The use of driven equilibrium conditions in the measurement of NMR relaxation times

The further development of the use of NMR relaxation times in chemical, biological and medical research has perhaps been curtailed by the length of time these measurements often take. The DESPOT (Driven Equilibrium Single Pulse Observation of T1) method has been developed, which reduces the time required to make a T1 measurement by a factor of up to 100. The technique has been studied extensively herein and the thesis contains recommendations for its successful experimental application. Modified DESPOT type equations for use when T2 relaxation is incomplete or where off-resonance effects are thought to be significant are also presented. A recently reported application of the DESPOT technique to MR imaging gave good initial results but suffered from the fact that the images were derived from spin systems that were not driven to equilibrium. An approach which allows equilibrium to be obtained with only one non-acquisition sequence is presented herein and should prove invaluable in variable contrast imaging. A DESPOT type approach has also been successfully applied to the measurement of T1. T_1's can be measured, using this approach significantly faster than by the use of the classical method. The new method also provides a value for T1 simultaneously and therefore the technique should prove valuable in intermediate energy barrier chemical exchange studies. The method also gives rise to the possibility of obtaining simultaneous T1 and T1 MR images. The DESPOT technique depends on rapid multipulsing at nutation angles, normally less than 90^o. Work in this area has highlighted the possible time saving for spectral acquisition over the classical technique (90^o-5T_1)_n. A new method based on these principles has been developed which permits the rapid multipulsing of samples to give T_1 and M_0 ratio information. The time needed, however, is only slightly longer than would be required to determine the M_0 ratio alone using the classical technique. In ^1H decoupled ^13C spectroscopy the method also gives nOe ratio information for the individual absorptions in the spectrum.

Reactive processing of polymers: structural characterization of products by 1H and 13C NMR spectroscopy for glycidyl methacrylate grafting onto EPR in the absence and presence of a reactive comonomer

Grafted GMA on EPR samples were prepared in a Thermo-Haake internal mixer by free radical melt grafting reactions in the absence (conventional system; EPR-g-GMA(CONV)) and presence of the reactive comonomer divinyl benzene, DVB (EPR-g-GMA(DVB)). The GMA-homopolymer (poly-GMA), a major side reaction product in the conventional system, was almost completely absent in the DVB-containing system, the latter also resulted in a much higher level of GMA grafting. A comprehensive microstructure analysis of the formed poly-GMA was performed based on one-dimensional H-1 and C-13 NMR spectroscopy and the complete spectral assignments were supported by two-dimensional NMR techniques based on long range two and three bond order carbon-proton couplings from HMBC (Heteronuclear Multiple Bond Coherence) and that of one bond carbon-proton couplings from HSQC (Heteronuclear Single Quantum Coherence), as well as the use of Distortionless Enhancement by Polarization Transfer (DEPT) NMR spectroscopy. The unambiguous analysis of the stereochemical configuration of poly-GMA was further used to help understand the microstructures of the GMA-grafts obtained in the two different free radical melt grafting reactions, the conventional and comonomer-containing systems. In the grafted GMA, in the conventional system (EPR-g-GMA(CONV)), the methylene protons of the GMA were found to be sensitive to tetrad configurational sequences and the results showed that 56% of the GMA sequence in the graft is in atactic configuration and 42% is in syndiotactic configuration whereas the poly-GMA was predominantly syndiotactic. The differences in the microstructures of the graft in the conventional EPR-g-GMA(CONV) and the DVB-containing (EPR-g-GMA(DVB)) systems is also reported (C) 2009 Elsevier Ltd. All rights reserved.

A structural investigation of the alkali metal site distribution within bioactive glass using neutron diffraction and multinuclear solid state NMR

The atomic-scale structure of Bioglass and the effect of substituting lithium for sodium within these glasses have been investigated using neutron diffraction and solid state magic angle spinning (MAS) NMR. Applying an effective isomorphic substitution difference function to the neutron diffraction data has enabled the Na-O and Li-O nearest-neighbour correlations to be isolated from the overlapping Ca-O, O-(P)-O and O-(Si)-O correlations. These results reveal that Na and Li behave in a similar manner within the glassy matrix and do not disrupt the short range order of the network former. Residual differences are attributed solely to the variation in ionic radius between the two species. Successful simplification of the 2

An examination of the calcium and strontium site distribution in bioactive glasses through isomorphic neutron diffraction, X-ray diffraction, EXAFS and multinuclear solid state NMR.

