Performance Tuning Non-Uniform Sampling for Sensitivity Enhancement of Signal-Limited Biological NMR

Non-uniform sampling (NUS) has been established as a route to obtaining true sensitivity enhancements when recording indirect dimensions of decaying signals in the same total experimental time as traditional uniform incrementation of the indirect evolution period. Theory and experiments have shown that NUS can yield up to two-fold improvements in the intrinsic signal-to-noise ratio (SNR) of each dimension, while even conservative protocols can yield 20-40 % improvements in the intrinsic SNR of NMR data. Applications of biological NMR that can benefit from these improvements are emerging, and in this work we develop some practical aspects of applying NUS nD-NMR to studies that approach the traditional detection limit of nD-NMR spectroscopy. Conditions for obtaining high NUS sensitivity enhancements are considered here in the context of enabling H-1,N-15-HSQC experiments on natural abundance protein samples and H-1,C-13-HMBC experiments on a challenging natural product. Through systematic studies we arrive at more precise guidelines to contrast sensitivity enhancements with reduced line shape constraints, and report an alternative sampling density based on a quarter-wave sinusoidal distribution that returns the highest fidelity we have seen to date in line shapes obtained by maximum entropy processing of non-uniformly sampled data.

Molecular Dynamics Simulations of the d(TAT) Triple Helix

Molecular dynamics (MD) simulations have been used to study the dynamical and time-averaged characteristics of the DNA triple helix d(T)10âd(A)10âd(T)10. The structures sampled during the trajectory resemble closely the B-type model for the DNA triplex proposed on the basis of NMR data, although there are some subtle differences. Alternative P- and A-type conformations for the triplex, suggested from X-ray experiments, are not predicted to contribute significantly to the structure of the DNA triplex in solution. Comparison with the best available experimental data supports the correctnes of the MD-generated structures. The analysis of the collected data gives a detailed picture of the characteristics of triple-helix DNA. A new and interesting pattern of hydration, specific for triplex DNA, is an important observation. The results suggest that molecular dynamics can be useful for the study of novel nucleic acid structures.

The Effects of Pi-Pi Stacking on the Controlled Radical Polymerization of Vinyl Aromatics

The atom transfer radical polymerization (ATRP) of styrene (St) was conducted in the presence of varying equivalence (eq) of hexafluorobenzene (HFB) and octafluorotoluene (OFT) to probe the effects of pi-pi stacking on the rate of the polymerization and on the tacticity of the resulting polystyrene (PSt). The extent of the pi-pi stacking interaction between HFB/OFT and the terminal polystyrenic phenyl group was also investigated as a function of solvent, both non-aromatic solvents (THF and hexanes) and aromatic solvents (benzene and toluene). In all cases the presence of HFB or OFT resulted in a decrease in monomer conversion indicating a reduction in the rate of the polymerization with greater retardation of the rate with increase eq of HFB or OFT (0.5 eq to 1 eq HFB/OFT compared to St). Additionally, when aromatic solvents were used instead of non-aromatic solvents the effect of the HFB/OFT on the rate was minimized, consistent with the aromatic solvent competitively interacting with the HFB/OFT. The effects of temperature and ligand strength on the ATRP of St in the presence of HFB were also probed. It was found that when using N,N,N’,N’,N’’-pentamethyldiethylenetriamine (PMDETA) as the ligand the effects of HFB at 38o were the same as at 86oC. When tris[2-(dimethylamino)ethyl]-amine (Me6TREN) was used as the ligand at 38o there was a decrease in monomer conversion similar to the analogous PMDETA reaction. When the polymerization was conducted at 86oC there was no effect on the monomer conversion with HFB present compared to when HFB was absent. To investigate the pi-pi stacking effect even further, the reverse pi-pi stacking system was observed by conducting the ATRP of pentafluorostyrene (PFSt) in the presence of varying eq of benzene and toluene, which in both cases resulted in an increase in monomer conversion compared to when benzene or toluene were absent; in summary the rate of the ATRP of PFSt increases when benzene or toluene waas present in the reaction. The pi-pi stacking interaction between the HFB/OFT and the dormant alkyl bromide of the polymer chain was verified by 1H-NMR with 1-bromoethylbenzene as the alkyl bromide. Also verified by 1H-NMR was the interaction between HFB/OFT and St and the interaction between PFSt and benzene. In all 1H-NMR spectra a perturbation in the aromatic and/or vinyl peaks was observed when the pi-pi stacking agent was present compared to when it was absent. The tacticity of the PSt formed in the presence of 1 eq of HFB was compared to the PSt formed in the absence of HFB by observing the C1 signal in their 13C-NMR spectra, but no change in shape or chemical shift of the signal was observed indicating that there was no change in tacticity.

