Exploring weak ligand-protein interactions by relaxometry of long-lived spin order

Relaxation times of nuclear spins often serve as a valuable source of information on the dynamics of various biochemical processes. Measuring relaxation as a function of the external magnetic field turned out to be extremely useful for the studies of weak ligand-protein interactions. We demonstrate that observing the relaxation of the long-lived spin order instead of longitudinal magnetization extends the capability of this approach. We studied the field-dependent relaxation of the longitudinal magnetization and the singlet order (SO) of methylene protons in alanine-glycine dipeptide and citrate in the presence of human serum albumin (HSA). As a result, SO relaxation proved to be more sensitive to ligand-protein interaction, providing higher relaxation contrast for various HSA concentrations. To assess the parameters of the binding process in more details, we utilized a simple analytical relaxation model to fit the experimental field dependences for both SO and T1 relaxation. We also tested the validity of our approach in the experiments with trimethylsilylpropanoic acid (TSP) used as a competitor in ligand binding with HSA.

Rapid and Simple 13C-Hyperpolarization by 1H Dissolution Dynamic Nuclear Polarization Followed by an Inline Magnetic Field Inversion

Dissolution dynamic nuclear polarization (dDNP) is a method of choice for preparing hyperpolarized 13C metabolites such as 1-13C-pyruvate used for in vivo applications, including the real-time monitoring of cancer cell metabolism in human patients. The approach consists of transferring the high polarization of electron spins to nuclear spins via microwave irradiation at low temperatures (1.0-1.5 K) and moderate magnetic fields (3.3-7 T). The solid sample is then dissolved and transferred to an NMR spectrometer or MRI scanner for detection in the liquid state. Common dDNP protocols use direct hyperpolarization of 13C spins reaching polarizations of >50% in ∼1-2 h. Alternatively, 1H spins are polarized before transferring their polarization to 13C spins using cross-polarization, reaching polarization levels similar to those of direct DNP in only ∼20 min. However, it relies on more complex instrumentation, requiring highly skilled personnel. Here, we explore an alternative route using 1H dDNP followed by inline adiabatic magnetic field inversion in the liquid state during the transfer. 1H polarizations of >70% in the solid state are obtained in ∼5-10 min. As the hyperpolarized sample travels from the dDNP polarizer to the NMR spectrometer, it goes through a field inversion chamber, which causes the 1H → 13C polarization transfer. This transfer is made possible by the J-coupling between the heteronuclei, which mixes the Zeeman states at zero-field and causes an antilevel crossing. We report liquid-state 13C polarization up to ∼17% for 3-13C-pyruvate and 13C-formate. The instrumentation needed to perform this experiment in addition to a conventional dDNP polarizer is simple and readily assembled.

Clinically Translatable Hyperpolarized 13C Bicarbonate pH Imaging Method for Use in Prostate Cancer

Solid tumors such as prostate cancer (PCa) commonly develop an acidic microenvironment with pH 6.5-7.2, owing to heterogeneous perfusion, high metabolic activity, and rapid cell proliferation. In preclinical prostate cancer models, disease progression is associated with a decrease in tumor extracellular pH, suggesting that pH imaging may reflect an imaging biomarker to detect aggressive and high-risk disease. Therefore, we developed a hyperpolarized carbon-13 MRI method to image the tumor extracellular pH (pHe) and prepared it for clinical translation for detection and risk stratification of PCa. This method relies on the rapid breakdown of hyperpolarized (HP) 1,2-glycerol carbonate (carbonyl-13C) via base-catalyzed hydrolysis to produce HP 13CO32-, which is neutralized and converted to HP H13CO3-. After injection, HP H13CO3- equilibrates with HP 13CO2 in vivo and enables the imaging of pHe. Using insights gleaned from mechanistic studies performed in the hyperpolarized state, we solved issues of polarization loss during preparation in a clinical polarizer system. We successfully customized a reaction apparatus suitable for clinical application, developed clinical standard operating procedures, and validated the radiofrequency pulse sequence and imaging data acquisition with a wide range of animal models. The results demonstrated that we can routinely produce a highly polarized and safe HP H13CO3- contrast agent suitable for human injection. Preclinical imaging studies validated the reliability and accuracy of measuring acidification in healthy kidney and prostate tumor tissue. These methods were used to support an Investigational New Drug application to the U.S. Food and Drug Administration. This methodology is now ready to be implemented in human trials, with the ultimate goal of improving the management of PCa.

