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.

Reduction of transient carnosine radicals depends on ß-alanyl amino group charge.

Reduction of transient carnosine (ß-alanyl-L-histidine) radicals by L-tryptophan, N-acetyl tryptophan, and the Trp-Gly peptide in neutral and basic aqueous solutions was studied using the technique of time-resolved chemically induced dynamic nuclear polarization (TR CIDNP). Carnosine radicals were generated in the photoinduced reaction with triplet excited 3,3',4,4'-tetracarboxy benzophenone. In this reaction, carnosine radicals with their radical center at the histidine residue are formed. Modeling of CIDNP kinetic data allowed for the determination of pH-dependent rate constants of the reduction reaction. It was shown that the protonation state of the amino group of the non-reacting ß-alanine residue of the carnosine radical affects the rate constant of the reduction reaction. The results were compared to those obtained previously for the reduction of histidine and N-acetyl histidine free radicals and to newly obtained results for the reduction of radicals derived from Gly-His, a homologue of carnosine. Clear differences were demonstrated.

Quantitative analysis of cross-talk in partly deuterated samples of nuclear spins hyperpolarized by dynamic nuclear polarization (DNP) in the thermal mixing regime.

Dynamical nuclear polarization (DNP) is a powerful method that allows one to polarize virtually any spin-bearing nucleus by transferring electron polarization by microwave irradiation of the electron Zeeman transitions. Under certain conditions, the DNP process can be described in thermodynamical terms using the thermal mixing (TM) model. Different nuclear species can exchange energy indirectly through their interactions with the electron spins and reach a common spin temperature. Such "cross-talk" effects can occur between proton (H) and deuterium (D) nuclei in de- and re-polarization experiments. In this work, we investigate such effects experimentally, using either protonated or deuterated TEMPOL radicals as polarizing agents. An analysis of these experiments based on Provotorov's equations allows one to extract the relevant kinetic parameters, such as the rates of energy transfer between the different reservoirs, and the heat capacity of the non-Zeeman (NZ) electron reservoir, while the heat capacities of the proton and deuterium reservoirs can be estimated based on their usual expressions. These parameters allow one to make predictions of the behaviour of heteronuclei such as carbon-13 or phosphorous-31, provided that their heat capacities are negligible. Finally, we present an experimental study of the dependence of Provotorov's kinetic parameters on the TEMPOL concentration and on the H/D ratio, thus providing insight into the nature of "hidden" spins that are not observable directly because of their proximity to the radicals.

Marcus Cross-Relationship Probed by Time-Resolved CIDNP.

The time-resolved CIDNP method can provide information about degenerate exchange reactions (DEEs) involving short-lived radicals. In the temperature range from 8 to 65 °C, the DEE reactions of the guanosine-5'-monophosphate anion GMP(-H)- with the neutral radical GMP(-H)•, of the N-acetyl tyrosine anion N-AcTyrO- with a neutral radical N-AcTyrO•, and of the tyrosine anion TyrO- with a neutral radical TyrO• were studied. In all the studied cases, the radicals were formed in the reaction of quenching triplet 2,2'-dipyridyl. The reorganization energies were obtained from Arrhenius plots. The rate constant of the reductive electron transfer reaction in the pair GMP(-H)•/TyrO- was determined at T = 25 °C. Rate constants of the GMP(-H)• radical reduction reactions with TyrO- and N-AcTyrO- anions calculated by the Marcus cross-relation differ from the experimental ones by two orders of magnitude. The rate constants of several other electron transfer reactions involving GMP(-H)-/GMP(-H)•, N-AcTyrO-/N-AcTyrO•, and TyrO-/TyrO• pairs calculated by cross-relation agree well with the experimental values. The rate of nuclear paramagnetic relaxation was found for the 3,5 and ß-protons of TyrO• and N-AcTyrO•, the 8-proton of GMP(-H)•, and the 3,4-protons of DPH• at each temperature. In all cases, the dependences of the rate of nuclear paramagnetic relaxation on temperature are described by the Arrhenius dependence.

Heavily Gd-Doped Non-Toxic Cerium Oxide Nanoparticles for MRI Labelling of Stem Cells.

