Paramagnetic Relaxation Research Articles

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.

Steroid‐Derived Isonitriles are Potent Cytochrome P450 Ligands that Should Enable Solution NMR as a Structural Technique to Probe P450 Dynamics

Human cytochrome P450 (CYP) enzymes are versatile, dynamic, and essential to many aspects of human health. The catalytic versatility of this superfamily of enzymes is driven by structural dynamics, which are often elusive to static structural techniques. For this reason, solution nuclear magnetic resonance (NMR) is likely to provide useful structural information orthogonal to X‐ray crystallography. The challenges of human P450 NMR studies are two‐pronged: 1) Human P450 enzymes are membrane‐bound, and often aggregate or precipitate in aqueous environments, and 2) P450 enzymes contain a paramagnetic heme iron buried within the active site, leading to decreased intensity of NMR correlations corresponding to nearby amino acid residues. We have overcome both obstacles with the human steroidogenic P450 enzyme CYP17A1 in complex with a novel substrate derivative, 3‐formyl pregnane‐20‐isonitrile1. The steroid skeleton of this ligand is similar to that of CYP17A1 endogenous substrates and therapeutics, but in this case the C20 isonitrile functional group directly coordinates both the oxidized (Fe3+) and the reduced (Fe2+) diamagnetic states of the heme iron. As a result, this compound both stabilizes CYP17A1 and suppresses paramagnetic relaxation and will facilitate application of multidimensional solution NMR to CYP17A1. The dissociation constant (Kd) and inhibition (IC50) of this isonitrile have been determined and compared to the prostate cancer drug abiraterone, which is the tightest‐binding CYP17A1 inhibitor to date. Structural characterization of this complex by solution NMR is ongoing, but this strategy should open the door to new methods of structural analysis of dynamic human P450 enzymes.

Relative domain orientation of the L289K HIV-1 reverse transcriptase monomer.

HIV-1 reverse transcriptase (RT) is a heterodimer comprised p66 and p51 subunits (p66/p51). Several single amino acid substitutions in RT, including L289K, decrease p66/p51 dimer affinity, and reduce enzymatic functioning. Here, small-angle X-ray scattering (SAXS) with proton paramagnetic relaxation enhancement (PRE), 19 F site-specific NMR, and size exclusion chromatography (SEC) were performed for the p66 monomer with the L289K mutation, p66L289K . NMR and SAXS experiments clearly elucidated that the thumb and RNH domains in the monomer do not rigidly interact with each other but are spatially close to the RNH domain. Based on this structural model of the monomer, p66L289K and p51 were predicted to form a heterodimer while p66 and p51L289K not. We tested this hypothesis by SEC analysis of p66 and p51 containing L289K in different combinations and clearly demonstrated that L289K substitution in the p51 subunit, but not in the p66 subunit, reduces p66/p51 formation. Based on the derived monomer model and the importance of the inter-subunit RNH-thumb domain interaction in p66/p51, validated by SEC, the mechanism of p66 homodimer formation was discussed.

Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins

NMR spectroscopy allows the study of biomolecules in close-to-native conditions. Structural information can be inferred from the NMR spectra when an assignment is available. Protein assignment is usually a time-consuming task, being specially challenging in the case of large, supramolecular systems. Here, we present an extension of existing state-of-the-art strategies for methyl group assignment that partially overcomes signal overlapping and other difficulties associated to isolated methyl groups. Our approach exploits the ability of proteins to populate two or more conformational states, allowing for unique NOE restraints in each protein conformer. The method is compatible with automated assignment algorithms, granting assignments beyond the limits of a single protein state. The approach also benefits from long-range structural restraints obtained from metal-induced pseudocontact shifts (PCS) and paramagnetic relaxation enhancements (PREs). We illustrate the method with the complete assignment of the 199 methyl groups of a MILproSVproSAT methyl-labeled sample of the UDP-glucose pyrophosphorylase enzyme from Leishmania major (LmUGP). Protozoan parasites of the genus Leishmania causes Leishmaniasis, a neglected disease affecting over 12 million people worldwide. LmUGP is responsible for the de novo biosynthesis of uridine diphosphate-glucose, a precursor in the biosynthesis of the dense surface glycocalyx involved in parasite survival and infectivity. NMR experiments with LmUGP and related enzymes have the potential to unravel new insights in the host resistance mechanisms used by Leishmania major. Our efforts will help in the development of selective and efficient drugs against Leishmania.

