Investigation of binding of UDP-Galf and UDP-[3-F]Galf to UDP-galactopyranose mutase by STD-NMR spectroscopy, molecular dynamics, and CORCEMA-ST calculations

UDP-galactopyranose mutase (UGM) is the key enzyme involved in the biosynthesis of Galf. UDP-Galp and UDP-Galf are two natural substrates of UGM. A protocol that combines the use of STD-NMR spectroscopy, molecular modeling, and CORCEMA-ST calculations was applied to the investigation of the binding of UDP-Galf and its C3-fluorinated analogue to UGM from Klebsiella pneumoniae. UDP-Galf and UDP-[3-F]Galf were bound to UGM in a manner similar to that of UDP-Galp. The interconversions of UDP-Galf and UDP-[3-F]Galf to their galactopyranose counterparts were catalyzed by the reduced (active) UGM with different catalytic efficiencies, as observed by NMR spectroscopy. The binding affinities of UDP-Galf and UDP-[3-F]Galf were also compared with those of UDP-Galp and UDP by competition STD-NMR experiments. When UGM was in the oxidized (inactive) state, the binding affinities of UDP-Galf, UDP-Galp, and UDP-[3-F]Galf were of similar magnitudes and were lower than that of UDP. However, when UGM was in the reduced state, UDP-Galp had higher binding affinity compared with UDP. Molecular dynamics (MD) simulations indicated that the "open" mobile loop in UGM "closes" upon binding of the substrates. Combined MD simulations and STD-NMR experiments were used to create models of UGM with UDP-Galf and UDP-[3-F]Galf as bound ligands. Calculated values of saturation-transfer effects with CORCEMA-ST (complete relaxation and conformational exchange matrix analysis of saturation transfer) were compared to the experimental STD effects and permitted differentiation between two main conformational families of the bound ligands. Taken together, these results are used to rationalize the different rates of catalytic turnover of UDP-Galf and UDP-[3-F]Galf and shed light on the mechanism of action of UGM.     

Reactivity of the triple ion and separated ion pair of tris(trimethylsilyl)methyllithium with aldehydes: a RINMR study

Low-temperature rapid-injection NMR (RINMR) experiments were performed on tris(trimethylsilyl)methyllithium. In THF/Me2O solutions, the separated ion (1S) reacted faster than can be measured at -130 degrees C with MeI and substituted benzaldehydes (k >/= 2 s -1), whereas the contact ion (1C) dissociated to 1S before reacting. Unexpectedly, the triple ion reacted faster with electron-rich benzaldehydes relative to electron-deficient ones. The addition of HMPA had no effect on the rate of reaction of the triple ion with p-diethylaminobenzaldehyde, and the immediate product of the reaction was the HMPA-solvated separated ion 1S, with the Peterson product forming only slowly. Thus, the aldehyde is catalyzing the dissociation of the triple ion. HMPA greatly decelerated the reaction of 1S (<10 -10), providing an estimate of the Lewis acid activating effect of a THF-solvated lithium cation in an organolithium addition to an aldehyde.     

Structures and solution dynamics of pseudorotaxanes mediated by alkali-metal cations

Kinetic stability studies of a series of pseudorotaxanes formed from electron-rich crown ethers (hosts and ) and naphthalene diimide (guest ) in the presence of alkali salt templates MX (where M(+) = Li(+) and Na(+), and X(-) = Cl(-), Br(-), I(-), NO(3)(-) and CF(3)SO(3)(-)) were performed by (1)H NMR. The switching between the (bound) host and its linkage isomer host (free) was monitored in solution in the presence and absence of alkali salts, to establish the relative thermodynamic stabilities in the series. We also report here six new crystal structures, for pseudorotaxanes of type: [.], [M(2)..](2+) and [M(2)..](2+). Their solution-phase structures are in good agreement with the solid-state structures determined by X-ray crystallography.     

On spanning trees and walks of low maximum degree

This article uses the discharging method to obtain the best possible results that a 3‐connected graph embeddable on a surface of Euler characteristic χ ≤ −46 has a spanning tree of maximum degree at most and a closed, spanning walk meetting each vertex at most times. Each of these results is shown to be best possible. © 2001 John Wiley & Sons, Inc. J Graph Theory 36: 67–74, 2001     

Metalloporphyrin Dendrimers with Folding Arms

Rigid and flexible linkers are combined in the new dendrimer shown schematically in the picture, which contains nine metalloporphyrin units (Porph). The construction is such that the four “arms” of the dendrimer can fold in a cooperative and predetermined manner in response to added 1,4-diazabicyclo[2.2.2]octane (DABCO).     

Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes

Bisphosphonates are a class of molecules in widespread use in treating bone resorption diseases and are also of interest as immunomodulators and anti-infectives. They function by inhibiting the enzyme farnesyl diphosphate synthase (FPPS), but the details of how these molecules bind are not fully understood. Here, we report the results of a solid-state (13)C, (15)N, and (31)P magic-angle sample spinning (MAS) NMR and quantum chemical investigation of several bisphosphonates, both as pure compounds and when bound to FPPS, to provide information about side-chain and phosphonate backbone protonation states when bound to the enzyme. We then used computational docking methods (with the charges assigned by NMR) to predict how several bisphosphonates bind to FPPS. Finally, we used X-ray crystallography to determine the structures of two potent bisphosphonate inhibitors, finding good agreement with the computational results, opening up the possibility of using the combination of NMR, quantum chemistry and molecular docking to facilitate the design of other, novel prenytransferase inhibitors.