Studying Electrophoretic Separations Using Cholate Micelles: Effects Of Ph, Temperature, And Composition

Micelle-forming bile salts have previously been shown to be effective pseudo-stationary phases for separating the chiral isomers of binaphthyl compounds with micellar electrokinetic capillary chromatography (MEKC). Here, cholate micelles are systematically investigated via electrophoretic separations and NMR using R, S-1, 1¿- binaphthyl- 2, 2¿-diylhydrogenphosphate (BNDHP) as a model chiral analyte. The pH, temperature, and concentration of BNDHP were systematically varied while monitoring the chiral resolution obtained with MEKC and the chemical shift of various protons in NMR. NMR data for each proton on BNDHP is monitored as a function of cholate concentration: as cholate monomers begin to aggregate and the analyte molecules begin to sample the micelle aggregate we observe changes in the cholate methyl and S-BNDHP proton chemical shifts. From such NMR data, the apparent CMC of cholate at pH 12 is found to be about 13-14 mM, but this value decreases at higher pH, suggesting that more extreme pHs may give rise to more effective separations. In general, CMCs increase with temperature indicating that one may be able to obtain better separations at lower temperatures. S-BNDHP concentrations ranging from 50 ¿M to 400 ¿M (pH 12.8) gave rise to apparent cholate CMC values from 10 mM to 8 mM, respectively, indicating that S-BNDHP, the chiral analyte molecule, may play an active role in stabilizing cholate aggregates. In all, these data show that NMR can be used to systematically investigate a complex multi-variable landscape of potential optimizations of chiral separations.

Understanding Bile Micelle Chiral Interactions

Bile salts are known to aggregate into micelles in biological systems; however, the fundamental structure and dynamics of bile molecule micelle formation are poorly understood. Previous studies have established that the bile salt cholate is capable of performing chirally selective micellar electrokinetic capillary chromatography (MEKC) separations of model racemic binaphthyl compounds 1,1¿-binaphthyl-2,2¿-diyl hydrogen phosphate (R,S-BNDHP) and 1,1¿-bi-2-naphthol (R,S-BN). Nuclear magnetic resonance (NMR) has been established as a complementary technique for understanding chiral selectivity and micelle formation events based on changes in proton chemical shifts of the probe molecules BNDHP and BN as well as of cholate. This work investigated the effects of the probe molecule, the alkali cation identity and temperature on cholate micelle aggregation and MEKC separations of R,S-BN and R,S-BNDHP. The probe molecule was found to mediate micelle formation by MEKC and proton NMR. A low (0.1 mM) concentration of probe was found to have minimal effects on micellization events detected by proton NMR while higher probe concentration (2.5 mM) was found to mediate micellization causing micellization events to occur at lower cholate concentrations. This work also investigated the effects of alkali counterion on chiral separation. Generally, counterions with larger crystal cationic radius were found to cause greater chiral separation power. NMR data suggest that protons near the surface of the cholate micelle are most sensitive to the cation identity, suggesting a model of improved separation based on the cation sterically inhibiting binding of one isomer. Finally, the effect of temperature on MEKC separation was investigated. Separation power of R,S-BN and R,S-BNDHP appeared to increase linearly with temperature for 22.0 mM to 50.0 mM pH 12.0 cholate. In total, these results indicate that cholate aggregation is dependent on multiple conditions. Understanding the roles that these factors play in influencing cholate micellization can inform better separation in MEKC.

