Pulsed dipolar EPR spectroscopy offers the ability to measure distances between spin labels in the 1-8 nm distance range. The pulsed EPR technique DEER is particularly useful for highly disordered systems where x-ray crystallography and NMR cannot yet be applied. By modeling the dipolar coupling between two spin labels, we can obtain a distance distribution across the biomolecule. The main disadvantage of DEER is that it is common for experiments to require more than 24 hours of averaging to achieve reasonable signal to noise. In this work, we utilize the recent development of high-speed (>1GHz) DAC boards which now operate at high enough frequencies to offer significant performance increases to pulsed EPR experiments. By using shaped microwave pulses instead of rectangular pulses, one can demonstrate (1) dramatically increased excitation bandwidth, (2) increased selectivity of excitation, and (3) calibration of pulses for resonator bandwidth compensation. We demonstrate the performance improvement of arbitrarily shaped pulses for various pulsed EPR applications on a home-build AWG spectrometer as well as commercial spectrometers. In addition, we apply arbitrarily shaped pulses to study tau protein aggregation, which is involved in Alzheimer’s disease and particularly difficult to study because of its broad distance distribution and short spin-spin relaxation times. Other methods to offer signal to noise improvements to the DEER experiment including denoising and alternative methods for calculating the distance distribution are investigated.

Tau is an intrinsically disordered protein found in neurons that binds and stabilizes microtubules. Under pathological conditions, tau aggregates into amyloid fibrils and this process is central to several neurodegenerative diseases, collectively known as tauopathies. It has been proposed that tau pathology occurs in a "prion-like" mechanism, where pathological tau conformers (termed "seeds" or "strains") recruit native monomeric tau to form amyloid aggregates by templated seeding. Recently, a high-resolution clue that distinct tau strains underpin different tauopathies came to light: tau fibrils isolated from tauopathies were found to have distinct core structures by cryo-electron microscopy. These fibril core structures are unique to and homogeneous within one disease, but typically different between different tauopathies. This dissertation is aimed to answer two key questions, which remain unclear in the current state of knowledge: (1) what are the defining properties or conditions that determine the shape of a fibril (e.g. physicochemical conditions, tau state such as mutations, fragmentation, and/or the presence of cofactors)? (2) What structural properties of the fibril are replicated and propagated in seeding, if at all? This work will guide you through a tour to establish the experimental conditions that enable in vitro tau seeding and use these conditions to gain a molecular understanding of tau structures in seeded fibrils.

Dynamic nuclear polarization (DNP) has re-emerged as a method to increase NMR signal by orders of magnitude in the past two decades. The recent developments in high frequency microwave (μw) sources, instrumentation, and radical synthesis have substantially enhanced the NMR signal at standard NMR fields via polarization transfer from unpaired electron spins to their coupled nuclei. Since the re-emergence of DNP, there has been a four-fold increase in publications associated with DNP compared to its initial discovery in 1953. This immense interest in understanding and optimizing the DNP mechanisms has led to numerous biological-, materials-, and imaging-based applications. However, only a limited set of sample formulations result in reliable and significant enhancement of the NMR signal – primarily nitroxide-based radicals in aqueous solvents. Furthermore, with recent technological developments, NMR spectrometers at magnetic fields > 20 T are now operational, where the standard DNP mechanisms governed by continuous wave μw irradiation, namely the solid-effect and cross-effect become less efficient. In order to broaden the scope of sample formulations and develop DNP methods for high magnetic fields, the underlying electron-nuclear spin dynamics must be better understood. However, there are limited instruments that can simultaneously acquire the spin dynamics of both the electron and nuclear spins under identical experimental conditions due to the instrumental challenges associated with acquiring these spin dynamics. Therefore, the aim of this work is to implement developments on our home-built static 194 GHz DNP system to allow for dual NMR and EPR detection, 2-source electron-electron double resonance, and arbitrary waveform generation. With these improvements, we can gain insight into the DNP mechanisms, how experimental conditions affect them, and explain odd phenomenon in experimental results.

