Molecular modelling has become widely used in chemistry and biology. The aim of this project is to use a range of molecular modelling techniques to study enzymic actions. This thesis consists of two parts. Part A of this thesis describes computational studies conducted for the calpain-calpastatin system. Calpain is a cysteine protease. Over-expression of calpain is associated with many diseases. Calpastatin is the naturally occurring specific regulator of calpain activity. In this part of the thesis, the dynamic conformational preferences of region B of the inhibitory domain in calpastatin were examined in detail by using molecular dynamics simulations and stochastic dynamic simulations with Monte Carlo sampling. Part B of the thesis explores the structure and function of the enzyme 3-dexoy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtuDAH7PS). MtuDAH7PS catalyses the first reaction of the shikimate pathway and is a target for the development of anti-tuberculosis drugs. MtuDAH7PS is found to be synergistically inhibited by combinations of aromatic amino acids (Trp+Phe or Trp+Tyr), but not by any single aromatic amino acids. In this part of the thesis, this unique mechanism of allosteric regulation in MtuDAH7PS was investigated by using a range molecular modelling techniques. Firstly protein crystal structure refinements were conducted and those crystal structures of MtuDAH7PS in complex with various ligand molecules are described in Chapter 4. Secondly, the reaction mechanism and roles of active site residues were investigated in Chapter 5, through docking calculations (both rigid docking and induced fit docking) of a series of designed active site inhibitors. Finally, Chapter 6 discusses the molecular basis of the communication mechanism of allosteric regulation in MtuDAH7PS.

Allosteric regulation of important enzymes is a mechanism frequently employed by organisms to exert control over their metabolism. The shikimate pathway is ultimately responsible for the biosynthesis of the aromatic amino acids in plants, microorganisms and apicomplexans. Two enzymes of the pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) and chorismate mutase (CM) are located at critical positions along the aromatic amino acid biosynthetic pathway and are often tightly feedback regulated in order to control the flux of metabolites through the pathway. This research presents studies on the allosteric function of these two enzymes. These studies emphasise the complexity of the intersecting network of allosteric response, which alters the catalytic activity of each enzyme in response to metabolic demand for the aromatic amino acids.

The shikimate pathway is a biosynthetic pathway that is responsible for producing a variety of organic compounds that are necessary for life in plants and microorganisms. The pathway consists of seven enzyme catalysed reactions beginning with the condensation reaction between D-erythrose 4-phosphate (E4P) and phosphoenolpyruvate (PEP) to give the seven-carbon sugar DAH7P. This thesis describes the design, synthesis and evaluation of a range of alternative non-natural four-carbon analogues of E4P (2- and 3-deoxyE4P, 3-methylE4P, phosphonate analogues of E4P) to probe the substrate specificity of different types of DAH7P synthases [such as Mycobacterium tuberculosis (a type II DAH7PS), Escherichia coli (a type Ialpha DAH7PS) and Pyrococcus furiosus (a type Ibeta DAH7PS)].