Paramagnetic relaxation enhancement NMR as a tool to probe guest binding and exchange in metallohosts

Paramagnetic metallohost systems can bind guest molecules and find application as biomimetic catalysts. Due to the presence of the paramagnetic metal center, rigorous characterization of these systems by NMR spectroscopy can be very difficult. We report here that metallohost-guest systems can be studied by using the paramagnetic relaxation enhancement (PRE) effect. Manganese(III) porphyrin cage compounds are shown through their PRE to thread and bind viologen guests, including a polymeric one. The binding constants and dethreading activation parameters are lower than those of the metal-free porphyrin cage compounds, which is proposed to be a result of charge repulsion of the trivalent metal center and dicationic viologen guest. The threading rate of the manganese(III) porphyrin cage onto the polymer is more than 10 times faster than that of the non-metallated one, which is ascribed to initial binding of the cage to the polymer chain prior to threading, and to an entron effect.

Photoinduced Superhydrophilicity of Gd-Doped TiO2 Ellipsoidal Nanoparticles Boosts T1 Contrast Enhancement for Magnetic Resonance Imaging.

The unsatisfactory performance of current gadolinium chelate based T1 contrast agents (CAs) for magnetic resonance imaging (MRI) stimulates the search for better alternatives. Herein, we report a new strategy to substantially improve the capacity of nanoparticle-based T1 CAs by exploiting the photoinduced superhydrophilic assistance (PISA) effect. As a proof of concept, we synthesized citrate-coated Gd-doped TiO2 ellipsoidal nanoparticles (GdTi-SC NPs), whose r1 increases significantly upon UV irradiation. The reduced water contact angle and the increased number of surface hydroxyl groups substantiate the existence of the PISA effect, which considerably promotes the efficiency of paramagnetic relaxation enhancement (PRE) and thus the imaging performance of GdTi-SC NPs. In vivo MRI of SD rats with GdTi-SC NPs further demonstrates that GdTi-SC NPs could serve as a high-performance CA for sensitive imaging of blood vessels and accurate diagnosis of vascular lesions, indicating the success of our strategy.

Improving Martini 3 for Disordered and Multidomain Proteins.

Coarse-grained molecular dynamics simulations are a useful tool to determine conformational ensembles of proteins. Here, we show that the coarse-grained force field Martini 3 underestimates the global dimensions of intrinsically disordered proteins (IDPs) and multidomain proteins when compared with small-angle X-ray scattering (SAXS) data and that increasing the strength of protein-water interactions favors more expanded conformations. We find that increasing the strength of interactions between protein and water by ca. 10% results in improved agreement with the SAXS data for IDPs and multidomain proteins. We also show that this correction results in a more accurate description of self-association of IDPs and folded proteins and better agreement with paramagnetic relaxation enhancement data for most IDPs. While simulations with this revised force field still show deviations to experiments for some systems, our results suggest that it is overall a substantial improvement for coarse-grained simulations of soluble proteins.

Visualizing Proteins in Mammalian Cells by 19 F NMR Spectroscopy.

In-cell NMR spectroscopy is a powerful tool to investigate protein behavior in physiologically relevant environments. Although proven valuable for disordered proteins, we show that in commonly used 1 H-15 N HSQC spectra of globular proteins, interactions with cellular components often broaden resonances beyond detection. This contrasts 19 F spectra in mammalian cells, in which signals are readily observed. Using several proteins, we demonstrate that surface charges and interaction with cellular binding partners modulate linewidths and resonance frequencies. Importantly, we establish that 19 F paramagnetic relaxation enhancements using stable, rigid Ln(III) chelate pendants, attached via non-reducible thioether bonds, provide an effective means to obtain accurate distances for assessing protein conformations in the cellular milieu.

