Research

Our research builds upon 30+ years of continuously funded work on ligand binding theory (1, 2), the kinetics of molecular recognition (3, 4), and structural enzymology (5-7), especially of proteins involved in blood coagulation (8-10). A notable development has been the rational engineering of a thrombin mutant with anticoagulant properties currently in Phase II testing (NCT03963895).

Ongoing research includes:

  1. Structure and dynamics of prothrombin (HL049413)
  2. Mechanism of protein C activation (HL139554)
  3. Molecular determinants of thrombin allostery (HL147821)

We are interested in two basic interactions of the blood coagulation cascade, i.e., the interaction of prothrombin with prothrombinase leading to generation of thrombin and blood clotting, and the interaction of the thrombin-thrombomodulin complex with protein C initiating the negative feed-back loop that shuts down the coagulation response. Both of these interactions have been studied for decades by several groups but remain in need of structural information.

Our experimental approach merges classical enzymology, protein engineering, and X-ray structural biology with innovative techniques like smFRET, 19F NMR, and cryo-EM. Our goal is to solve the molecular architecture of prothrombin and protein C, free and bound to their biological activators, and to gain information on underlying dynamics, mechanism of activation and epitopes involved in the interactions.

Bibliography

  1. Di Cera E. Thermodynamic Theory of Site-Specific Binding Processes in Biological Macromolecules. (1995) Cambridge University Press, Cambridge, UK.
  2. Di Cera E. Site-specific analysis of mutational effects in proteins. Adv Protein Chem (1998) 51, 59-119.
  3. Vogt AD, Di Cera E. Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism. Biochemistry (2012) 51, 5894-5902.
  4. Vogt AD, Di Cera E. Conformational Selection Is a Dominant Mechanism of Ligand Binding. Biochemistry (2013) 52, 5723-5729.
  5. Page MJ, Di Cera E. Role of Na+ and K+ in enzyme function. Physiol Rev (2006) 86, 1049-1092.
  6. Page MJ, Di Cera E. Serine peptidases: classification, structure and function. Cell Mol Life Sci (2008) 65, 1220-1236.
  7. Pozzi N, Vogt AD, Gohara DW, Di Cera E. Conformational selection in trypsin-like proteases. Curr Opin Struct Biol (2012) 22, 421-431.
  8. Chen Z, Pelc LA, Di Cera E. Crystal structure of prethrombin-1. Proc Natl Acad Sci U S A (2010) 107, 19278-19283.
  9. Di Cera E, Guinto ER, Vindigni A, Dang QD, Ayala YM, Wuyi M, Tulinsky A. The Na+ binding site of thrombin. J Biol Chem (1995) 270, 22089-22092.
  10. Pozzi N, Chen Z, Pelc LA, Shropshire DB, Di Cera E. The linker connecting the two kringles plays a key role in prothrombin activation. Proc Natl Acad Sci U S A (2014) 111, 7630-7635.

Complete Bibliography via PubMed: Di Cera E