John Wilkie

A Design for Life: Prokaryotic Metal-binding MerR Family Regulators

The MerR family of metal-binding, metal-responsive proteins is unique in that they activate transcription from unusual promoters and coordinate metals through cysteine (and in the case of ZntR, histidine) residues. They have conserved primary structures yet can effectively discriminate metals in vivo.

Anion complexation via C–H⋯X interactions using a palladacyclic receptor

A novel organometallic receptor binds anions in solution and in the solid state, with complexes stabilised through a series of C-HX interactions, as evidenced by 1H NMR spectroscopy, X-ray crystallography and computational models.

The role of metal ions in phosphate ester hydrolysis

Many phosphatases make use of metal ions to aid catalysis of phosphate ester hydrolysis. Here, we investigate the impact of metal ions on the potential energy surface (PES), and hence the preferred reaction mechanism, for a simple model for hydrolysis of phosphate ester monoanions. We show that, while both associative (A(N) + D(N)) and dissociative (D(N) + A(N)) mechanisms are represented on the potential energy surfaces both in the presence and absence of metal ions, the D(N) + A(N) process is favoured when there are no metal ions present and the A(N) + D(N) process is favoured in the presence of two metal ions. A concerted (A(N)D(N)) process is also available in the presence of two metal ions, but proceeds via a high-energy transition state. In the presence of only a single metal ion the A(N)D(N) process is the most favoured, but still proceeds via a high-energy transition state. Thus, we conclude that metallo-enzyme phosphatases are likely to utilise an associative process, while those that function without metal ions may well follow a dissociative process.

De Novo Design of Ln(III) Coiled Coils for Imaging Applications

A new peptide sequence (MB1) has been designed which, in the presence of a trivalent lanthanide ion, has been programmed to self-assemble to form a three stranded metallo-coiled coil, Ln(III)(MB1)3. The binding site has been incorporated into the hydrophobic core using natural amino acids, restricting water access to the lanthanide. The resulting terbium coiled coil displays luminescent properties consistent with a lack of first coordination sphere water molecules. Despite this the gadolinium coiled coil, the first to be reported, displays promising magnetic resonance contrast capabilities.

NMR and molecular dynamics study of the size, shape, and composition of reverse micelles in a cetyltrimethylammonium bromide (CTAB)/n-hexane/pentanol/water microemulsion.

The size, shape, and composition of reverse micelles (RMs) in a cetyltrimethylammonium bromide (CTAB)/pentanol/n-hexane/water microemulsion were investigated using pulsed gradient stimulated echo (PGSTE) nuclear magnetic resonance (NMR) measurements and molecular modeling. PGSTE data were collected at observation times (Δ) of 10, 40, and 450 ms. At long observation times, CTAB and pentanol exhibited single diffusion coefficients. However, at short (Δ ≤ 40 ms) observation times both CTAB and pentanol exhibited slow and fast diffusion coefficients. These NMR data indicate that both CTAB and pentanol molecules reside in different environments within the microemulsion and that there is exchange between regions on the millisecond time scale. Molecular dynamic simulations of the CTAB RM, in a solvent box containing n-hexane and pentanol, produced an ellipsoid shaped RM. Using structural parameters from these simulations and the Stokes-Einstein relation, the structure factor and dimensions of the reverse micelle were determined. Analysis of the composition of the interphase also showed that there was a variation in the ratio of surfactant to cosurfactant molecules depending on the curvature of the interphase.

Mechanism of CB1954 reduction by Escherichia coli nitroreductase.

NTR (nitroreductase NfsB from Escherichia coli) is a flavoprotein with broad substrate specificity, reducing nitroaromatics and quinones using either NADPH or NADH. One of its substrates is the prodrug CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide), which is converted into a cytotoxic agent; so NTR/CB1954 has potential for use in cancer gene therapy. However, wild-type NTR has poor kinetics and binding with CB1954, and the mechanism for the reduction of CB1954 by NTR is poorly understood. Computational methods have been utilized to study potential underlying reaction mechanisms so as to identify the order of electron and proton transfers that make up the initial reduction step and the sources of the protons. We have used Molecular Dynamics to examine the nature of the active site of the wild-type enzyme and the preferred binding mode of the substrate. A combination of these results has allowed us to unequivocally identify the reaction mechanism for the reduction of CB1954 by NTR.

Magnetic resonance studies of a redox probe in a reverse sodium bis(2-ethylhexyl)sulfosuccinate/octane/water microemulsion.