Strontium has been substituted for calcium in the glass series (SiO2)49.46(Na2O)26.38(P2O5)1.07(CaO)23.08x(SrO)x (where x = 0, 11.54, 23.08) to elucidate their underlying atomic-scale structural characteristics as a basis for understanding features related to the bioactivity. These bioactive glasses have been investigated using isomorphic neutron and X-ray diffraction, Sr K-edge EXAFS and solid state 17O, 23Na, 29Si, 31P and 43Ca magic-angle-spinning (MAS) NMR. An effective isomorphic substitution first-order difference function has been applied to the neutron diffraction data, confirming that Ca and Sr behave in a similar manner within the glass network, with residual differences attributed to solely the variation in ionic radius between the two species. The diffraction data provides the first direct experimental evidence of split Ca–O nearest-neighbour correlations in these melt quench bioactive glasses, together with an analogous splitting of the Sr–O correlations; the correlations are attributed to the metal ions correlated either to bridging or to non-bridging oxygen atoms. Triple quantum (3Q) 43Ca MAS NMR corroborates the split Ca–O correlations. Successful simplification of the 2 < r (A) < 3 region via the difference method has also revealed two distinct Na environments. These environments are attributed to sodium correlated either to bridging or to nonbridging oxygen atoms. Complementary multinuclear MAS NMR, Sr K-edge EXAFS and X-ray diffraction data supports the structural model presented. The structural sites present will be intimately related to their release properties in physiological fluids such as plasma and saliva, and hence the bioactivity of the material. Detailed structural knowledge is therefore a prerequisite for optimising material design.

Matrix-assisted diffusion-ordered spectroscopy:mixture resolution by NMR using SDSmicelles

Diffusion-ordered spectroscopy (DOSY) is a powerful technique for mixture analysis, but in its basic form it cannot separate the component spectra for species with very similar diffusion coefficients. It has been recently demonstrated that the component spectra of a mixture of isomers with nearly identical diffusion coefficients (the three dihydroxybenzenes) can be resolved using matrix-assisted DOSY (MAD), in which diffusion is perturbed by the addition of a co-solute such as a surfactant [R. Evans, S. Haiber, M. Nilsson, G. A. Morris, Anal. Chem. 2009, 81, 4548-4550]. However, little is known about the conditions required for such a separation, for example, the concentrations and concentration ratios of surfactant and solutes. The aim of this study was to explore the concentration range over whichmatrix-assisted DOSY using the surfactant SDS can achieve diffusion resolution of a simple model set of isomers, the monomethoxyphenols. The results show that the separation is remarkably robust with respect to both the concentrations and the concentration ratios of surfactant and solutes, supporting the idea that MAD may become a valuable tool formixture analysis. © 2010 John Wiley & Sons, Ltd.

Quantitative interpretation of diffusion-ordered NMR spectra:can we rationalize small molecule diffusion coefficients?

Appealingly simple: A new method is described that allows the diffusion coefficient of a small molecule to be estimated given only the molecular weight and the viscosity of the solvent used. This method makes possible the quantitative interpretation of the diffusion domain of diffusion-ordered NMR spectra (see picture). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dimethylsulfoxide oxidizes glutathione in vitro and in human erythrocytes:kinetic analysis by 1H NMR

The interaction of dimethylsulfoxide (Me2SO) with glutathione was investigated under non-equilibrium conditions in solution using 1H NMR and in intact erythrocytes using 1H spin-echo NMR. In solution the reaction was observed to follow second-order kinetics (Rate = k1[glutathione][Me2SO]) at 300 K pH 7.4, ksol = 4.7 × 10-5 mol -1 L1 s-1. In intact erythrocytes the rate constant for the cellular environment, kcell, was found to be slightly larger at 8.1 × 10-5 mol-1 L1 s-1. Furthermore, the reaction of Me2SO with erythrocyte glutathione showed a biphasic dependence on the Me2SO concentration, with little oxidation of glutathione occurring until the Me2SO concentration exceeded 0.5 mol L-1. The results suggest that at lower concentrations, Me2SO can be effectively removed, most probably by reaction with glutathione, which is regenerated by glutathione reductase, although preferential reaction with other cellular components (e.g., membrane or cellular thiols) cannot be ruled out. Thus the concentrations of Me2SO that are commonly used in cryopreservation of mammalian cells (∼1.4 mol L-1) can cause oxidation of intracellular glutathione.