Fingerprinting and profiling in metabolomics of biosamples

This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.

Paramagnetic relaxivity of delocalized long-lived states of protons in chains of CH2 groups

Long-lived states (LLSs) have lifetimes T LLS that can be much longer than longitudinal relaxation times T 1 . In molecules containing several geminal pairs of protons in neighboring CH2 groups, it has been shown that delocalized LLSs can be excited by converting magnetization into imbalances between the populations of singlet and triplet states of each pair. Since the empirical yield of the conversion and reconversion of observable magnetization into LLSs and back is on the order of 10 % if one uses spin-lock induced crossing (SLIC), it would be desirable to boost the sensitivity by dissolution dynamic nuclear polarization (d-DNP). To enhance the magnetization of nuclear spins by d-DNP, the analytes must be mixed with radicals such as 4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPOL). After dissolution, these radicals lead to an undesirable paramagnetic relaxation enhancement (PRE) which shortens not only the longitudinal relaxation times T 1 but also the lifetimes T LLS of LLSs. It is shown in this work that PRE by TEMPOL is less deleterious for LLSs than for longitudinal magnetization for four different molecules: 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), homotaurine, taurine, and acetylcholine. The relaxivities r LLS (i.e., the slopes of the relaxation rate constants R LLS as a function of the radical concentration) are 3 to 5 times smaller than the relaxivities r 1 of longitudinal magnetization. Partial delocalization of the LLSs across neighboring CH2 groups may decrease this advantage, but in practice, this effect was observed to be small, for example, when comparing taurine containing two CH2 groups and homotaurine with three CH2 groups. Regardless of whether the LLSs are delocalized or not, it is shown that PRE should not be a major problem for experiments combining d-DNP and LLSs, provided the concentration of paramagnetic species after dissolution does not exceed 1 mM, a condition that is readily fulfilled in typical d-DNP experiments. In bullet d-DNP experiments however, it may be necessary to decrease the concentration of TEMPOL or to add ascorbate for chemical reduction.

Frémy’s Salt as a Low-Persistence Hyperpolarization Agent: Efficient Dynamic Nuclear Polarization Plus Rapid Radical Scavenging

Nuclear magnetic resonance (NMR) spectroscopy is a key technique for molecular structure determination in solution. However, due to its low sensitivity, many efforts have been made to improve signal strengths and reduce the required substrate amounts. In this regard, dissolution dynamic nuclear polarization (DDNP) is a versatile approach as signal enhancements of over 10 000-fold are achievable. Samples are signal-enhanced ex situ by transferring electronic polarization from radicals to nuclear spins before dissolving and shuttling the boosted sample to an NMR spectrometer for detection. However, the applicability of DDNP suffers from one major drawback, namely, paramagnetic relaxation enhancements (PREs) that critically reduce relaxation times due to the codissolved radicals. PREs are the primary source of polarization losses canceling the signal improvements obtained by DNP. We solve this problem by using potassium nitrosodisulfonate (Frémy’s salt) as polarization agent (PA), which provides high nuclear spin polarization and allows for rapid scavenging under mild reducing conditions. We demonstrate the potential of Frémy’s salt, (i) showing that both ¹H and ¹³C polarization of ∼30% can be achieved and (ii) describing a hybrid sample shuttling system (HySSS) that can be used with any DDNP/NMR combination to remove the PA before NMR detection. This gadget mixes the hyperpolarized solution with a radical scavenger and injects it into an NMR tube, providing, within a few seconds, quantitatively radical-free, highly polarized solutions. The cost efficiency and broad availability of Frémy’s salt might facilitate the use of DDNP in many fields of research.