The location and dynamics of the [Ru(bpy)(3)](2+) complex inside sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/octane/water microemulsions were studied, over a range of droplet sizes, using magnetic resonance spectroscopy, dynamic light scattering, and molecular modeling. The T(1) magnetic resonance relaxation times of water inside the AOT reverse micelles (RMs) were measured in both the presence and the absence of the [Ru(bpy)(3)](2+) complex. Large size droplet RMs (ω(0) > 20) were found to be sensitive to the presence of the [Ru(bpy)(3)](2+) complex, which was detected through a decrease in the T(1) relaxation time of the water inside the RM core, as compared to RMs containing no [Ru(bpy)(3)](2+). However, no difference in T(1) relaxation time was observed for water in small RMs (ω(0) < 20). Two-dimensional (1)H-(1)H NOESY spectroscopy was performed to probe the location of the [Ru(bpy)(3)](2+) complex in both small (ω(0) = 9.2) and large droplets (ω(0) = 34.9). Cross-peaks between protons in the AOT tail groups and bipyridyl ligands were observed, showing that the [Ru(bpy)(3)](2+) complex resided in the RM interface. Finally, molecular modeling simulations were performed to probe the location of the [Ru(bpy)(3)](2+) complex and the structure of the RM. Molecular dynamics simulations confirmed the location of the [Ru(bpy)(3)](2+) complex in the RM interface and detected differences in the surfactant layer and the amount of water penetration into this layer with changing droplet size.

The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis.

We present 2-dimensional potential energy surfaces and optimised transition states (TS) for water attack on a series of substituted phosphate monoester monoanions at the DFT level of theory, comparing a standard 6-31++g(d,p) basis set with a larger triple-zeta (augmented cc-pVTZ) basis set. Small fluorinated model compounds are used to simulate increasing leaving group stability without adding further geometrical complexity to the system. We demonstrate that whilst changing the leaving group causes little qualitative change in the potential energy surfaces (with the exception of the system with the most electron withdrawing leaving group, CF(3)O(-), in which the associative pathway changes from a stepwise A(N) + D(N) pathway to a concerted A(N)D(N) pathway), there is a quantitative change in relative gas-phase and solution barriers for the two competing pathways. In line with previous studies, in the case of OCH(3), the barriers for the associative and dissociative pathways are similar in solution, and the two pathways are equally viable and indistinguishable in solution. However, significantly increasing the stability of the leaving group (decreasing proton affinity, PA) results in the progressive favouring of a stepwise dissociative, D(N) + A(N), mechanism over associative mechanisms.

Probes for the position and mechanistic role of the second ‘catalytic’ magnesium ion in the inositol monophosphatase reaction

Two magnesium ions are required for the enzymic hydrolysis of phosphate monoester substrates of inositol monophosphatase. It has been suggested that one (buried) Mg2+ ion binds to the enzyme and the phosphate dianion moiety of the substrate through one or more of its negatively charged O-atoms while the second Mg2+ ion binds to the substrate bridging phosphate ester O-atom and one other substrate-derived O-atom. This second Mg2+ ion may also position and activate the attacking nucleophilic water molecule (A. G. Cole and D. Gani, J. Chem. Soc., Perkin Trans. 1, 1995, previous article). To determine the minimum structural requirements for a substrate, as deduced from the proposed interactions for natural and synthetic substrates with both Mg2+ ions, ethane-1,2-diol 1-phosphate was prepared and was found to be a substrate. The design and preparation of a range of minimal structure synthetic probes based on this new substrate including propyl, 2-methoxyethyl, 2-(2-hydroxyethoxy)ethyl and 5-hydroxypentyl monophosphate ester and both antipodes of 1,5-dihydroxypentan-2-yl phosphate allowed the specific interactions between the substrate and the enzyme and/or the second Mg2+ ion to be assessed. The results support the proposed roles for the metal ions and provide information on the position of the second Mg2+ ion. This information rationalises the properties of known organophosphate substrates and inhibitors for the enzyme and, furthermore, facilitates the construction of a 3-D catalytic mechanism for the inositol monophosphatase reaction which is described. This new catalytic mechanism explains why Li+ behaves as an inhibitor and accounts for its unusual inhibitory properties.

BTN3A1 discriminates γδ T cell phosphoantigens from non-antigenic small molecules via a conformational sensor in its B30.2 domain

Human Vγ9/Vδ2 T-cells detect tumor cells and microbial infections by recognizing small phosphorylated prenyl metabolites termed phosphoantigens (P-Ag). The type-1 transmembrane protein Butyrophilin 3A1 (BTN3A1) is critical to the P-Ag-mediated activation of Vγ9/Vδ2 T-cells; however, the molecular mechanisms involved in BTN3A1-mediated metabolite sensing are unclear, including how P-Ags are discriminated from nonantigenic small molecules. Here, we utilized NMR and X-ray crystallography to probe P-Ag sensing by BTN3A1. Whereas the BTN3A1 immunoglobulin variable domain failed to bind P-Ag, the intracellular B30.2 domain bound a range of negatively charged small molecules, including P-Ag, in a positively charged surface pocket. However, NMR chemical shift perturbations indicated BTN3A1 discriminated P-Ag from nonantigenic small molecules by their ability to induce a specific conformational change in the B30.2 domain that propagated from the P-Ag binding site to distal parts of the domain. These results suggest BTN3A1 selectively detects P-Ag intracellularly via a conformational antigenic sensor in its B30.2 domain and have implications for rational design of antigens for Vγ9/Vδ2-based T-cell immunotherapies.