Structural and dynamic requirements for optimal activity of the essential bacterial enzyme dihydrodipicolinate synthase.

Dihydrodipicolinate synthase (DHDPS) is an essential enzyme involved in the lysine biosynthesis pathway. DHDPS from E. coli is a homotetramer consisting of a 'dimer of dimers', with the catalytic residues found at the tight-dimer interface. Crystallographic and biophysical evidence suggest that the dimers associate to stabilise the active site configuration, and mutation of a central dimer-dimer interface residue destabilises the tetramer, thus increasing the flexibility and reducing catalytic efficiency and substrate specificity. This has led to the hypothesis that the tetramer evolved to optimise the dynamics within the tight-dimer. In order to gain insights into DHDPS flexibility and its relationship to quaternary structure and function, we performed comparative Molecular Dynamics simulation studies of native tetrameric and dimeric forms of DHDPS from E. coli and also the native dimeric form from methicillin-resistant Staphylococcus aureus (MRSA). These reveal a striking contrast between the dynamics of tetrameric and dimeric forms. Whereas the E. coli DHDPS tetramer is relatively rigid, both the E. coli and MRSA DHDPS dimers display high flexibility, resulting in monomer reorientation within the dimer and increased flexibility at the tight-dimer interface. The mutant E. coli DHDPS dimer exhibits disorder within its active site with deformation of critical catalytic residues and removal of key hydrogen bonds that render it inactive, whereas the similarly flexible MRSA DHDPS dimer maintains its catalytic geometry and is thus fully functional. Our data support the hypothesis that in both bacterial species optimal activity is achieved by fine tuning protein dynamics in different ways: E. coli DHDPS buttresses together two dimers, whereas MRSA dampens the motion using an extended tight-dimer interface.

Characterisation of dihydrodipicolinate synthase (DHDPS) from Bacillus anthracis.

Bacillus anthracis is a Gram-positive spore-forming bacterium that is the causative agent of anthrax disease. The use of anthrax as a bioweapon has increased pressure for the development of an effective treatment. Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step in the biosynthetic pathway yielding two essential bacterial metabolites, meso-diaminopimelate (DAP) and (S)-lysine. DHDPS is therefore a potential antibiotic target, as microbes require either lysine or DAP as a component of the cell wall. This paper is the first biochemical description of DHDPS from B. anthracis. Enzyme kinetic analyses, isothermal titration calorimetry (ITC), mass spectrometry and differential scanning fluorimetry (DSF) were used to characterise B. anthracis DHDPS and compare it with the well characterised Escherichia coli enzyme. B. anthracis DHDPS exhibited different kinetic behaviour compared with E. coli DHDPS, in particular, substrate inhibition by (S)-aspartate semi-aldehyde was observed for the B. anthracis enzyme (K(si(ASA))=5.4+/-0.5 mM), but not for the E. coli enzyme. As predicted from a comparison of the X-ray crystal structures, the B. anthracis enzyme was not inhibited by lysine. The B. anthracis enzyme was thermally stabilised by the first substrate, pyruvate, to a greater extent than its E. coli counterpart, but has a weaker affinity for pyruvate based on enzyme kinetics and ITC studies. This characterisation will provide useful information for the design of inhibitors as new antibiotics targeting B. anthracis.

Inhibiting protein-protein interactions as an emerging paradigm for drug discovery.

Association of proteins into homo- and hetero-oligomers plays an important role in a plethora of biological phenomena. Inhibition of these interactions is increasingly recognized as a valuable new direction in drug design. In this mini-review we consider inhibition of protein misfolding and aggregation, molecules that disrupt enzyme quaternary structure, and signaling inhibitors, as emerging drugs.

Protein cross-linking in food.

The aims of this paper are (1) to probe the relationship between molecular structure and protein cross-linking ability for a range of small molecules; (2) to establish whether this relationship holds within a food matrix; and (3) to test the impact of Maillard cross-linking on food functionality, particularly texture, in wheat- and soy-based food systems. A variety of molecules were obtained, either commercially or via organic synthesis. Cross-linking ability was tested using our standard model system, employing ribonuclease A and analyzing the results by SDS-PAGE. Molecules of varying reactivity were tested in wheat- and soy-based products, and the changes in functionality were correlated with changes in protein cross-linking. No simple relationship was found between molecular structure and ability to cross-link ribonuclease. Only the most reactive reagents were able to cross-link within the food matrix. Nevertheless, a low degree of cross-linking was shown to have significant consequences on the properties of wheat- and soy-based foods, suggesting that the Maillard reaction may represent a means to control food texture.

Covalent protein adduct formation and protein cross-linking resulting from the maillard reaction between cyclotene and a model food protein.