Inversion of Hyperpolarized 13C NMR Signals through Cross-Correlated Cross-Relaxation in Dissolution DNP Experiments

Dissolution dynamic nuclear polarization (DDNP) is a versatile tool to boost signal amplitudes in solution-state nuclear magnetic resonance (NMR) spectroscopy. For DDNP, nuclei are spin-hyperpolarized "ex situ" in a dedicated DNP device and then transferred to an NMR spectrometer for detection. Dramatic signal enhancements can be achieved, enabling shorter acquisition times, real-time monitoring of fast reactions, and reduced sample concentrations. Here, we show how the sample transfer in DDNP experiments can affect NMR spectra through cross-correlated cross-relaxation (CCR), especially in the case of low-field passages. Such processes can selectively invert signals of ¹³C spins in proton-carrying moieties. For their investigations, we use schemes for simultaneous or "parallel" detection of hyperpolarized ¹H and ¹³C nuclei. We find that ¹H → ¹³C CCR can invert signals of ¹³C spins if the proton polarization is close to 100%. We deduce that low-field passage in a DDNP experiment, a common occurrence due to the introduction of so-called "ultra-shielded" magnets, accelerates these effects due to field-dependent paramagnetic relaxation enhancements that can influence CCR. The reported effects are demonstrated for various molecules, laboratory layouts, and DDNP systems. As coupled ¹³C-¹H spin systems are ubiquitous, we expect similar effects to be observed in various DDNP experiments. This might be exploited for selective spectroscopic labeling of hydrocarbons.

Hyperpolarized water as universal sensitivity booster in biomolecular NMR

NMR spectroscopy is the only method to access the structural dynamics of biomolecules at high (atomistic) resolution in their native solution state. However, this method's low sensitivity has two important consequences: (i) typically experiments have to be performed at high concentrations that increase sensitivity but are not physiological, and (ii) signals have to be accumulated over long periods, complicating the determination of interaction kinetics on the order of seconds and impeding studies of unstable systems. Both limitations are of equal, fundamental relevance: non-native conditions are of limited pharmacological relevance, and the function of proteins, enzymes and nucleic acids often relies on their interaction kinetics. To overcome these limitations, we have developed applications that involve 'hyperpolarized water' to boost signal intensities in NMR of proteins and nucleic acids. The technique includes four stages: (i) preparation of the biomolecule in partially deuterated buffers, (ii) preparation of 'hyperpolarized' water featuring enhanced ¹H NMR signals via cryogenic dynamic nuclear polarization, (iii) sudden melting of the cryogenic pellet and dissolution of the protein or nucleic acid in the hyperpolarized water (enabling spontaneous exchanges of protons between water and target) and (iv) recording signal-amplified NMR spectra targeting either labile ¹H or neighboring ¹⁵N/¹³C nuclei in the biomolecule. Water in the ensuing experiments is used as a universal 'hyperpolarization' agent, rendering the approach versatile and applicable to any biomolecule possessing labile hydrogens. Thus, questions can be addressed, ranging from protein and RNA folding problems to resolving structure-function relationships of intrinsically disordered proteins to investigating membrane interactions.

Practical dissolution dynamic nuclear polarization

This review article intends to provide insightful advice for dissolution-dynamic nuclear polarization in the form of a practical handbook. The goal is to aid research groups to effectively perform such experiments in their own laboratories. Previous review articles on this subject have covered a large number of useful topics including instrumentation, experimentation, theory, etc. The topics to be addressed here will include tips for sample preparation and for checking sample health; a checklist to correctly diagnose system faults and perform general maintenance; the necessary mechanical requirements regarding sample dissolution; and aids for accurate, fast and reliable polarization quantification. Herein, the challenges and limitations of each stage of a typical dissolution-dynamic nuclear polarization experiment are presented, with the focus being on how to quickly and simply overcome some of the limitations often encountered in the laboratory.