Here this dual-purpose instrument is specifically used to investigate the impact electron-electron (e-e) interactions have on DNP and the underlying spin dynamics. It has previously been assumed that the radicals containing the unpaired electron necessary for DNP were homogeneously distributed through the sample volume; however, we have found that both the solvents’ propensity to form glass polymorphs and the radical type can significantly alter the distribution of mono-radicals throughout the sample. Subsequently, the heterogeneity and clustering of the electron spins will significantly alter the e-e interactions, and therefore, the DNP enhancement and spin dynamics. We find that many e-e interactions (even if they are relatively weak) can cause a significant reduction in nuclear relaxation due to e-e-n mediated relaxation, which allows for a faster build-up of hyperpolarized NMR signal and can decrease acquisition times.

The aim of the work presented here has been to optimize the sensitivity of nuclear magnetic resonance (NMR) through the use of the technique of dynamic nuclear polarization (DNP) and magic angle spinning (MAS). DNP is a technique where the polarization from free electron “DNP agent” can be transferred to hyperfine coupled nuclei through microwave irradiation of the sample. The greatest nuclear polarizations are to be expected when the starting thermal electron and nuclear polarization is maximized by operating MAS at a helium cryogenic temperatures. Through a collaboration with Revolution NMR LLC and Bruker Biospin we have development a Cryo DNP-MAS probe operation at a temperature of 25 K and spin rates of 8 kHz. We have measured the microwave beam transmission through each component of the Cryo DNP-MAS probe and optimized the NMR coil and rotor material to maximize the microwave transmission to the sample. We have found that changing the geometry of the radio frequency NMR coil allowing for greater transmission of microwaves doubled the resulting nuclear signal enhancement.

Much of the current development in DNP has focused on tethered nitroxide radicals as the DNP agents, but the design of potent radicals for DNP, in particular under magic angle spinning (MAS) conditions, is still debated and relies on empirical trial and error as the contributing factors for MAS DNP enhancement are not entirely understood. Significant instrumental effort is needed to measure the electron paramagnetic resonance EPR parameters at magnetic fields of 7 T or greater. This work presents the development of an EPR spectrometer at 7 T in order to measure the electron spin dynamics contribution factors to DNP. We have found that the nuclear depolarization induced by MAS is determined by the spin-lattice relaxation time of the nitroxide DNP agent, and once this depolarization is accounted for different tethered nitroxide radical designs have the same DNP signal enhancement. Finally the signal enhancement capabilities of the Han labs home built DNP system is demonstrated through direct enhancement of aluminum spins on the surface of a mesoporous material targeting catalytically active aluminum spins on the surface. When the nitroxide radical is tailored to have a favorable electrostatic interaction with the surface species, the aluminum NMR signal enhancement can be up to 10 fold.

Solid-state nuclear magnetic resonance (NMR) is an essential tool for the study of biological solids, catalysts, and other functional materials. However, NMR has intrinsically low signal sensitivity and dynamic nuclear polarization (DNP) is one of the most effective approaches to enhance NMR sensitivity. DNP enhances NMR signal sensitivity through transferring the high polarization of electron spins to nuclear spins using microwave (mw) irradiation as a perturbation via different DNP mechanisms. As current DNP efficiency is still far from the theoretical limit (660 for 1H NMR), a major focus in DNP research is to develop methods that can maximize DNP enhancements at conditions germane to solid-state NMR, at high magnetic fields, with fast magic angle spinning (MAS), and under variable temperatures. There are many aspects involved in DNP methods development, including the DNP mechanisms clarification and improvement, instrumentation development, better samples preparation methods, and new data processing techniques.

DNP mechanisms development is one of the most important aspects in the DNP methods development area. Current diagnostics of DNP mostly rely on the analysis of the nuclear spin dynamics as a function of mw irradiation parameters which provides incomplete (sometimes even misleading) insights into the mechanism diagnosis process. With the help of continuous wave and pulsed electron paramagnetic resonance (EPR) spectrometers at various fields (from 0.35 to 7 Tesla) as well as quantum mechanical simulations, I have developed and standardized a workflow to diagnose DNP mechanisms and improve their efficiencies. Using the developed workflow, I have improved the existing Cross Effect (CE) DNP efficiency significantly by rationally tuning the the EPR spectral density of mixed broad (TEMPO) and narrow (Trityl)-line radicals, suggesting a novel polarizing agent design of one Trityl tethered to at least two TEMPO moieties. With the help of this novel workflow, a new truncated CE DNP mechanisms was discovered that has the apparent features of an Overhauser Effect. This discovery not only expanded the scope of the theoretical understanding of DNP mechanisms but also provided a technique to probe paramagnetic materials with very fast electron spin lattice relaxation rates. Furthermore, I have discovered an unexpected 1H Thermal Mixing (TM) DNP mechanism with narrow line radicals Trityl and BDPA, providing a new direction of future DNP radical design utilizing the TM DNP mechanism.

