Dr. James K. Stoops

Structure-Function Studies of Macromolecules of Biological Interest

Research activities involve studies of the structural organization and function of macromolecules such as the fatty acid synthase, pyruvate dehydrogenase, urease, human a2-macroglobulin, and CaM-kinases. The multifaceted approaches described below and the diversity of topics under investigation offer the student an excellent back-ground in structural biology. Cryo- and stain electron microscopy are employed to record the images of the macromolecules. Electron micrographs are processed in our computer science laboratory to enhance structural features of the molecule and to reconstruct its three-dimensional structure. Functional studies utilize physico-chemical methods to investigate the mechanisms of some of these proteins. An adequately equipped biochemistry laboratory complements this research.

We have recently completed three-dimensional (3D) reconstructions of various forms of human a2-macroglobulin. a2-Macroglobulin is a glycoprotein (Mr=720 kD) that functions as one of the major proteinase inhibitors in the plasma of vertebrates. It is thought to serve as a general scavenger of proteinases, thereby protecting blood and tissue proteins from degradation. Inhibition of a proteinase by a2-macroglobulin is unique in that the molecule undergoes a large structural change on reaction with a proteinase resulting in its entrapment. Our 3D structures of native and the a2-macroglobulin proteinase complex delineated the position of the bound proteinase in the structure and showed the manner in which a2 - m a c r o -globulin sequesters the proteinase.

Selected References

Structural organization of CaM Kinase IIa determined by 3-D electron microscopy and protein engineering.

The unique structure consists of twelve subunits that form a gear-shaped core to which are tethered six foot-like functional domains at both ends of the core.

The x-ray ribbon structure of CaM Kinase I is docked in one of the functional domains and shows that the catalytic site is near the central portion of the foot.

Zhou, Z.H., McCarthy, D.B., O'Connor, C.M., Reed, L.J., and Stoops, J.K. "The Remarkable Structural and Functional Organization of the Eukaryotic Pyruvate Dehydrogenase Complexes." Proc. Nat'l. Acad.. Sci., U.S.A. 98: 14802-14807. 2001.

Zhou, Z. H., Liao, W., Cheng, R. H., Lawson, J.E., McCarthy, D. B., Reed, L. J., and Stoops, J. K. "Direct Evidence for the Size and Conformational Variability of the Pyruvate Dehydrogenase Complex Revealed by 3-D Electron Microscopy: the "Breathing" Core and Its Functional Relationship to Protein Dynamics." J. Biol. Chem. 276: 21704-21713, 2001.

Qazi, U., Kolodziej, S.J., Gettins, P.G.W., and Stoops, J.K. "The Structure of the C949S Mutant Human _2-Macroglobulin Demonstrates the Critical Role of the Internal Thiol Esters in its Proteinase-Entrapping Structural Transformation". J. Struct. Biol. 131:19-26, 2000.

Kolodziej S.J., Hudmon A., Waxham M.N. and Stoops J.K.: Three-dimensional reconstructions of Cam kinase II a and truncated Cam kinase II a reveal an unique organization for its structural core and functional domains. J. Biol. Chem. 275:14354-14359, 2000.