Recently, human mesenchymal stem cells (hMSc) have attracted a great deal of attention as potential therapeutic agents in the treatment of socially significant diseases. Despite substantial advances in stem-cell therapy, the biological mechanisms of hMSc action after transplantation remain unclear. The use of magnetic resonance imaging (MRI) as a non-invasive method for tracking stem cells in the body is very important for analysing their distribution in tissues and organs, as well as for ensuring control of their lifetime after injection. Herein, detailed experimental data are reported on the biocompatibility towards hMSc of heavily gadolinium-doped cerium oxide nanoparticles (Ce0.8Gd0.2O2-x) synthesised using two synthetic protocols. The relaxivity of the nanoparticles was measured in a magnetic field range from 1 mT to 16.4 T. The relaxivity values (r1 = 11 ± 1.2 mM-1 s-1 and r1 = 7 ± 1.2 mM-1 s-1 in magnetic fields typical of 1.5 and 3 T MRI scanners, respectively) are considerably higher than those of the commercial Omniscan MRI contrast agent. The low toxicity of gadolinium-doped ceria nanoparticles to hMSc enables their use as an effective theranostic tool with improved MRI-contrasting properties.

Unravelling structures of radicals of kynurenic acid formed in the photoinduced reactions with tryptophan and N-acetyl tyrosine.

Kynurenic acid (KNA) in the triplet state reacts with tryptophan (Trp) at neutral pH via proton-coupled electron transfer (PCET), which includes the stepwise transition of both electron and proton from Trp to triplet KNA. In the case of tyrosine (Tyr), the quenching reaction is H-transfer, a simultaneous transfer of electron and proton. In this work, we used the time-resolved chemically induced dynamic nuclear polarization (TR CIDNP) method to unveil the sites of H/H+ transfer within KNA. For this purpose, we obtained the values of 1H hyperfine coupling constants (HFCCs) and g-factors for different tautomeric forms of KNA radicals by the DFT method, then calculated CIDNP intensities using these g-factors and HFCCs according to the Adrian model. The calculated CIDNP intensities for different protons were correlated with their CIDNP intensities in the geminate spectra detected in the photoreactions of KNA with Trp, N-acetyl Trp, and N-acetyl Tyr. Best-fit proportionality relationships between calculated and experimental CIDNP intensities have shown that the KNA anion radical is present in two of the three possible tautomeric forms, which result from the H/H+ movement to the carbonyl oxygen of keto- and oxo-quinolinate forms of KNA, without any visible contribution of the H/H+ transfer to the nitrogen of the enol form. For 4-hydroxyquinoline (4HQN), being the chromophoric core of KNA and exhibiting the same PCET and H-transfer reactions with Trp and Tyr, a single possible tautomeric form of its radical has been revealed as H/H+ transfer to the carbonyl oxygen of the keto-form.

Polarizing insensitive nuclei at ultralow magnetic fields using parahydrogen: A facile route to optimize adiabatic magnetic field sweeps.

Parahydrogen induced polarization (PHIP) provides a powerful tool to enhance inherently weak nuclear magnetic resonance signals, particularly in biologically relevant compounds. The initial source of PHIP is the non-equilibrium spin order of parahydrogen, i.e., dihydrogen, where the two protons make up a singlet spin state. Conversion of this spin order into net magnetization of magnetic heteronuclei, e.g., 13C, provides one of the most efficient ways to exploit PHIP. We propose a facile route to increase the performance of PHIP transfer in experiments with adiabatic sweeps of the ultralow magnetic field. To date, this technique yields the highest efficiency of PHIP transfer, yet, it has been mostly utilized with linear field sweeps, which does not consider the underlying spin dynamics, resulting in sub-optimal polarization. This issue was previously addressed by using the "constant" adiabaticity method, which, however, requires extensive calculations for large spin systems. In this work, the field sweep is optimized by utilizing the field dependence of the average 13C polarization. Both the experimental detection and the numerical simulation of this dependence are straightforward, even for complex multi-spin systems. This work provides a comprehensive survey of PHIP transfer dynamics at ultralow fields for two molecular systems that are relevant for PHIP, namely, maleic acid and allyl pyruvate. The proposed optimization allowed us to increase the resulting 13C polarization in 13C-allyl pyruvate from 6.8% with a linear profile to 8.7% with an "optimal" profile. Such facile optimization routines are valuable for adiabatic experiments in complex spin systems undergoing rapid relaxation or chemical exchange.

Parahydrogen-Induced Hyperpolarization of Unsaturated Phosphoric Acid Derivatives.