Visualizing Proteins in Mammalian Cells by 19F NMR Spectroscopy

AbstractIn‐cell NMR spectroscopy is a powerful tool to investigate protein behavior in physiologically relevant environments. Although proven valuable for disordered proteins, we show that in commonly used 1H‐15N HSQC spectra of globular proteins, interactions with cellular components often broaden resonances beyond detection. This contrasts 19F spectra in mammalian cells, in which signals are readily observed. Using several proteins, we demonstrate that surface charges and interaction with cellular binding partners modulate linewidths and resonance frequencies. Importantly, we establish that 19F paramagnetic relaxation enhancements using stable, rigid Ln(III) chelate pendants, attached via non‐reducible thioether bonds, provide an effective means to obtain accurate distances for assessing protein conformations in the cellular milieu.

Stacking Faults Assist Lithium-Ion Conduction in a Halide-Based Superionic Conductor.

In the pursuit of urgently needed, energy dense solid-state batteries for electric vehicle and portable electronics applications, halide solid electrolytes offer a promising path forward with exceptional compatibility against high-voltage oxide electrodes, tunable ionic conductivities, and facile processing. For this family of compounds, synthesis protocols strongly affect cation site disorder and modulate Li+ mobility. In this work, we reveal the presence of a high concentration of stacking faults in the superionic conductor Li3YCl6 and demonstrate a method of controlling its Li+ conductivity by tuning the defect concentration with synthesis and heat treatments at select temperatures. Leveraging complementary insights from variable temperature synchrotron X-ray diffraction, neutron diffraction, cryogenic transmission electron microscopy, solid-state nuclear magnetic resonance, density functional theory, and electrochemical impedance spectroscopy, we identify the nature of planar defects and the role of nonstoichiometry in lowering Li+ migration barriers and increasing Li site connectivity in mechanochemically synthesized Li3YCl6. We harness paramagnetic relaxation enhancement to enable 89Y solid-state NMR and directly contrast the Y cation site disorder resulting from different preparation methods, demonstrating a potent tool for other researchers studying Y-containing compositions. With heat treatments at temperatures as low as 333 K (60 °C), we decrease the concentration of planar defects, demonstrating a simple method for tuning the Li+ conductivity. Findings from this work are expected to be generalizable to other halide solid electrolyte candidates and provide an improved understanding of defect-enabled Li+ conduction in this class of Li-ion conductors.

1H NMR spectral analysis of structural features in a series of paramagnetic homoleptic binuclear triple-decker phthalocyaninato lanthanide complexes

The search for efficient methods of comparative structural investigations of coordination compounds in solid state and solutions is a very relevant task. In this study, structural assignments in a series of Ln2[(15C5)4Pc]3 complexes (where [(15C5)4Pc]2- is 2,3,9,10,16,17,24,25-tetrakis(15-crown-5)phthalocyaninato-dianion, Ln = Nd3+, Tb3+, Dy3+, Ho3+, Er3+ and Tm3+) was performed using NMR relaxation and paramagnetic lanthanide-induced shifts (LIS) data. Analysis of the paramagnetic chemical shifts and relaxation rates evidenced of isostructurality of the complete series of the investigated triple-decker complexes in the solutions. The performed systematic DFT calculations for a series of model complexes with methoxy-substituted ligands Ln2[(MeO)8Pc]3 demonstrate that the calculated geometrical factors are in agreement with characteristics extracted from experimental NMR data.

Protein Electrostatics Investigated through Paramagnetic NMR for Nonpolar Groups.

