Quantitative at-line monitoring of enzymatic hydrolysis using benchtop diffusion nuclear magnetic resonance spectroscopy.

Benchtop diffusion nuclear magnetic resonance (NMR) spectroscopy was used to perform quantitative monitoring of enzymatic hydrolysis. The study aimed to test the feasibility of the technology to characterize enzymatic hydrolysis processes in real time. Diffusion ordered spectroscopy (DOSY) was used to measure the signal intensity and apparent self-diffusion constant of solubilized protein in hydrolysate. The NMR technique was tested on an enzymatic hydrolysis reaction of red cod, a lean white fish, by the endopeptidase alcalase at 50°C. Hydrolysate samples were manually transferred from the reaction vessel to the NMR equipment. Measurement time was approximately 3 min per time point. The signal intensity from the DOSY experiment was used to measure protein concentration and the apparent self-diffusion constant was converted into an average molecular weight and an estimated degree of hydrolysis. These values were plotted as a function of time and both the rate of solubilization and the rate of protein breakdown could be calculated. In addition to being rapid and noninvasive, DOSY using benchtop NMR spectroscopy has an advantage compared with other enzymatic hydrolysis characterization methods as it gives a direct measure of average protein size; many functional properties of proteins are strongly influenced by protein size. Therefore, a method to give protein concentration and average size in real time will allow operators to more tightly control production from enzymatic hydrolysis. Although only one type of material was tested, it is anticipated that the method should be applicable to a broad variety of enzymatic hydrolysis feedstocks.

Benchtop nuclear magnetic resonance spectroscopy in forensic chemistry.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique well known for its ability to elucidate structures and analyse mixtures and its quantitative nature. However, the cost and maintenance of high field NMR instruments prevent its widespread use by forensic chemists. The introduction of benchtop NMR spectrometers to the market operating at 40-80 MHz have a small footprint, are easy to use and cost much less than high field instruments, which makes them well suited to meet the needs of forensic chemists. These modern low field spectrometers are often capable of running multiple nuclei including 1 H, 13 C, 19 F and 31 P; 2D NMR experiments and advanced experiments such as solvent suppression and diffusion-ordered spectroscopy (DOSY) are possible. This has resulted in a number of publications in the area of forensic chemistry using benchtop NMR spectroscopy in the last 5 years that was previously missing from the literature. This mini review summarises this research including examples of benchtop NMR being used to identify and quantify compounds relevant to forensics and some advanced methods that may be used to overcome some of the limitations of these instruments for forensic analysis. Further validation and automation are likely required for widespread uptake of benchtop NMR in industry; however, it has been demonstrated as a useful complement to other analytical techniques commonplace of forensic laboratories.

Measurement of the hydrodynamic radii of PEE-G dendrons by diffusion spectroscopy on a benchtop NMR spectrometer.

Benchtop nuclear magnetic resonance (NMR) spectroscopy is a useful tool for the rapid determination of the self-diffusion coefficient and the hydrodynamic radius of dendrons. The self-diffusion coefficients of the first four generations of poly ethoxy ethyl glycinamide (PEE-G) dendrons are measured by diffusion-ordered spectroscopy (DOSY) on a benchtop NMR equipped with diffusion gradient coils. The hydrodynamic radii of the dendrons are calculated via the Stokes-Einstein equation. The effects of solvent and pH are determined with the hydrodynamic radius increasing with generation and decreasing upon neutralization of an acidic solution. These measurements provide valuable information for biological and pharmaceutical applications of dendrons.

Evaluation of benchtop NMR Diffusion Ordered Spectroscopy for small molecule mixture analysis.

Diffusion Ordered Spectroscopy (DOSY) is an attractive method for analyzing chemical mixtures in the liquid state because it separates spectra by the molecular weight of the associated molecule. It has been compared with hyphenated chromatographic and analytical methods such LC-MS and has broad potential in servicing those same applications including forensics, reaction analysis, quality control, and fraud detection. Benchtop NMR can collect quality spectra on small molecules, however, lacks the chemical shift dispersion of high field instruments, can suffer from spectral overlap common in mixtures, and the diminished sensitivity of the lower field compounds these problems. In this work, we show that existing high field pulse sequences and processing methods perform well at 43 MHz. Spectra from molecular mixtures where the constituents had 20% differences in diffusion coefficients and significant overlap were able to be matched to a bespoke spectral library and identified correctly. In addition, spectra from mixtures with constituents that have severe overlap in the spectrum and differ by 50% in diffusion coefficients were also able to be match and identified correctly. The combination of benchtop NMR and easy implementation of modern pulse sequences and processing show promise of bringing these useful methods to chemistry laboratories in research and industrial environments.

Site-specific dynamic nuclear polarization of hydration water as a generally applicable approach to monitor protein aggregation.

