Residue-specific contributions to the energetics of the catalytic cycle of PGK

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Biological molecules interact through multiple weak bonds, which define the specificity and the affinity of the interaction. One would expect that the total strength of this interaction would equal the sum of all the contributing weak bonds in isolation. However this is not the case, and interactions are often much weaker or stronger than expected (known as cooperativity). This often corresponds with the function of the molecules. The majority of functional biological molecules are proteins, the large macromolecules that are encoded by DNA. Proteins that bind to rare nutrients (biotin or iron) or highly unstable structures (rate-defining intermediates of chemical reactions) bind more tightly than expected, whereas other proteins bind and release abundant molecules quickly (for example the reactants and products of biochemical reactions, like glucose or lactate), but must still bind specifically. This is most striking in enzymes, which speed up biochemical reactions by binding to rate-defining intermediates of chemical reactions (transition states). They must also bind to the reactants and products of the reactions, which are very similar in chemistry to the transition state, but must be bound much more weakly. The focus of this study is how enzymes combine these two modes of binding in their reaction cycles, and how they use their intrinsic flexibility to do so. We wish to test whether structural tightening provides a mechanism of achieving this discrimination. NMR allows the measurement of the properties of individual atoms within large molecules, but there is a size limit to the size of molecules that can be studied. Over time this size limit is increasing as technology improves and is now at a stage where large enzymes like phosphoglycerate kinase (PGK) can be studied. This project will use this technology to determine the contributions that different atoms within this enzyme make to the binding of the transition state of the reaction it catalyses, using stable chemicals that resemble it (called transition state analogues). The conclusions should be broadly applicable to other enzymes. An understanding of this process is vital to the design inhibitors of enzymes for use as therapeutic agents (drugs) and to technologies that use enzymes out of their biological context, for example bioremediation. It will also help the theoretical understanding of how important biological molecules work.