Parahydrogen-induced nuclear polarization offers a significant increase in the sensitivity of NMR spectroscopy to create new probes for medical diagnostics by magnetic resonance imaging. As precursors of the biocompatible hyperpolarized probes, unsaturated derivatives of phosphoric acid, propargyl and allyl phosphates, are proposed. The polarization transfer to 1H and 31P nuclei of the products of their hydrogenation by parahydrogen under the ALTADENA and PASADENA conditions, and by the PH-ECHO-INEPT+ pulse sequence of NMR spectroscopy, resulted in a very high signal amplification, which is among the largest for parahydrogen-induced nuclear polarization transfer to the 31P nucleus.

15 N SABRE Hyperpolarization of Metronidazole at Natural Isotope Abundance.

Signal Amplification By Reversible Exchange (SABRE) is gaining increased attention as a tool to enhance weak Nuclear Magnetic Resonance (NMR) signals. In SABRE, spin order is transferred from parahydrogen (H2 in its nuclear singlet spin state) to a substrate molecule in a transient Ir-based complex. In recent years, SABRE polarization of biologically active substrates has been demonstrated, notably of metronidazole - an antibiotic and antiprotozoal drug. In this work, we study 15 N SABRE polarization of metronidazole at natural isotope abundance. We are able to demonstrate significant 15 N polarization reaching 15 %, which corresponds to a signal enhancement of 46,000 at 9.4 T for the nitrogen atom with lone electron pair. Additionally, the other two N-atoms can be polarized, although less efficiently. We present a detailed study of the field dependence of polarization and explain the maxima in the field dependence using the concept of coherent polarization transfer at level anti-crossings in the SABRE complex. A study of spin relaxation phenomena presented here enables optimization of the magnetic field for efficient storage of non-thermal polarization.

Hyperpolarization of cis-15 N2 -Azobenzene by Parahydrogen at Ultralow Magnetic Fields*.

The development of nuclear spins hyperpolarization, and the search for molecules that can be efficiently hyperpolarized is an active area in nuclear magnetic resonance. In this work we present a detailed study of SABRE SHEATH (signal amplification by reversible exchange in shield enabled alignment transfer to heteronuclei) experiments on 15 N2 -azobenzene. In SABRE SHEATH experiments the nuclear spins of the target are hyperpolarized through transfer of spin polarization from parahydrogen at ultralow fields during a reversible chemical process. Azobenzene exists in two isomers, trans and cis. We show that all nuclear spins in cis-azobenzene can be efficiently hyperpolarized by SABRE at suitable magnetic fields. Enhancement factors (relative to 9.4 T) reach up to 3000 for 15 N spins and up to 30 for the 1 H spins. We compare two approaches to observe either hyperpolarized magnetization of 15 N/1 H spins, or hyperpolarized singlet order of the 15 N spin pair. The results presented here will be useful for further experiments in which hyperpolarized cis-15 N2 -azobenzene is switched by light to trans-15 N2 -azobenzene for storing the produced hyperpolarization in the long-lived spin state of the 15 N pair of trans-15 N2 -azobenzene.

Reduction of transient histidine radicals by tryptophan: influence of the amino group charge.

Second-order rate constants of the reduction of histidine radicals by tryptophan were obtained for all combinations of the two amino acids and their N-acetyl derivatives. For the dipeptide N-acetyl histidine-tryptophan, contributions from inter- and intramolecular reduction were revealed. The pH dependences of the rate constants were found to be determined by the protonation state of the amino group of tryptophan. Proton coupled electron transfer is proposed as a reaction mechanism.

Kynurenic acid and its chromophoric core 4-hydroxyquinoline react with tryptophan via proton-coupled electron transfer, and with tyrosine via H-transfer.

Kynurenic acid (KNA) and 4-hydroxyquinoline (4HQN) are photochemically active products of tryptophan catabolism that readily react with tryptophan (Trp) and tyrosine (Tyr) after optical excitation. Recently, transient absorption experiments have shown that at neutral pH Trp reacts with triplet KNA via proton-coupled electron transfer (PCET), and not via electron transfer (ET) as it was suggested before. PCET includes the stepwise transition of both electrons and protons from Trp to triplet KNA. In this work, we confirmed that PCET is the reaction mechanism by the alternative method of time-resolved chemically induced dynamic nuclear polarization (TR-CIDNP). Further studies by TR-CIDNP revealed hydrogen transfer as the mechanism of the reaction between triplet KNA and Tyr in neutral solutions and a transition of both PCET and H-transfer mechanisms to ET under acidic conditions. 4HQN, being the chromophoric core of KNA, exhibits different spectral and photophysical properties from KNA but employs the same mechanisms for the reactions of its triplet state with Trp and Tyr at neutral and acidic pH.

