Much of the machinery of the cell -- enzymes, transport factors, signaling complex, transcriptional and translational devices -- involve proteins’ interaction with other proteins, with other bio-macromolecules and with low molecular weight ligands. The large scale systems analysis of these interactions is highly complex. Using and developing the tools of structural biology, molecular dynamics simulation, molecular biology and protein engineering, we are attempting to provide such analysis in leading edge systems of practical biological interest.
In many proteins the role of ‘unstructured' regions can be assessed using improved NMR and scattering measurements probing how multiple weak interactions can give rise to specificity and selectivity of biological activity. These interactions can also be probed in cell using direct observation of multiple expressed protein systems by NMR, for a direct study of protein-protein interactions. A new area of application is using these methods to understand the dynamic structures of the FG-rich Nuclear Pore proteins, and their interactions with carriers and cargo. Novel functional roles of ‘unfoldable’ protein regions are being discovered. The nuclear pore transport mechanism contains potential significant targets for next generation therapeutics in cancer and infectious disease, which are being targeted for validation.
The mechanism of the intein reaction, internal splicing of proteins, is of general interest for protein engineering and as a model for several posttranslational modification mechanisms involving thioesterification. NMR is being used as an essential tool for probing this unusual reaction involving breaking and making peptide bonds, with substantial flexibility of the coordinating entities. All these studies also involve developing new analytical applied mathematical methods.
Protein kinases are critical mediators in development, differentiation, and homeostasis. Genetic and phenotypic modifications of their activities and of related phosphatases are commonly associated with many diseases states including infections, cancers, autoimmunity and developmental disorders. Recent advances have introduced selective inhibitors to these enzymes, and the potential for understanding the chemical biology of their interactions and for therapeutics are significant. A substantial part of their regulation and substrate interactions involve major molecular movements (“dynamics”) which are probed using NMR and other methods adding to static structural information from NMR or crystallography.
Selected References
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