Experimental validation of theoretical models for protein electrostatics remains rare. Recently, we have developed a paramagnetic NMR-based method for de novo determination of effective near-surface electrostatic potentials, which allows for straightforward examination of electrostatic models for biomolecules. In the current work, we expand this method and demonstrate that effective near-surface electrostatic potentials can readily be determined from 1H paramagnetic relaxation enhancement (PRE) data for protein CαH and CH3 groups. The experimental data were compared with those predicted from the Poisson-Boltzmann theory. The impact of structural dynamics on the effective near-surface electrostatic potentials was also assessed. The agreement between the experimental and theoretical data was particularly good for methyl 1H nuclei. Compared to the conventional pKa-based validation, our paramagnetic NMR-based approach can provide a far larger number of experimental data that can directly be used to examine the validity of theoretical electrostatic models for proteins.

Protein Dynamics to Define and Refine Disordered Protein Ensembles.

Intrinsically disordered proteins and unfolded proteins have fluctuating conformational ensembles that are fundamental to their biological function and impact protein folding, stability, and misfolding. Despite the importance of protein dynamics and conformational sampling, time-dependent data types are not fully exploited when defining and refining disordered protein ensembles. Here we introduce a computational framework using an elastic network model and normal-mode displacements to generate a dynamic disordered ensemble consistent with NMR-derived dynamics parameters, including transverse R2 relaxation rates and Lipari-Szabo order parameters (S2 values). We illustrate our approach using the unfolded state of the drkN SH3 domain to show that the dynamical ensembles give better agreement than a static ensemble for a wide range of experimental validation data including NMR chemical shifts, J-couplings, nuclear Overhauser effects, paramagnetic relaxation enhancements, residual dipolar couplings, hydrodynamic radii, single-molecule fluorescence Förster resonance energy transfer, and small-angle X-ray scattering.

Architecture of the two metal-binding sites in prolactin

Metal binding by members of the growth hormone (GH) family of hematopoietic cytokines has been a subject of considerable interest. However, beyond appreciation of its role in reversible packing of GH proteins in secretory granules, the molecular mechanisms of metal binding and granule formation remain poorly understood. Here, we investigate metal binding by a GH family member prolactin (PRL) using paramagnetic metal titration and chelation experiments. Cu2+-mediated paramagnetic relaxation enhancement measurements identified two partial metal-binding sites on the opposite faces of PRL composed of residues H30/H180 and E93/H97, respectively. Coordination of metal ions by these two sites causes formation of inter-molecular bridges between the PRL protomers and enables formation of reversible higher aggregates. These findings in vitro suggest a model for reversible packaging of PRL in secretory granules. The proposed mechanism of metal-promoted PRL aggregation lends insight and support to the previously suggested role of metal coordination in secretory granule formation by GH proteins.

Probing the PIP2 dependence of the ASAP1 PH domain membrane binding by NMR and MD simulations

Association of the ASAP1 Pleckstrin homology (PH) domain with multiple PI(4,5)P2 at the membrane surface participates to the regulation of the small GTPase Arf1 activity. However, the effect of local PI(4,5)P2 enrichment at the membrane is unclear beyond an increased affinity of ASAP1 PH for the membrane. In particular, how PI(4,5)P2 concentration affects the docking geometry of ASAP1 PH is unknown. To determine the orientation of ASAP1 PH at the membrane interface, we explored the use of pseudo distance constraints obtained from NMR Paramagnetic Relaxation Enhancement (PRE) experiments.

Paramagnetic relaxation enhancement NMR reveals the structures and ribosome interactions of nascent chains during biosynthesis

The crucial process of protein folding begins co-translationally on the ribosome. Emerging evidence is demonstrating that the ribosome itself is an active player in regulating the folding of nascent chains, a process that is vital for proteostasis. However, surprisingly little is known structurally about the conformations of nascent polypeptides on their parent ribosome during vectorial emergence and how the ribosome modulates co-translational folding.

Paramagnetic Chemical Probes for Studying Biological Macromolecules.

Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

Electron paramagnetic resonance characterization and electron spin relaxation of manganate ion in glassy alkaline LiCl solution and doped into Cs2SO4

Manganate ion, MnO42−, has important roles in catalysis and potential roles in water treatment. EPR spectra of MnO42− in a glassy alkaline solution of concentrated LiCl at X-band and Q-band at 80 K exhibit g1 = 1.9776 ± 0.001, g2 = 1.9677 ± 0.001, g3 = 1.9560 ± 0.001 and A1 = 182 ± 9, A2 = 275 ± 15, and A3 = 400 ± 15 MHz. In Cs2SO4 the spectra were simulated with 1.908 ± 0.001, g2 = 1.909 ± 0.001, g3 = 1.937 ± 0.001 and A1 = 90 ± 20, A2 = 100 ± 20, and A3 = 400 ± 15 MHz. Simulations required large distributions in A values which suggests that hyperfine splittings are sensitive to differences in geometry. Continuous wave spectra are observable at 80 K in glassy alkaline LiCl, but only up to about 20 K in Cs2SO4. In glassy alkaline LiCl electron spin relaxation was measured at X-band using spin echo and inversion recovery from 4.2 to 60 K. Tm is 4.6 μs at 4.2 K and decreases at higher temperatures as it becomes driven by T1. T1 decreases from ca. 34 ms at 4.2 K to ca. 240 ns at 60 K. Tm and T1 in Cs2SO4 are too short to measure by electron spin echo. The distorted tetrahedral geometry of MnO42− results in faster relaxation than for other 3d1 spin systems that have square pyramidal (C4v) or distorted octahedral geometries.

Monitoring electron spin fluctuations with paramagnetic relaxation enhancement

The magnetic interactions between the spin of an unpaired electron and the surrounding nuclear spins can be exploited to gain structural information, to reduce nuclear relaxation times as well as to create nuclear hyperpolarization via dynamic nuclear polarization (DNP). A central aspect that determines how these interactions manifest from the point of view of NMR is the timescale of the fluctuations of the magnetic moment of the electron spins. These fluctuations, however, are elusive, particularly when electron relaxation times are short or interactions among electronic spins are strong. Here we map the fluctuations by analyzing the ratio between longitudinal and transverse nuclear relaxation times T1/T2, a quantity which depends uniquely on the rate of the electron fluctuations and the Larmor frequency of the involved nuclei. This analysis enables rationalizing the evolution of NMR lineshapes, signal quenching as well as DNP enhancements as a function of the concentration of the paramagnetic species and the temperature, demonstrated here for LiMg1−xMnxPO4 and Fe(III) doped Li4Ti5O12, respectively. For the latter, we observe a linear dependence of the DNP enhancement and the electron relaxation time within a temperature range between 100 and 300 K.

Insights into the Gelation Mechanism of Metal-Coordinated Hydrogels by Paramagnetic NMR Spectroscopy and Molecular Dynamics

Metal-coordination complexes are attracting increasing attention as supramolecular cross-linkers to develop polymeric hydrogel networks with tunable and dynamic mechanical properties. Nonetheless, the rational design of these materials is still hindered by the limited mechanistic understanding of how metal–ligand interactions influence the structure and properties of the hydrogel. Here, we report a detailed mechanistic investigation using nuclear magnetic resonance (NMR) spectroscopy combined with molecular dynamics (MD) simulations to explore the formation of cellulose-based hydrogels induced by coordination with paramagnetic Fe3+ ions. We demonstrate how NMR paramagnetic relaxation enhancement can be used to probe the distances between the metal center and NMR active nuclei on the polymer chain, informing on the metal–ligand coordination network. Experimental results, together with supporting MD simulations, allow us to uncover a structuration of water around the cross-linked metals within the hydrogel, in addition to the establishment of different orientations of the chains governed by hydrogen bonds networks. Progress in understanding the gelation mechanism of metal-coordinated hydrogels will fuel their exploitation for a wide variety of biomedical applications.