frederick, MD, 21702, U.S.A

    David G. Covell & Anders Wallqvist

  3. The Wallenberg Laboratory, Dept. of Clinical Chemistry, University Hospital, Malmö, Lund University, S-205 02, Malmö, Sweden

    Anna M. Blom, Ute Friedrich & Björn Dahlbäck

Authors
  1. Bruno O. Villoutreix
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  2. David G. Covell
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  4. Anders Wallqvist
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  5. Ute Friedrich
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  6. Björn Dahlbäck
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Villoutreix, B.O., Covell, D.G., Blom, A.M. et al. Screening the molecular surface of human anticoagulant protein C: A search for interaction sites. J Comput Aided Mol Des 15, 13–27 (2001). https://doi.org/10.1023/A:1011158717139

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