Insights into enzyme allosteric inhibition mechanisms using computational studies
Degree GrantorUniversity of Canterbury
Degree NameDoctor of Philosophy
Allostery, the process by which action of an effector at one site of the protein provokes a functional response at a distant site, is critical in the regulation of metabolic pathways. Yet, despite its importance, allostery remains enigmatic and little detailed information is known about how the function of the protein is affected, how the allosteric signal is communicated or how allosteric regulation evolves in a protein. The overall objective of this thesis is to provide new insights into the understanding of allostery by studying computationally allosteric regulation in the metabolic enzyme 3-deoxy- D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) which catalyses the first committed step in the biosynthesis of aromatic amino acids. Not only is DAH7PS a promising antimicrobial drug target, owing to its presence in microorganisms but not in animals, but also, the unique variety of allosteric regulation mechanisms found in this protein family makes it the ideal playground to study allostery. Firstly, in Chapter 2, using a variety of sequence and phylogenetic analysis tools, the evolution of allosteric regulation in the DAH7PS family was explored. New subgroups of the DAH7PS family were identified and it was found that DAH7PS is likely to have acquired allostery by the recruitment of an N- or C-terminal regulatory domain via gene fusion. Loop extensions and N-terminal domain mutations then gave rise to more complex allosteric regulation mechanisms. In Chapter 3, a new computational method, which is based on the monitoring of calculated pKa variations of ionisable residues over the course of molecular dynamics simulations, is used to identify allosteric communication pathways in protein relying on dynamic allosteric regulation. This approach is used to decipher the subtle allosteric regulation mechanism of DAH7PS from pathogen Neisseria meningitidis. A number of key charge-charge and hydrogen bond interactions were identified as being responsible for the communication of the allosteric signal in this protein. These predictions were verified experimentally and showed that pH variations can mimic the allosteric control, by changing the protonation state of the residues involved in the identified key interactions. The allosteric regulation of the DAH7PS from hyperthermophile Thermotoga maritima, which relies on major domain motions, is explored using molecular dynamics simulations in Chapter 4. It was found that the flexibility of the allosteric domains impedes the entrance to the active site, explaining the lower catalytic activity observed experimentally when compared to a mutant lacking the regulatory domains. Furthermore, the simulations revealed that although the inhibition of the enzyme is achieved by blocking the access to the active site, the residual activity of the enzyme at high inhibitor concentrations observed experimentally, can be explained by the opening of a back door providing direct access to the catalytic site. In Chapter 5, using a combination of X-ray crystallography, homology modelling and small-angle X-ray scattering, the allosteric regulation mechanism of DAH7PS from thermophilic soil bacterium Geobacillus sp. was studied. These methods revealed that binding of the allosteric ligand to the allosteric regulatory domains stabilises a more compact conformation of the protein, limiting the catalytic functionality of the DAH7PS domain active site. In addition, molecular dynamics simulations are currently in progress to further explore the allosteric regulation of this enzyme are presented. In Chapter 6, the different attempts to model the first step of the reaction catalysed by DAH7PS, using hybrid quantum mechanics / molecular mechanics simulations, are presented and recommendations for future work toward the complete modelling of the reaction are provided. Finally, the implications of this work are discussed in the general context of allosteric regulation mechanisms.