Covalent Maillard products of the reactions of carbonyl compounds with proteins are often described in the literature, but, until recently, evidence for their existence has been indirect. Cyclotene (2-hydroxy-3-methylcyclopent-2-enone), a common flavor compound, was incubated with a model food protein, ribonuclease, and found to cross-link the protein. Size exclusion high-performance liquid chromatrography and electrospray mass spectrometry of the early stages of the reaction provide strong evidence for covalent adducts that we believe to be intermediates in the cross-linking reaction.

Versatile multi-functionalization of protein nanofibrils for biosensor applications.

Protein nanofibrils offer advantages over other nanostructures due to the ease in their self-assembly and the versatility of surface chemistry available. Yet, an efficient and general methodology for their post-assembly functionalization remains a significant challenge. We introduce a generic approach, based on biotinylation and thiolation, for the multi-functionalization of protein nanofibrils self-assembled from whey proteins. Biochemical characterization shows the effects of the functionalization onto the nanofibrils' surface, giving insights into the changes in surface chemistry of the nanostructures. We show how these methods can be used to decorate whey protein nanofibrils with several components such as fluorescent quantum dots, enzymes, and metal nanoparticles. A multi-functionalization approach is used, as a proof of principle, for the development of a glucose biosensor platform, where the protein nanofibrils act as nanoscaffolds for glucose oxidase. Biotinylation is used for enzyme attachment and thiolation for nanoscaffold anchoring onto a gold electrode surface. Characterization via cyclic voltammetry shows an increase in glucose-oxidase mediated current response due to thiol-metal interactions with the gold electrode. The presented approach for protein nanofibril multi-functionalization is novel and has the potential of being applied to other protein nanostructures with similar surface chemistry.

Stability of the insecticide cypermethrin during tomato processing and implications for endocrine activity.

The thermal and pH stabilities of cypermethrin during food processing were investigated using tomato as a model food system and high-performance liquid chromatography as the analytical method. Cypermethrin was thermally unstable in aqueous conditions, where the hydrolysis of the pesticide was accelerated by heat. The mean proportion remaining after heating cypermethrin in water for 10 min was 66%, falling to 27% after 1 h. Similarly, thermal processing of canned tomatoes caused cypermethrin to degrade, with remaining levels in the final product ranging from 30 to 60% of the original. Cypermethrin was unstable at extreme pHs, with acid hydrolysis occurring faster than alkaline hydrolysis in phosphate buffers. The acidity of tomato paste (pH 4.3) caused cypermethrin levels to decrease by 30% within 12 days at 5 degrees C. The studies indicate that cypermethrin residues are likely to degrade by hydrolysis during food processing, thus reducing the exposure of consumers to cypermethrin. 3-Phenoxybenzaldehyde, a hydrolysis breakdown product of cypermethrin, was detected in the tomato paste and from the heating of cypermethrin in water at 100 degrees C. There is concern that the risk of breakdown products in terms of endocrine activity is unknown since in vitro studies reported that cypermethrin breakdown products display endocrine activity.

The effect of Saccharomyces cerevisiae on the stability of the herbicide glyphosate during bread leavening.

AIMS: To investigate the ability of baker's yeast (Saccharomyces cerevisiae) to degrade the herbicide glyphosate during the fermentation cycle of the breadmaking process. METHODS AND RESULTS: Aqueous glyphosate was added to bread ingredients and kneaded by commercially available breadmaking equipment into dough cultures. Cultures were incubated in the breadmaker throughout the fermentation cycle. The recovery of glyphosate levels following fermentation was determined, thus allowing an estimation of glyphosate degradation by yeast. CONCLUSIONS: It was shown, for the first time, that S. cerevisiae plays a role in metabolizing glyphosate during the fermentation stages of breadmaking. Approximately 21% was degraded within 1 h. SIGNIFICANCE AND IMPACT OF THE STUDY: As a result of projected increases in the glyphosate use on wheat and the role of bread as a dietary staple, this may contribute to more informed decisions being made relating to the use of glyphosate on glyphosate-resistant wheat, from a public health/regulatory perspective.

Kinetic characterisation of ene-diol-based inhibitors of alpha-amylase.

A kinetic analysis of the inhibition of malt alpha-amylase by compounds based on ascorbic acid has shown the mode of inhibition to be competitive for the parent compound, but more complex for its derivatives. We have further simplified the ascorbic acid ene-diol pharmacophore by demonstrating that dihydroxyfumaric acid is also a good inhibitor of malt alpha-amylase.

Novel approaches to the analysis of the Maillard reaction of proteins.

The Maillard reaction comprises a complex network of reactions which has proven to be of great importance in both food science and medicine. The majority of methods developed for studying the Maillard reaction in food have focused on model systems containing amino acids and monosaccharides. In this study, a number of electrophoretic techniques, including two-dimensional gel electrophoresis and capillary electrophoresis, are presented. These have been developed specifically for the analysis of the Maillard reaction of food proteins, and are giving important insights into this complex process.