Kinetic evidence for the transiently shifted acidity constant of histidine linked to paramagnetic tyrosine probed by intramolecular electron transfer in oxidized peptides.

The kinetics of electron transfer (ET) from tyrosine (Tyr) to short-lived histidine (His) radicals in peptides of different structures was monitored using time-resolved chemically induced dynamic nuclear polarization (CIDNP) to follow the reduction of the His radicals using NMR detection of the diamagnetic hyperpolarized reaction products. In aqueous solution over a wide pH range, His radicals were generated in situ in the photo-induced reaction with the photosensitizer, 3,3',4,4'-tetracarboxy benzophenone. Model simulations of the CIDNP kinetics provided pH-dependent rate constants of intra- and intermolecular ET, and the pH dependencies of the reaction under study were interpreted in terms of protonation states of the reactants and the product, His with either protonated or neutral imidazole. In some cases, an increase of pKa of imidazole in the presence of the short-lived radical center at a nearby Tyr residue was revealed. Interpretation of the obtained pH dependencies made is possible to quantify the degree of paramagnetic shift of the acidity constant of the imidazole of the His residue in the peptides with a Tyr residue in its paramagnetic state, and to correlate this degree with the intramolecular ET rate constant - a higher intramolecular ET rate constant corresponded to a greater acidity constant shift.

Sequential assignment of NMR spectra of peptides at natural isotopic abundance with zero- and ultra-low-field total correlation spectroscopy (ZULF-TOCSY).

A novel method dubbed ZULF-TOCSY results from the combination of Zero and Ultra-Low Field (ZULF) with high-field, high-resolution NMR, leading to a generalization of the concept of total correlation spectroscopy (TOCSY). ZULF-TOCSY is a new building block for NMR methods, which has the unique property that the polarization is evenly distributed among all NMR-active nuclei such as 1H, 13C, 15N, 31P, etc., provided that they belong to the same coupling network, and provided that their relaxation is not too fast at low fields, as may occur in macromolecules. Here, we show that ZULF-TOCSY correlations can be observed for peptides at natural isotopic abundance, such as the protected hexapeptide Boc-Met-enkephalin. The analysis of ZULF-TOCSY spectra readily allows one to make sequential assignments, thus offering an alternative to established heteronuclear 2D experiments like HMBC. For Boc-Met-enkephalin, we show that ZULF-TOCSY allows one to observe all expected cross-peaks between carbonyl carbons and α-CH protons, while the popular HMBC method provides insufficient information.

Singlet to triplet conversion in molecular hydrogen and its role in parahydrogen induced polarization.

Detailed experimental and comprehensive theoretical analysis of singlet-triplet conversion in molecular hydrogen dissolved in a solution together with organometallic complexes used in experiments with parahydrogen (the H2 molecule in its nuclear singlet spin state) is reported. We demonstrate that this conversion, which gives rise to formation of orthohydrogen (the H2 molecule in its nuclear triplet spin state), is a remarkably efficient process that strongly reduces the resulting NMR (nuclear magnetic resonance) signal enhancement, here of 15N nuclei polarized at high fields using suitable NMR pulse sequences. We make use of a simple improvement of traditional pulse sequences, utilizing a single pulse on the proton channel that gives rise to an additional strong increase of the signal. Furthermore, analysis of the enhancement as a function of the pulse length allows one to estimate the actual population of the spin states of H2. We are also able to demonstrate that the spin conversion process in H2 is strongly affected by the concentration of 15N nuclei. This observation allows us to explain the dependence of the 15N signal enhancement on the abundance of 15N isotopes.

Correlation of high-field and zero- to ultralow-field NMR properties using 2D spectroscopy.

The field of zero- to ultralow-field (ZULF) nuclear magnetic resonance (NMR) is currently experiencing rapid growth, owing to progress in optical magnetometry and attractive features of ZULF-NMR such as low hardware cost and excellent spectral resolution achieved under ZULF conditions. In this work, an approach is proposed and demonstrated for simultaneous acquisition of ZULF-NMR spectra of individual 13C-containing isotopomers of chemical compounds in a complex mixture. The method makes use of fast field cycling such that the spin evolution takes place under ZULF conditions, whereas signal detection is performed in a high-field NMR spectrometer. This method has excellent sensitivity, also allowing easy assignment of ZULF-NMR spectra to specific analytes in the mixture. We demonstrate that the spectral information is the same as that given by ZULF-NMR, which makes the method suitable for creating a library of ZULF-NMR spectra of various compounds and their isotopomers. The results of the field-cycling experiments can be presented in a convenient way as 2D-NMR spectra with the direct dimension giving the high-field 13C-NMR spectrum (carrying the chemical-shift information) and the indirect dimension giving the ZULF-NMR spectrum (containing information about proton-carbon J-couplings). Hence, the method can be seen as a variant of heteronuclear J-resolved spectroscopy, one of the first 2D-NMR techniques.

