The long term objective of this proposal is the development of an accurate method of structure prediction of biologically-important, homologous proteins to elucidate their function and to aid in design of therapeutic drugs and of profitable mutations. This goal is supported by the careful testing of predictions against crystal structures and spectral data.
The specific aims are to test the our prediction of the membrane- active, hemolytic toxin structures against the crystal structures we are determining. We will extend predictions and testing of the method to the larger, homologous systems of the kringles from plasminogen (particularly Kringle 4 for which we have collected diffraction data) and the phycobiliproteins from blue-green algae, proteins for which we currently have crystals. Health-relatedness of the method is the structure predictions of the kringles (important in regulating clot formation and lysis), of plasminogen (a primary physiological fibrinolytic agent involved in the maintenance of blood fluidity) from the kringle and serine protease structures (this proposal), and of the kringle in tissue plasminogen activator (currently in trials for prevention of second heart attacks). all predictions should aid in development of drugs to optimize plasminogen activation. The prediction method is based on computer graphics modeling combined with in vacuo global energy minimization with AMBER. Calculations will be extended to include solvent and molecular dynamics. Potential energy functions will be tested against the well-determined (0.83A) crambin structure. Unique to this proposal and critical to the method development is the test of a predicted structure against the crystal structure and data form solution methods (circular dichroism, nmr and Raman spectra) that are sensitive to 2 degree and 3 degree structure. Systems under study are models for protein-lipid interactions (hemolytic toxins), have well-characterized lysine-binding (kringles) and have been crystallized in our laboratory. We will solve the crystal structure of one of the small proteins (5000 MW) and progress to larger, more complex structures (10,000 and 17,5090 MW).