We present a generally applicable approach for monitoring protein aggregation by detecting changes in surface hydration water dynamics and the changes in solvent accessibility of specific protein sites, as protein aggregation proceeds in solution state. This is made possible through the Overhauser dynamic nuclear polarization (DNP) of water interacting with stable nitroxide spin labels tethered to specific proteins sites. This effect is highly localized due to the magnetic dipolar nature of the electron-proton spin interaction, with >80% of their interaction occurring within 5 A between the unpaired electron of the spin label and the proton of water. We showcase our tool on the aggregation of tau proteins, whose fibrillization is linked to neurodegenerative disease pathologies known as taupathies. We demonstrate that the DNP approach to monitor local changes in hydration dynamics with residue specificity and local contrast can distinguish specific and neat protein-protein packing leading to fibers from non-specific protein agglomeration or precipitation. The ability to monitor tau assembly with local, residue-specific, resolution, under ambient conditions and in solution state will help unravel the mechanism and structural characteristics of the gradual process of tau aggregation into amyloid fibers, which remains unclear to this day.

Dynamic nuclear polarization enhanced nuclear magnetic resonance and electron spin resonance studies of hydration and local water dynamics in micelle and vesicle assemblies.

We present a unique analysis tool for the selective detection of local water inside soft molecular assemblies (hydrophobic cores, vesicular bilayers, and micellar structures) suspended in bulk water. Through the use of dynamic nuclear polarization (DNP), the (1)H NMR signal of water is amplified, as it interacts with stable radicals that possess approximately 658 times higher spin polarization. We utilized stable nitroxide radicals covalently attached along the hydrophobic tail of stearic acid molecules that incorporate themselves into surfactant-based micelle or vesicle structures. Here, we present a study of local water content and fluid viscosity inside oleate micelles and vesicles and Triton X-100 micelles to serve as model systems for soft molecular assemblies. This approach is unique because the amplification of the NMR signal is performed in bulk solution and under ambient conditions with site-specific spin labels that only detect the water that is directly interacting with the localized spin labels. Continuous wave (cw) electron spin resonance (ESR) analysis provides rotational dynamics of the spin-labeled molecular chain segments and local polarity parameters that can be related to hydration properties, whereas we show that DNP-enhanced (1)H NMR analysis of fluid samples directly provides translational water dynamics and permeability of the local environment probed by the spin label. Our technique therefore has the potential to become a powerful analysis tool, complementary to cw ESR, to study hydration characteristics of surfactant assemblies, lipid bilayers, or protein aggregates, where water dynamics is a key parameter of their structure and function. In this study, we find that there is significant penetration of water inside the oleate micelles with a higher average local water viscosity (approximately 1.8 cP) than in bulk water, and Triton X-100 micelles and oleate vesicle bilayers mostly exclude water while allowing for considerable surfactant chain motion and measurable water permeation through the soft structure.

Portable X-band system for solution state dynamic nuclear polarization.

This paper concerns instrumental approaches to obtain large dynamic nuclear polarization (DNP) enhancements in a completely portable system. We show that at fields of 0.35 T under ambient conditions and at X-band frequencies, 1H enhancements of >100-fold can be achieved using nitroxide radical systems, which is near the theoretical maximum for 1H polarization using the Overhauser effect at this field. These large enhancements were obtained using a custom built microwave transmitter and a commercial TE102 X-band resonant cavity. The custom built microwave transmitter is compact, so when combined with a permanent magnet it is readily transportable. Our commercial X-band resonator was modified to be tunable over a range of approximately 9.5-10 GHz, giving added versatility to our fixed field portable DNP system. In addition, a field adjustable Halbach permanent magnet has also been employed as another means for matching the electron spin resonance condition. Both portable setups provide large signal enhancements and with improvements in design and engineering, greater than 100-fold 1H enhancements are feasible.

Spin-labeled gel for the production of radical-free dynamic nuclear polarization enhanced molecules for NMR spectroscopy and imaging.

Dynamic nuclear polarization (DNP) has recently received much attention as a viable approach to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and the contrast of magnetic resonance imaging (MRI), where the significantly higher electron spin polarization of stable radicals is transferred to nuclear spins. In order to apply DNP-enhanced NMR and MRI signal to biological and in vivo systems, it is crucial to obtain highly polarized solution samples at ambient temperatures. As stable radicals are employed as the source for the DNP polarization transfer, it is also crucial that the highly polarized sample lacks residual radical concentration because the polarized molecules will be introduced to a biological system that will be sensitive to the presence of radicals. We developed an agarose-based porous media that is covalently spin-labeled with stable radicals. The loading of solvent accessible radical is sufficiently high and their mobility approximates that in solution, which ensures high efficiency for Overhauser mechanism induced DNP without physically releasing any measurable radical into the solution. Under ambient conditions at 0.35 T magnetic field, we measure the DNP enhancement efficiency of (1)H signal of stagnant and continuously flowing water utilizing immobilized stable nitroxide radicals that contain two or three ESR hyperfine splitting lines and compare them to the performance of freely dissolved radicals.