Simultaneous 15 N polarization of several biocompatible substrates in ethanol-water mixtures by signal amplification by reversible exchange (SABRE) method.

Signal amplification by reversible exchange (SABRE) is a popular method for generating strong signal enhancements in nuclear magnetic resonance (NMR). In SABRE experiments, the source of polarization is provided by the nonthermal spin order of parahydrogen (pH2 , the H2 molecule in its nuclear singlet spin state). Polarization formation requires that both pH2 and a substrate molecule bind to an Ir-based complex where polarization transfer occurs. Subsequently, the complex dissociates and free polarized substrate molecules are formed. In this work, we present approaches towards biocompatible SABRE, meaning that several small biomolecules are simultaneously polarized by using the SABRE method in water-ethanol solutions at room temperature. We are able to demonstrate significant 15 N-NMR signal enhancements in water-ethanol solutions for biomolecules like nicotinamide, metronidazole, adenosine-5'-monophosphate, and 4-methylimidazole and found that the first three substrates are polarized at the same level as a well-known pyridine. We show that simultaneous polarization of several molecules is indeed feasible when the reactions are carried out at an ultralow field of about 400-500 nT. The achieved enhancements are between 100-fold and 15,000-fold. The resulting 15 N polarization (maximal value about 4% achieved for metronidazole and pyridine at 45°C) strongly depends on the sample temperature, pH2 bubbling pressure, and pH2 flow. One more parameter, which is important for optimizing the enhancement, is the solvent pH. Hence, this study presents a step in developing biocompatible SABRE polarization and gives a clue on how such SABRE experiments should be optimized to achieve the highest NMR signal enhancement.

Spin dynamics in experiments on orthodeuterium induced polarization (ODIP).

A comprehensive description of the spin dynamics underlying the formation of Ortho-Deuterium Induced Polarization (ODIP) is presented. ODIP can serve as a tool for enhancing Nuclear Magnetic Resonance (NMR) signals of 2H nuclei, being important probes of molecular structure and dynamics. To produce ODIP, in the first step, the D2 gas is brought to thermal equilibrium at low temperature, here 30 K, so that the ortho-component, corresponding to the total spin of the 2H nuclei equal to 0 and 2, is enriched, here to 92%. In the second step, the orthodeuterium molecule is attached to a substrate molecule using a suitable hydrogenation catalyst such that the symmetry of the two 2H nuclei is broken. As a result, the non-thermal spin order of orthodeuterium is converted into enhancement of observable NMR signals. In this work, we perform a theoretical study of ODIP and calculate the shape of ODIP spectra and their dependence on the magnetization flip angle. These results are compared with experiments performed for a number of substrates; good agreement between experimental and calculated ODIP spectra is found. We also discuss the performance of NMR techniques for converting anti-phase ODIP spectral patterns into in-phase patterns, which are more suitable for signal detection and for transferring ODIP to heteronuclei, here to 13C spins. Experimental procedures reported here allowed us to reach signal enhancement factors of more than 1000 for 2H nuclei in the liquid phase. These results are useful for extending the scope of spin hyperpolarization to the widely used 2H nuclei.

Algorithmic cooling of nuclear spins using long-lived singlet order.

Algorithmic cooling methods manipulate an open quantum system in order to lower its temperature below that of the environment. We achieve significant cooling of an ensemble of nuclear spin-pair systems by exploiting the long-lived nuclear singlet state, which is an antisymmetric quantum superposition of the "up" and "down" Zeeman states. The effect is demonstrated by nuclear magnetic resonance experiments on a molecular system containing a coupled pair of near-equivalent 13C nuclei. The populations of the system are subjected to a repeating sequence of cyclic permutations separated by relaxation intervals. The long-lived nuclear singlet order is pumped well beyond the unitary limit. The pumped singlet order is converted into nuclear magnetization which is enhanced by 21% relative to its thermal equilibrium value.

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.

DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3' to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.