Biochemistry and Molecular Biology

Macromolecular binding event is not simply a two-state exchange between free and bound states. In fact, previous kinetic investigations have suggested that the process of the specific complex formation goes through intermediate states called as target search or encounter complexes and the presence of such intermediates greatly accelerates the overall process. In terms of structure, how do individual components bind to each other at the intermediates states? How dynamic are they? These are fundamentally important questions for understanding macromolecular recognitions, while structural biology has not given adequate answers yet. It is because the very low population at equilibrium and dynamic nature of such states make the investigations extremely difficult. We have developed a number of powerful NMR methods that permit characterization of the intermediates in macromolecular binding at equilibrium. Applying the new techniques, we investigate structural and dynamic aspects of binding intermediates. Currently, the focus in our research is on the target search process whereby gene-regulatory proteins are able to efficiently and rapidly locate their specific DNA target sequence in a sea of non-specific DNA.