Enhanced Sensitivity by Nonuniform Sampling Enables Multidimensional MAS NMR Spectroscopy of Protein Assemblies

We report dramatic sensitivity enhancements in multidimensional MAS NMR spectra by the use of nonuniform sampling (NUS) and introduce maximum entropy interpolation (MINT) processing that assures the linearity between the time and frequency domains of the NUS acquired data sets. A systematic analysis of sensitivity and resolution in 2D and 3D NUS spectra reveals that with NUS, at least 1.5- to 2-fold sensitivity enhancement can be attained in each indirect dimension without compromising the spectral resolution. These enhancements are similar to or higher than those attained by the newest-generation commercial cryogenic probes. We explore the benefits of this NUS/MaxEnt approach in proteins and protein assemblies using 1-73-(U-C-13,N-15)/74-108-(U-N-15) Escherichia coil thioredoxin reassembly. We demonstrate that in thioredoxin reassembly, NUS permits acquisition of high-quality 3D-NCACX spectra, which are inaccessible with conventional sampling due to prohibitively long experiment times. Of critical importance, issues that hinder NUS-based SNR enhancement in 3D-NMR of liquids are mitigated in the study of solid samples in which theoretical enhancements on the order of 3-4 fold are accessible by compounding the NUS-based SNR enhancement of each indirect dimension. NUS/MINT is anticipated to be widely applicable and advantageous for multidimensional heteronuclear MAS NMR spectroscopy of proteins, protein assemblies, and other biological systems.

Enhancing Sensitivity In Natural Product Nmr: Exploring Optimal Non-Uniform Sampling

Recent optimizations of NMR spectroscopy have focused their attention on innovations in new hardware, such as novel probes and higher field strengths. Only recently has the potential to enhance the sensitivity of NMR through data acquisition strategies been investigated. This thesis has focused on the practice of enhancing the signal-to-noise ratio (SNR) of NMR using non-uniform sampling (NUS). After first establishing the concept and exact theory of compounding sensitivity enhancements in multiple non-uniformly sampled indirect dimensions, a new result was derived that NUS enhances both SNR and resolution at any given signal evolution time. In contrast, uniform sampling alternately optimizes SNR (t < 1.26T2) or resolution (t~3T2), each at the expense of the other. Experiments were designed and conducted on a plant natural product to explore this behavior of NUS in which the SNR and resolution continue to improve as acquisition time increases. Possible absolute sensitivity improvements of 1.5 and 1.9 are possible in each indirect dimension for matched and 2x biased exponentially decaying sampling densities, respectively, at an acquisition time of ¿T2. Recommendations for breaking into the linear regime of maximum entropy (MaxEnt) are proposed. Furthermore, examination into a novel sinusoidal sampling density resulted in improved line shapes in MaxEnt reconstructions of NUS data and comparable enhancement to a matched exponential sampling density. The Absolute Sample Sensitivity derived and demonstrated here for NUS holds great promise in expanding the adoption of non-uniform sampling.

Hydrodynamic Characterization of Bile Salt Host-Guest Complexes by Pulsed Field Gradient NMR Spectroscopy

The work described herein is aimed at understanding primary and secondary aggregation of bile salt micelles and how micelles can perform chiral recognition of binapthyl analytes. Previous work with cholate and deoxycholate using micellar electrokinetic chromatography (MEKC) and nuclear magnetic resonance (NMR) has provided insightinto cholate and deoxycholate micelle formation, especially with respect to the critical micelle concentration (CMC). Chiral separations of the model analyte, 1,1â??-binaphthyl-2,2â??-diyl hydrogen phosphate (BNDHP), via cholate (C) and deoxycholate (DC) mediated MEKC separataions previously have shown the DC CMC to be 7-10 mM andthe cholate CMC at 14 mM at ph 12. A second model analyte,1,1â??-binaphthol (BN), was also previously investigated to probe micellar structure, but the MEKC data for this analyte implied a higher CMC, which may be interpreted as secondary aggregation. Thiswork extends the investigation of bile salts to include pulsed field gradient spin echo (PFGSE) NMR experiments being used to gain information about the size and degree of polydispersity of cholate and deoxycholate micelles. Concentrations of cholate below 10mM show a large variation in effective radius likely due to the existence of transient preliminary aggregates. The onset of the primary micelle shows a dramatic increase in effective radius of the micelle in cholate and deoxycholate. In the region of expectedsecondary aggregation a gradual increase of effective radius was observed with cholate; deoxycholate showed a persistent aggregate size in the secondary micelle region that is modulated by the presence of an analyte molecule. Effective radii of cholate anddeoxycholate (individually) were compared with and without R- and S-BNDHP in order to observe the effective radius difference of micelles with and without analyte present. The presence of S-BNDHP consistently resulted in a larger effective aggregate radius incholate and deoxycholate, confirming previous data of the S-BNDHP interacting more with the micelle than R-BNDHP. In total, various NMR techniques, like diffusion NMR can be used to gain a greater understanding of the bile salt micellization process and chiral resolution.