Instrumentation development is another key aspect in the DNP methods development. In this aspect, being able to operate at ultra low temperature (ULT, 100 K) is one of the major challenges. In collaboration with JEOL RESONANCE Inc., Japan and JEOL USA Inc, we have successfully installed the first commercial 14.1 Tesla NMR spectrometer equipped with a closed-cycle helium ULT-MAS system. To demonstrate the feasibility of doing DNP/NMR at ULT using the newly installed system, I conducted a comprehensive NMR characterization of a hydrated [U-13C]alanine standard sample at variable temperatures (25 – 100 K) and different spinning speeds (1.5 – 100 kHz). I confirmed that the 13C CP-MAS NMR of [U-13C]alanine obtained a large sensitivity gain at ULT resulting from the Boltzmann factor, radio frequency circuitry quality factor improvement and the suppression of its methyl group rotation. I further observed that the addition of organic biradicals widely used for CE DNP significantly shortened the 1H T1 spin lattice relaxation time at ULT via the two-electron-one-nucleus triple flip transition, without further broadening the 13C spectral linewidth. My experimental observations suggest that the prospects of DNP/NMR under ULT conditions established with a closed-cycle helium MAS system are bright.

With the DNP mechanisms improvements and instrumentation advancements, I have further applied DNP enhanced NMR to study biological samples as well as inorganic silica nano-particles, where tens to hundreds of DNP enhancements have been achieved in all the tested samples. Preliminary DNP study has already provided unprecedented information of the presence of a minor –Si(OH)3 species in the hydrated natural abundant silica nanoparticle materials. However, the applications of DNP in bio-solid materials need more than sensitivity enhancement, where NMR spectral resolution is another critical factor. To eventually apply DNP in bio-solids, better sample preparation methods to obtain homogeneous Tau amyloid protein fibrils and better data processing using wavelet denoising techniques are underdevelopment.

Hydration water is necessary for protein function. It was long thought that the hydration water was simply an innocent solvent. However, current findings show that water is not an innocent solvent but an active player. It is now thought that hydration water plays a crucial role in biomolecular recognition by mediating the thermodynamic interaction between a protein and its ligand. The current challenge is to measure the hydration water and protein side chain thermodynamical properties.

In this thesis we present site-specific measurements of hydration water motion on an array of biomolecular surfaces. We rationalize the hydration water motion in terms of the biomolecular surface properties. We find that the hydration water surrounding globular proteins contains information about the chemical and geometrical topology of the protein surface. We then present instrumentation developments to the Overhauser dynamic nuclear polarization (ODNP) methodology that made such measurements possible.

We then introduce a new technique to measure the protein dynamic transition site- specifically and thus a new way to probe the coupling between a protein and the sur- rounding hydration water. We present measurements made on a small folded peptide system, the Trp Cage, and find that the hydration water motion and the protein dy- namic transition temperature are homogeneous across the surface of the peptide.

Finally we discuss the development of a high field pulse EPR spectrometer that features arbitrary waveform generation capabilities. We showcase the applicability of this instrument and discuss the applicability of this instrument to the study of protein structure and dynamics.

Tau protein binds and stabilizes microtubules in the neurons of human brain. Its aggregation into amyloid fibrils is a hallmark of Alzheimer’s disease and associated with many other neurodegenerative diseases. Revealing its aggregation mechanism is key to understanding the disease progress and developing therapies. Tau is recently found by us and others to form droplet, a condense, fluidic and dynamic structure resulting from liquid-liquid phase separation of proteins, RNA and other molecules. Droplet has been shown to promote amyloid aggregation of several other neurodegenerative disease-associated proteins including FUS and hnRNPA1. In the case of tau droplet, however, its principles and its relationship with tau aggregation are still unclear. This dissertation will guide you through a tour to build physical models that explain the driving forces of tau forming droplets, and to use these models to inform our new understandings of tau aggregation.

