The role of dynamics in enzyme mechanism and allostery

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Abstract – The role of dynamics in enzyme mechanism and allostery Enzymes are complex molecules that perform difficult chemical transformations and regulate biochemical activities that maintain cell health. Although many structures of enzymes are available, numerous aspects of enzyme function remain hidden in their dynamics and transient deformations. NMR spectroscopy, in concert with other methods, has helped to realize how dynamics assists protein function on a variety of timescales. However, such studies have been largely limited to small enzymes and proteins. Typically, enzymes are large with complex features, and they are often oligomeric and symmetric in ways that are intimately tied to their allosteric regulation/function. There is thus a need to increase access to the rich dynamics and other NMR-sensitive parameters that exist in complex enzymes and larger proteins. The work proposed here aims to 1) solve long- standing problems in the general study of allostery in symmetric homodimers and 2) gain crucial information on highly flexible regions important for the function of a (large) metabolic enzyme that is a primary target for chemotherapies. Structural and dynamic processes will be examined in the human (70 kDa) and E. coli (62 kDa) versions of thymidylate synthase (TS), which methylates deoxyuridine monophosphate (dUMP) to produce the dTMP nucleotide. TS is a symmetric homodimer that is “half-the-sites reactive”, which is interesting from the perspective of allostery since the active sites are separated by 35 Å. Although the half-the-sites nature of TS gives an expectation of negative thermodynamic cooperativity between the two subunits, we have showed that substrate binding cooperativity is nonexistent or small in ecTS. By contrast, hTS has pronounced negative binding cooperativity, as well as more conformational changes and additional sequence segments of high flexibility. Comparison of residue-specific behavior in the ecTS and hTS systems will yield insights into mechanisms of allostery in symmetric homodimers. Our previous work on ecTS produced an NMR strategy that enables clean, protomer-selective observation of step-wise ligand binding that is necessary to evaluate intersubunit allosteric mechanisms in homodimers. This work will be extended to further characterize intersubunit communication in ecTS in Aim 1 and applied separately to hTS in Aim 3, along with computational work to supply molecular details of the dynamics. The knowledge gained will advance the delineation of principles of allosteric communication, which are needed to engineer or control it in proteins and improve design of allosteric drugs. In Aim 2, structural and dynamic features of function of hTS will be determined, including the role of the highly flexible and hitherto invisible 29-residue N-terminus. In addition, the means by which a tumor-derived resistance mutation weakens affinity to cancer drug 5-FU will be investigated. In summary, this work will use a combination of NMR, ITC, crystallography, and MD simulations to reveal dynamics-based function and mechanisms of allostery in a complex, symmetric, enzyme homodimer.