The enzyme 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyses the stereospecific aldol-like condensation between phosphoenolpyruvate (PEP) and the five-carbon sugar D-arabinose 5-phosphate (A5P). This is the first biosynthetic step in the formation of 3-deoxy-D-manno-octulosonate (KDO), an essential lipopolysaccharide component of all Gram-negative bacteria. KDO8PS is evolutionarily related to the shikimate pathway enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), which catalyses a similar condensation reaction between PEP and the four-carbon sugar D-erythrose 4-phosphate (E4P), in the first step of the shikimate pathway to aromatic compounds in plants and microorganisms. As well as being a one-carbon shorter substrate, E4P has the opposite C2-OH configuration to A5P. While there are both metal-dependent and metal-independent forms of KDO8PS, in contrast, all DAH7PS are metal-dependent enzymes. Little is understood about the key sequence features that distinguish KDO8PS and DAH7PS. These features, particularly those that contribute to A5P or E4P binding, are thought to be responsible for the differences in substrate specificity between the two enzymes. This thesis describes the functional and structural studies of KDO8PS mutants to examine the roles of these residues, using the metal-dependent KDO8PS from Acidithiobacillus ferrooxidans and the metal-independent KDO8PS from Neisseria meningitidis. In Chapter 2 an extensive KDO8PS and DAH7PS sequence analysis is presented. The results, which identify sequence conservation in both enzymes, are discussed in the context of the (β/α)8 TIM-barrel structure. Some of the differences in conservation between the two enzymes were highlighted as being obvious in having a role or contributing to the different substrate selection preferences of the two enzymes, such as an extended β7α7 loop in KDO8PS, and motif differences on the β2α2 and β4α4 loops. A similar analysis was also used to compare metal-dependent and metal-independent KDO8PSs, and it was found the two forms differ in the conservation of only three residues. Chapter 3 describes the characterisation of A. ferrooxidans KDO8PS (AfeKDO8PS) and investigates aspects of metal dependency in KDO8PS. The enzyme was found to be metal dependent, and like all other KDO8PS enzymes, to possess a tetrameric quaternary structure, and display tight substrate specificity. The β8α8 loop was found to have a critical role in binding and positioning the substrates, and AfeKDO8PS could not be engineered to be a metal-independent enzyme. The role of the KDO8PS-conserved KANRS motif, present on the β2α2 loop and one of the main contributors to the A5P binding site, is probed in Chapter 4. Individual residues of the motif were mutated to investigate function, and the motif was converted to the equivalent motif found in DAH7PS (KPRS). It was found that the Lys plays a critical role in enzymatic catalysis, and is likely intimately involved in the enzyme mechanism. The Asn residue of the motif in KDO8PS was found to be an important contributor to KDO8PS stereospecificity. The work described in Chapter 5 investigates the role of the β7α7 loop in KDO8PS. This long active-site loop, which exists in a shorter version in DAH7PS, was found not to be essential for catalysis in KDO8PS, but was necessary for efficient catalysis. The two conserved residues on the loop provide interactions to A5P, but the presence of the extended loop as a whole was found to be most important for catalytic efficiency. In Chapter 6 a conserved residue on the re face of PEP is investigated. In KDO8PS the residue is conserved as Asp, and in DAH7PS the same residue is conserved as a Glu. Mutational analysis found that in KDO8PS the Asp residue appears to be important for enzyme activity but unimportant for PEP binding. Mutating this Asp in KDO8PS to Glu was accommodated by KDO8PS, but it was found its introduction could potentially be optimised by coupling the change with mutation to other conserved differences. In KDO8PS, one of the interfaces between adjacent subunits in the tetrameric structure is partially composed of a conserved sequence motif, PAFLxR. In Chapter 7, the roles of the residues in this motif are explored. The Arg of the motif was found to be important for A5P binding. The equivalent (and also conserved) motif in DAH7PS is GARNxQ, and mutation of residues in the KDO8PS motif to the equivalent residues in DAH7PS was tolerated by KDO8PS, but negatively impacted upon the enzyme kinetic parameters. The sequence features investigated in the other chapters were combined with those to the subunit interface to create a DAH7PS-like protein. This extensively engineered protein lost all KDO8PS activity, but nor did it gain DAH7PS activity. Lastly, in Chapter 8 the results from all chapters are reviewed and ideas are discussed for advancing the research presented in this thesis.

The enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first reaction in the shikimate pathway, leading to the biosynthesis of aromatic compounds including the aromatic amino acids. The catalytic activity of DAH7PS is regulated through feedback inhibition and is the major control point for the pathway. DAH7PSs are divided into two families, type I and type II, based on molecular weight and amino acid sequence. Type I DAH7PSs can be further divided based on sequence similarity. All DAH7PS enzymes with their crystal structures solved share a basic (β/α)₈-barrel fold in which the key catalytic components are housed. Furthermore, all structurally characterised DAH7PSs, except Pyrococcus furiosus DAH7PS (PfuDAH7PS) and Aeropyrum pernix DAH7PS, have recruited extra structural motifs that are implicated in allosteric regulation. However, there are significant differences in the additional structural elements. This thesis investigates the hypothesis that the diverse regulation strategies for controlling DAH7PS activity have evolved by domain recruitment, whereby regulatory domains have been added to the catalytic barrel. Chapter 2 describes the functional characterisation of the type Iβ Thermotoga maritima DAH7PS (TmaDAH7PS), and the exploration of its response to inhibitors. The catalytic activity of TmaDAH7PS was found to be substantially inhibited by tyrosine (Tyr) and to a lesser extent, phenylalanine (Phe). The putative regulatory domain previously identified as a ferredoxin-like domain was recognised as an aspartate kinase-chorismate-mutase-tyrA (prephenate dehydrogenase) or ACT domain. Chapter 3 describes the characterisation of TmaDAH7PS with the N-terminal domain removed. The truncated enzyme was found to be more catalytically active than wild-type TmaDAH7PS and insensitive to inhibition by the aromatic amino acids, Tyr, Phe and tryptophan. Apart from the truncation of the ACT domain, the crystal structure of truncTmaDAH7PS showed no major changes to the monomer structure when compared to wild-type TmaDAH7PS. However, truncTmaDAH7PS crystallises as a dimer, unlike wild-type TmaDAH7PS. In Chapter 4, the solution of the crystal structure of TmaDAH7PS with Tyr bound is presented. Tyr binding was shown to induce a significant conformational change, and Tyr is observed to bind at the interface between the ACT domains from two diagonally located monomers of the tetramer. The major reorganisation of the regulatory domain with respect to the barrel observed in the crystal structure, was confirmed by small angle X-ray scattering. The closed conformation adopted by the protein on Tyr binding physically gates the neighbouring barrel and blocks substrate entry into the active site. Chapter 5 explores the interactions between TmaDAH7PS and the allosteric inhibitor, Tyr. The residues His29 and Ser31, which form hydrogen bonds with the hydroxyl moiety of the Tyr ligand, were examined for their impact on the sensitivity and selectivity of the enzyme for the inhibitors Tyr and Phe. The hydroxyl side chain of Ser31 was found to be important for both the preferential inhibition by Tyr over Phe and the inhibitory mechanism. His29 (the hydrogen-bonding partner of Ser31) appears to play a secondary role in determining ligand selectivity and the relative positioning of these two residues is crucial to the inhibition of the enzyme. Chapter 6 evaluates the transferability of allosteric control of catalytic activity. The ACT domain of TmaDAH7PS was fused onto the barrel of the unregulated PfuDAH7PS. This chimeric enzyme was found to be catalytically active, inhibited by Tyr (although less sensitive) and preliminary crystallographic results show inhibition occurs via the same conformational change observed for wild-type TmaDAH7PS.

3-Deoxy-D-arabino heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first step of the shikimate pathway, responsible for the biosynthesis of aromatic amino acids. This pathway is found in microorganisms, plants and apicomplexan parasites and its absence in mammals makes it a viable target for antimicrobial drug design. DAH7PS enzymes differ in the regulatory machinery that decorates the catalytic (β/α)8 barrel. Some DAH7PS enzymes are fused to chorismate mutase (CM), another enzyme in the shikimate pathway. This fusion protein is allosterically regulated by chorismate (CA) or prephenate (PA), the precursor of tyrosine and phenylalanine. It has been suggested that DAH7PS enzymes evolved these extensions to the core barrel for the sole purpose of regulation. Geobacillus sp DAH7PS (GspDAH7PSWT) is a thermophilic type Iβ DAH7PS enzyme with an N-terminal CM domain fused through a linker region. This thesis describes the functional