Solid state nuclear magnetic resonance (NMR) is a powerful technique that gives access to molecular structures and dynamics not accessible via other methods. However, the Achilles heal of NMR is the inherently low polarization of nuclei in a magnetic field in temperatures above the milli-Kelvin range, resulting in very poor sensitivity compared to other forms of spectroscopy. Fortunately, the much larger polarization of a paramagnetic electron can be transferred to the nuclei in a process known as dynamic nuclear polarization (DNP). However, the efficiency of state of the art DNP techniques drops of significantly at high magnetic fields $>$5T and fast magic angle spinning (MAS)-- conditions favourable for high resolution NMR spectroscopy. Furthermore the scope of state of the art DNP methodology has been limited to a narrow set of paramagnetic electrons, pulse sequences, and instrumentation, which has limited the widespread applicability of DNP

This dissertation will seek to enhance the efficiency of DNP high magnetic field and fast MAS via electron spin analysis and manipulation of the coupled electron spin network. Advanced DNP instrumentation was also developed and applied to novel DNP systems in an effort to expand the scope of DNP to presently "exotic" paramagnetic systems.

In an effort to rationalize DNP performance of current state of the art DNP radicals, an electron paramagnetic resonance (EPR) case study was undertaken that revealed a previously unknown distribution of magnetic spin-spin exchange coupling. The origin of this distribution was rationalized to be rotamer states via DFT calculations, and its effect on DNP was elucidated via quantum mechanical DNP simulations.

The magnetic properties of the spin system is only half the recipe for DNP, as $\mu$w irradiation of the EPR transitions is also necessary to facilitate polarization transfer. Thus, we have also developed a new method for shaped $\mu$w irradiation to boost the efficiency of DNP under MAS. This technique promises to be even more efficient compared to standard $\mu$w irradiation at higher temperatures, higher magnetic fields, and at higher $\mu$w power as new $\mu$w source technology is developed.

Finally, we have developed a new versatile cryogen free dual EPR/DNP probe for in situ EPR and NMR analysis of non-traditional DNP systems. This probe been designed to provide optimal $\mu$w (EPR) and radiofrequency (NMR) performance simultaneously for a broad range of nuclei and electron centers. This system has been used to analyze and demonstrate DNP between paramagnetic centers of different spin quantum number for the first time, opening up an entirely new avenues of DNP methodology using hetero-spin systems. The versatility of this system also allows testing of novel DNP instrumentation, as well as addition of various capabilities to enable a wide range of magnetic resonance experiments including ENDOR and light activated DNP.

Transmembrane proteins are essential biomolecules that reside in cell membranes and play important roles in biological functions including ion transport, signal transductions, and enzymatic reactions. These proteins are surrounded by a highly heterogeneous environment. They have hydrophilic domains that are exposed to water molecules and solutes in solution and hydrophobic membrane-spanning domains that are embedded within a lipophilic environment. This unique combination of environment around the transmembrane protein is not only required to preserve a proper folding of its structure but can also take part in regulating its functional activity. Due to the complexity of the environment, biophysicists are still developing approaches to elucidate the role of different factors in modulating the function of transmembrane proteins.

This dissertation aims to investigate the influence of environmental factors on the structure and function of transmembrane proteins by studies of Proteorhodopsin (PR), a light-activated proton pump that originated from marine bacteria. PR is an excellent model for studying transmembrane protein function as its proton transport function can be directly assessed by optical absorbance spectroscopic techniques. PR also shares the same seven-helical transmembrane (7TM) structure with a large family of human receptors, which makes the structural knowledge learned from PR studies potentially transferable to other physiologically important transmembrane proteins (e.g. G protein-coupled receptors). On the other hand, PR has excellent robustness and is found to be stable in a variety of environments. This allows it to be studied in environments not limited to native-like bacteria membrane but also other biomimetic platforms with different factors that can be independently controlled. PR also has its significance in protein engineering applications. The proton motive force generated by PR through its vectorial proton transport can be utilized as an approach to harvest solar energy. All these together make the studies of PR appeal to objectives of both fundamental biophysical understanding and bioengineering applications on transmembrane proteins.