Nuclear singlet relaxation by chemical exchange

The population imbalance between nuclear singlet states and triplet states of strongly coupled spin-1/2 pairs, also known as nuclear singlet order, is well protected against several common relaxation mechanisms. We study the nuclear singlet relaxation of ¹³C pairs in aqueous solutions of 1,2-¹³C₂ squarate over a range of pH values. The ¹³C singlet order is accessed by introducing ¹⁸O nuclei in order to break the chemical equivalence. The squarate dianion is in chemical equilibrium with hydrogen-squarate (SqH^-) and squaric acid (SqH₂) characterized by the dissociation constants pK₁ = 1.5 and pK₂ = 3.4. Surprisingly, we observe a striking increase in the singlet decay time constants T_S when the pH of the solution exceeds ∼10, which is far above the acid-base equilibrium points. We derive general rate expressions for chemical-exchange-induced nuclear singlet relaxation and provide a qualitative explanation of the T_S behavior of the squarate dianion. We identify a kinetic contribution to the singlet relaxation rate constant, which explicitly depends on kinetic rate constants. Qualitative agreement is achieved between the theory and the experimental data. This study shows that infrequent chemical events may have a strong effect on the relaxation of nuclear singlet order.

Use of dissolved hyperpolarized species in NMR: Practical considerations

Hyperpolarization techniques that can transiently boost nuclear spin polarization are generally carried out at low temperature - as in the case of dynamic nuclear polarization - or at high temperature in the gaseous state - as in the case of optically pumped noble gases. This review aims at describing the various issues and challenges that have been encountered during dissolution of hyperpolarized species, and solutions to these problems that have been or are currently proposed in the literature. During the transport of molecules from the polarizer to the NMR detection region, and when the hyperpolarized species or a precursor of hyperpolarization (e.g. parahydrogen) is introduced into the solution of interest, several obstacles need to be overcome to keep a high level of final magnetization. The choice of the magnetic field, the design of the dissolution setup, and ways to isolate hyperpolarized compounds from relaxation agents will be presented. Due to the non-equilibrium character of the hyperpolarization, new NMR pulse sequences that perform better than the classical ones will be described. Finally, three applications in the field of biology will be briefly mentioned.

Spin Thermometry: A Straightforward Measure of Millikelvin Deuterium Spin Temperatures Achieved by Dynamic Nuclear Polarization

Dynamic nuclear polarization of samples at low temperatures, typically between 1.2 and 4.2 K, allows one to achieve spin temperatures of as low as 2 mK so that for many nuclear isotopes the high-temperature approximation is violated for the nuclear Zeeman interaction. This leads to characteristic asymmetries in powder spectra. We show that the line shapes due to the quadrupolar couplings of deuterium spins present in virtually all solvents used for such experiments (DNP juice) allow the quick yet accurate determination of the deuterium spin temperature or, equivalently, the deuterium polarization. The observation of quadrupolar echoes excited by small flip-angle pulses allows one to monitor the build-up and decay of the positive or negative deuterium polarization.

Generalised magnetisation-to-singlet-order transfer in nuclear magnetic resonance

A variety of pulse sequences have been described for converting nuclear spin magnetisation into long-lived singlet order for nuclear spin-1/2 pairs. Existing sequences operate well in two extreme parameter regimes. The magnetisation-to-singlet (M2S) pulse sequence performs a robust conversion of nuclear spin magnetisation into singlet order in the near-equivalent limit, meaning that the difference in chemical shift frequencies of the two spins is much smaller than the spin-spin coupling. Other pulse sequences operate in the strong-inequivalence regime, where the shift difference is much larger than the spin-spin coupling. However both sets of pulse sequences fail in the intermediate regime, where the chemical shift difference and the spin-spin coupling are roughly equal in magnitude. We describe a generalised version of M2S, called gM2S, which achieves robust singlet order excitation for spin systems ranging from the near-equivalence limit well into the intermediate regime. This closes an important gap left by existing pulse sequences. The efficiency of the gM2S sequence is demonstrated numerically and experimentally for near-equivalent and intermediate-regime cases.

Experimental evidence for the role of paramagnetic oxygen concentration on the decay of long-lived nuclear spin order

The sensitivity of longitudinal magnetization and singlet order to relaxation from dissolved paramagnetic oxygen sources in solution is investigated experimentally.