characterisation work carried out on GspDAH7PSWT, in attempt to help determine how DAH7PS enzymes evolved such diverse methods of regulation. Chapter 2 describes the functional characterisation work carried out on the catalytic and regulatory domains of GspDAH7PSWT. The enzyme demonstrated both DAH7PS and CM activities with the DAH7PS domain determined to be metal dependent and most activated by Cd2+. PA completely inhibited the catalytic activity of GspDAH7PSWT, and AUC demonstrated an equilibrium exists between the dimeric and tetrameric quaternary states of the enzyme in solution. Chapter 3 describes the domain truncation of GspDAH7PSWT carried out at the linker region in order to obtain two separate protein domains, the catalytic domain lacking the N-terminal domain (GspDAH7PSDAH7PS) and the regulatory domain without the catalytic domain (GspDAH7PSCM). Both variants were fully characterised, and information obtained from each domain was compared to the respective catalytic and regulatory domains of the wild-type enzyme, which was also characterised. Like GspDAH7PSWT, GspDAH7PSDAH7PS showed greatest activation in the presence of Cd2+, with other metals having varying effects on activation rates and stability of the enzyme. Both truncated variants followed Michaelis-Menten kinetics where GspDAH7PSDAH7PS was found to be more active than GspDAH7PSWT and unaffected by PA, whereas GspDAH7PSCM was a less efficient catalyst than the CM domain of GspDAH7PSWT. AUC demonstrated that in solution an equilibrium occurs between the monomeric and tetrameric oligomeric states of GspDAH7PSDAH7PS. Chapter 4 summarises the findings of the thesis along with future directions of this research, combining the results obtained and expanding upon them. It is concluded that the catalytic regulatory CM domain supports both protein structure and allosteric regulation of GspDAH7PSWT

3-Deoxy-D-arabino heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first step of the shikimate pathway, responsible for the biosynthesis of aromatic amino acids. This pathway is found in microorganisms, plants and apicomplexan parasites and its absence in mammals makes it a viable target for antimicrobial drug design. DAH7PS enzymes differ in the regulatory machinery that decorates the catalytic (β/α)8 barrel. Some DAH7PS enzymes are fused to chorismate mutase (CM), another enzyme in the shikimate pathway. This fusion protein is allosterically regulated by chorismate (CA) or prephenate (PA), the precursor of tyrosine and phenylalanine. It has been suggested that DAH7PS enzymes evolved these extensions to the core barrel for the sole purpose of regulation. Geobacillus sp DAH7PS (GspDAH7PSWT) is a thermophilic type Iβ DAH7PS enzyme with an N-terminal CM domain fused through a linker region. This thesis describes the functional characterisation work carried out on GspDAH7PSWT, in attempt to help determine how DAH7PS enzymes evolved such diverse methods of regulation. Chapter 2 describes the functional characterisation work carried out on the catalytic and regulatory domains of GspDAH7PSWT. The enzyme demonstrated both DAH7PS and CM activities with the DAH7PS domain determined to be metal dependent and most activated by Cd2+. PA completely inhibited the catalytic activity of GspDAH7PSWT, and AUC demonstrated an equilibrium exists between the dimeric and tetrameric quaternary states of the enzyme in solution. Chapter 3 describes the domain truncation of GspDAH7PSWT carried out at the linker region in order to obtain two separate protein domains, the catalytic domain lacking the N-terminal domain (GspDAH7PSDAH7PS) and the regulatory domain without the catalytic domain (GspDAH7PSCM). Both variants were fully characterised, and information obtained from each domain was compared to the respective catalytic and regulatory domains of the wild-type enzyme, which was also characterised. Like GspDAH7PSWT, GspDAH7PSDAH7PS showed greatest activation in the presence of Cd2+, with other metals having varying effects on activation rates and stability of the enzyme. Both truncated variants followed Michaelis-Menten kinetics where GspDAH7PSDAH7PS was found to be more active than GspDAH7PSWT and unaffected by PA, whereas GspDAH7PSCM was a less efficient catalyst than the CM domain of GspDAH7PSWT. AUC demonstrated that in solution an equilibrium occurs between the monomeric and tetrameric oligomeric states of GspDAH7PSDAH7PS. Chapter 4 summarises the findings of the thesis along with future directions of this research, combining the results obtained and expanding upon them. It is concluded that the catalytic regulatory CM domain supports both protein structure and allosteric regulation of GspDAH7PSWT