To achieve our objectives, the functions of PR under the influences of different modulators are examined in biomimetic environments including synthetic liposomes, lipid nanodiscs, and synthetic host materials. With controls over the surrounding lipid composition and the oligomeric distribution of PR between its monomeric and oligomeric forms, we identify that protein-protein interaction (i.e. the formation of oligomers) is a key factor to determine the proton transport kinetic of PR. Nevertheless, in the lipid membrane environment, the protein-protein interaction shows no impact on the protonation behavior of PR’s embedded ionizable amino acid D97, a switch that controls the population of active PR with proton transport capability. Instead, we find that the electrostatic environment around PR (e.g. the ion type or concentration in the buffer and the net charge of lipid headgroups) can significantly modulate the pKa of this embedded D97 (pKaD97), and in turn affects the population of active PR. Most importantly, the same concept is found to be transferable to PR reconstituted in synthetic host materials with increased thermal and mechanical stability for bioengineering applications.

To further understand the correlation between the structure and function of transmembrane proteins, complementary magnetic resonance spectroscopic tools were used to acquire the structure of PR with different functional outcomes. This dissertation interrogates the structural rearrangement of PR associated with the pKaD97 modulation by different electrostatic environments. Local conformation changes at the third intracellular loop of PR are uncovered by using electron paramagnetic resonance (EPR) analysis and Overhauser dynamic nuclear polarization (ODNP) relaxometry through a change of local environment experienced by a site-directly introduced spin label on the loop. Moreover, by conducting dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (ssNMR) measurements on PR either site-specifically or uniformly labeled with NMR active nuclei, we identify the residues that rearranged while PR is in different electrostatic environments. On the other hand, to have a structural-based understanding of the functional impact of oligomerization, this dissertation also seeks to develop a novel approach to map out the structural rearrangement of PR activation by high field EPR spectroscopy with Gadolinium-based spin labels. The study of PR provides an opportunity of directly correlating the measured structural dynamics with the kinetics of proton transport function measured by its transient absorbance change.

Altogether, PR studies presented here elucidate the roles of oligomerization in modulating its proton transport function and underscore the importance of the biomimetic environment on affecting the function of transmembrane proteins. For bioengineering and biomedical applications relying on transmembrane protein systems, this dissertation offers a guideline for optimizing functions of proteins that are controlled by a similar mechanism as PR. Furthermore, the change of structural properties observed here by magnetic resonance tools from PR with different functional outcomes adds value to biophysical understandings on the relationship between structure and function of transmembrane proteins that share a similar structure as PR.

The aggregation of the human tau protein is heavily implicated in the progression of Alzhiemer’s Disease. In this study we examined the aggregation kinetics of a truncated segment of the longest tau isoform, Tau 187, and induced aggregation with the polyanion hepain. We applied cw-EPR in order to quantitatively measure the population of tau embedded in parallel β-sheet structure and compared these measurements to traditional kinetic measurement techniques, Tht fluorescence and turbidity. Cw-EPR revealed rapid formation of parallel β-sheet structure early in the aggregation process well before fibrils are thought to appear. We observe a large population of spins first exhibits reduced mobility upon mixing with heparin, which is later followed by an increase in β-sheet structure consistent with proposed models of nucleation followed by structural rearrangement. Additionally, comparing cw-EPR with Tht fluorescence demonstrates Tht binding is non-linear with respect to parallel β-sheet structure and the precise binding structure of Tht remains unclear.

The transfer of tau pathology from infected to healthy cells has been well established by the literature, however, little is known about the relationship between seed structure and seeding efficacy. Here we investigated the importance of β-sheet content as detected by cw-EPR on seeding efficacy, but were unable to establish a relationship due to the overriding effect of heparin. Previously our group has observed a conformational shift around the PHF6* hexapeptide from compact to extended state and we examined the stoichiometric effect of heparin on this extension to determine the potency of heparin for inducing changes in the tau system. Finally, dependence of tau aggregation kinetics on heparin stoichiometry was investigated. We discovered the extent of observable distance change depended on heparin stoichiometry, however, even dilute quantities of heparin are able to induce significant extension around the PHF6* hexapeptide. The amount of total fibril formation was also found to depend on the heparin stoichiometry with lower heparin concentrations generating less total fibril content. Our findings suggests even minute quantities of heparin exerts great influence on the tau system and future work will require ways of working around or limiting heparin’s influence in order to directly probe the underlying fundamentals of tau aggregation.