A nanoliter volume nuclear magnetic resonance (NMR) system using tunneling magneto-resistive (TMR) sensors to recognize biomolecules

The need to incorporate advanced engineering tools in biology, biochemistry and medicine is in great demand. Many of the existing instruments and tools are usually expensive and require special facilities.^ With the advent of nanotechnology in the past decade, new approaches to develop devices and tools have been generated by academia and industry. ^ One such technology, NMR spectroscopy, has been used by biochemists for more than 2 decades to study the molecular structure of chemical compounds. However, NMR spectrometers are very expensive and require special laboratory rooms for their proper operation. High magnetic fields with strengths in the order of several Tesla make these instruments unaffordable to most research groups.^ This doctoral research proposes a new technology to develop NMR spectrometers that can operate at field strengths of less than 0.5 Tesla using an inexpensive permanent magnet and spin dependent nanoscale magnetic devices. This portable NMR system is intended to analyze samples as small as a few nanoliters.^ The main problem to resolve when downscaling the variables is to obtain an NMR signal with high Signal-To-Noise-Ratio (SNR). A special Tunneling Magneto-Resistive (TMR) sensor design was developed to achieve this goal. The minimum specifications for each component of the proposed NMR system were established. A complete NMR system was designed based on these minimum requirements. The goat was always to find cost effective realistic components. The novel design of the NMR system uses technologies such as Direct Digital Synthesis (DDS), Digital Signal Processing (DSP) and a special Backpropagation Neural Network that finds the best match of the NMR spectrum. The system was designed, calculated and simulated with excellent results.^ In addition, a general method to design TMR Sensors was developed. The technique was automated and a computer program was written to help the designer perform this task interactively.^

Novel Purification of Archaeal Rnase P Protein, Pfu Rpp38, for Nmr Studies

Dr. Kenneth Murray, Ph.D. Assistant Professor of Biology Ribonuclease P (RNase P) is an essential and ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving 5' leader sequences during tRNA maturation. RNase P comprises one essential RNA, and one protein subunit in eubacteria, five proteins in archaea, and ten in humans. Due to its homology to human RNase P, its higher stability, and simpler structure; extensive studies have been conducted utilizing the enzyme from the archaeal hyperthermophile, Pyrococcus furious (Pfu). Previous studies identified only four protein subunits associated with the archaeal RNase P. This fourprotein reconstituted particle, however, had an optimal temperature of 55°C, compared to the optimal 70°C of the wild type RNase P. Additional probing of the organism's genome database revealed a fifth RNase P protein subunit, RPP38. To facilitate further investigations of Pfu RNase complexes, we sought to develop a protocol for the purification ofRPP38. Our results, presented herein, represent the first known expression.purification protocol developed for RPP38. Briefly, we synthesized an N-terminal6x-His RPP38 fusion construct, reengineered to contain a Tobacco Etch Virus (TEV) protease cleavage site. Purification was achieved via immobilized metal affinity chromatography and reversed phase high performance liquid chromatography. Following purification the 6X-His affinity tag was removed via TEV cleavage, thus regenerating the native RPP38 protein. Purity and identity of RPP38 were confirmed by sodium dodecylsulfate - polyacrylamide gel electrophoresis and mass spectrometry, respectively. Our work is expected to contribute to our understanding ofRNase P function and tRNA maturation by providing an efficient, facile technique to express and purify Pfu RNase protein RPP38 as a means to facilitate structural and functional analyses.

A Protein NMR Assistant

Postprint

A new SOS-DFPT approximation for NMR shielding calculations : the Loc.3 correction applied to the catalytic mechanism of Serine Proteases

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

A new SOS-DFPT approximation for NMR shielding calculations : the Loc.3 correction applied to the catalytic mechanism of Serine Proteases

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.