Increasing the resolution of single pair fluorescence resonance energy transfer measurements in solution via molecular cytometry.

We report a method to increase the resolution of single pair fluorescence resonance energy transfer (spFRET) measurements in aqueous solutions. Solution-based spFRET measurements of fluorescently labeled biological molecules (proteins, RNA, DNA) are often used to obtain histograms of molecular conformation without resorting to sample immobilization. However, for solution-phase spFRET studies, the number of photons detected from a single molecule as it diffuses through an open confocal volume element are quite limited. An "average" transit may yield on the order of 40 photons. Shot noise on the number of detected photons substantially limits the resolution of the measurement. The method reported here uses a hydrodynamically focused sample stream to ensure molecules traverse the full width of an excitation laser beam. This substantially increases the average number of photons detected per molecular transit (approximately 85 photons/molecule), which increases measurement precision. In addition, this method minimizes another source of heterogeneity present in diffusive measures of spFRET: the distribution of paths taken through the excitation laser beam. We demonstrate here using a FRET labeled protein sample (a FynSH3 domain) that superior resolution (a factor of approximately 2) can be obtained via molecular cytometry compared to spFRET measurements based upon diffusion through an open confocal volume element.

Hyperpolarized water as an authentic magnetic resonance imaging contrast agent.

Pure water in a highly (1)H spin-polarized state is proposed as a contrast-agent-free contrast agent to visualize its macroscopic evolution in aqueous media by MRI. Remotely enhanced liquids for image contrast (RELIC) utilizes a (1)H signal of water that is enhanced outside the sample in continuous-flow mode and immediately delivered to the sample to obtain maximum contrast between entering and bulk fluids. Hyperpolarization suggests an ideal contrast mechanism to highlight the ubiquitous and specific function of water in physiology, biology, and materials because the physiological, chemical, and macroscopic function of water is not altered by the degree of magnetization. We present an approach that is capable of instantaneously enhancing the (1)H MRI signal by up to 2 orders of magnitude through the Overhauser effect under ambient conditions at 0.35 tesla by using highly spin-polarized unpaired electrons that are covalently immobilized onto a porous, water-saturated gel matrix. The continuous polarization of radical-free flowing water allowed us to distinctively visualize vortices in model reactors and dispersion patterns through porous media. A (1)H signal enhancement of water by a factor of -10 and -100 provides for an observation time of >4 and 7 s, respectively, upon its injection into fluids with a T(1) relaxation time of >1.5 s. The implications for chemical engineering or biomedical applications of using hyperpolarized solvents or physiological fluids to visualize mass transport and perfusion with high and authentic MRI contrast originating from water itself, and not from foreign contrast agents, are immediate.

Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins.

First raised some 60 years ago, the question of whether chemically denatured proteins are fully unfolded has, in recent years, seen significantly renewed interest. This increased attention has been spurred, in large part, by new spectroscopic and computational approaches that suggest even the most highly denatured polypeptides contain significant residual structure. In contrast, the most recent scattering results uphold the long-standing view that chemically denatured proteins adopt random coil configurations. Here we review the evidence both for and against residual structure in chemically denatured proteins, and attempt to reconcile these seemingly contradictory observations.

Site-specific dimensions across a highly denatured protein; a single molecule study.

Do highly denatured proteins adopt random coil configurations? Here, we address this question by measuring residue-to-residue separations across the denatured FynSH3 domain. Using single-molecule Forster resonance energy transfer techniques, we have collected transfer efficiency probability distributions for dye-labeled, denatured protein. Applying maximum likelihood analysis to the interpretation of these distributions, we have determined the through-space distance between five residue pairs in the protein's guanidine hydrochloride-unfolded and trifluoroethanol-unfolded states. We find that, while the dimensions of the guanidine hydrochloride -unfolded molecule generally coincide with the dimensions predicted for a random coil ensemble, potentially statistically significant deviations from random coil behavior are also evident. These small, site-specific deviations may provide a means of reconciling earlier, scattering-based evidence for the random coil nature of the unfolded state with more site-specific spectroscopic evidence suggesting residual structure. We have also studied the unfolded ensemble populated in 50% trifluoroethanol, a denaturant that induces a highly helical unfolded state. We find that the size and shape of the unfolded ensemble under these conditions is effectively indistinguishable from that populated in guanidinium hydrochloride solutions, suggesting that the gross structure of the denatured state is, perhaps surprisingly, independent of the chemistry of the cosolvent.