Magnetic susceptibility and paramagnetism-based NMR

Enhancing the degradation rate and biomineralization nature of antiferromagnetic Fe-20Mn alloy by groove pressing

The Fe-Mn alloys are potential candidates for biodegradable implant applications. However, the very low degradation rates of Fe-Mn alloys in the physiological environment are a major disadvantage. In this study, the degradation rate of a Fe-20Mn alloy was improved using the groove pressing (GP) technique. Hot rolled sheets of 2 mm thickness were subjected to GP operation at 1000°C. Uniform fine-grained (UFG) Fe-Mn alloys were obtained using the GP technique. The influence of GP on the microstructure, mechanical properties, degradation behavior in simulated body fluid (SBF), surface wettability, biomineralization, and cytocompatibility was investigated and compared to the annealed (A Fe-Mn) and rolled (R Fe-Mn) sample. The groove-pressed Fe-Mn (G Fe-Mn) alloy had a grain size of approximately 40 ± 16 μm whereas the A Fe-Mn and R Fe-Mn samples had grain sizes of 303 ± 81 and 117 ± 14.5 μm, respectively. Enhanced strength and elongation were also observed with the G Fe-Mn sample. The potentiodynamic polarization test showed the highest Icorr, lowest polarization resistance, and lowest Ecorr for the G Fe-Mn sample among all other samples indicating its higher degradation rate. The weight loss data from immersion tests also shows that the percentage of weight loss increases with time indicating the accelerated degradation behavior of the sample. The static immersion test showed an enhancement in weight loss of 0.46 ± 0.02% and 1.02 ± 0.05% for R Fe-Mn and G Fe-Mn samples, respectively, than A Fe-Mn sample (0.31 ± 0.03%) after 56 days in immersion in SBF. The greater biomineralization tendency in UFG materials is confirmed by the G Fe-Mn sample's stronger hydroxyapatite deposition. When compared to the A Fe-Mn and R Fe-Mn samples, the G Fe-Mn sample has a better wettability, which promotes higher cell adhesion and vitality, showing higher biocompatibility. This study demonstrates that Fe-20Mn processed by GP has potential applications for the manufacture of biodegradable metallic implants.

Controlled synthesis and characterization of porous silicon nanoparticles for dynamic nuclear polarization

Si nanoparticles (NPs) have been actively developed as a hyperpolarized magnetic resonance imaging (MRI) contrast agent with an imaging window close to one hour. However, the progress in the development of NPs has been hampered by the incomplete understanding of their structural properties that correspond to efficient hyperpolarization buildup and long polarization decays. In this work we study dynamic nuclear polarization (DNP) of single crystal porous Si (PSi) NPs with defined doping densities ranging from nominally undoped to highly doped with boron or phosphorus. To develop such PSi NPs we perform low-load metal-assisted catalytic etching for electronic grade Si powder followed by thermal oxidation to form the dangling bonds in the Si/SiO2 interface, the Pb centers. Pb centers are the endogenous source of the unpaired electron spins necessary for DNP. The controlled fabrication and oxidation procedures allow us to thoroughly investigate the impact of the magnetic field, temperature and doping on the DNP process. We argue that the buildup and decay rate constants are independent of size of Si crystals between approximately 10 and 60 nm. Instead, the rates are limited by the polarization transfer across the nuclear spin diffusion barrier determined by the large hyperfine shift of the central 29Si nuclei of the Pb centers. The size-independent rates are then weakly affected by the doping degree for low and moderately doped Si although slight doping is required to achieve the highest polarization. Thus, we find the room temperature relaxation of low boron doped PSi NPs reaching 75 ± 3 minutes and nuclear polarization levels exceeding ∼6% when polarized at 6.7 T and 1.4 K. Our study thus establishes solid grounds for further development of Si NPs as hyperpolarized contrast agents.

Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins

Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.

Development of Ln(III) Derivatives as 19F Parashift Probes

19F parashift probes with paramagnetically shifted reporter nuclei provide attractive platforms to develop molecular imaging probes. These probes enable ratiometric detection of molecular disease markers using a direct detection technique. Here, we describe a series of trivalent lanthanide (Ln(III)) complexes that are structural analogues of the clinically approved MR contrast agent (CA) ProHance to obtain LnL 19F parashift probes. We evaluated trans-gadolinium paramagnetic lanthanides compared to diamagnetic YL for 19F chemical shift and relaxation rate enhancement. The paramagnetic contribution to chemical shift (δPCS) for paramagnetic LnL exhibited either shifts to lower frequency (δPCS < 0 for TbL, DyL, and HoL) or shifts to higher frequency (δPCS > 0 for ErL, TmL, and YbL) compared to YL 19F spectroscopic signal. Zero-echo time pulse sequences achieved 56-fold sensitivity enhancement for DyL over YL, while developing probe-specific pulse sequences with fast delay times and acquisition times achieved 0.6-fold enhancement in limit of detection for DyL. DyL provides an attractive platform to develop 19F parashift probes for ratiometric detection of enzymatic activity.

Effect of Magnetic Anisotropy on the 1H NMR Paramagnetic Shifts and Relaxation Rates of Small Dysprosium(III) Complexes

We present a detailed analysis of the 1H NMR chemical shifts and transverse relaxation rates of three small Dy(III) complexes having different symmetries (C3, D2 or C2). The complexes show sizeable emission in the visible region due to 4F9/2 → 6HJ transitions (J = 15/2 to 11/2). Additionally, NIR emission is observed at ca. 850 (4F9/2 → 6H7/2), 930 (4F9/2 → 6H5/2), 1010 (4F9/2 → 6F9/2), and 1175 nm (4F9/2 → 6F7/2). Emission quantum yields of 1-2% were determined in aqueous solutions. The emission lifetimes indicate that no water molecules are present in the inner coordination sphere of Dy(III), which in the case of [Dy(CB-TE2PA)]+ was confirmed through the X-ray crystal structure. The 1H NMR paramagnetic shifts induced by Dy(III) were found to be dominated by the pseudocontact mechanism, though, for some protons, contact shifts are not negligible. The analysis of the pseudocontact shifts provided the magnetic susceptibility tensors of the three complexes, which were also investigated using CASSCF calculations. The transverse 1H relaxation data follow a good linear correlation with 1/r6, where r is the distance between the Dy(III) ion and the observed proton. This indicates that magnetic anisotropy is not significantly affecting the relaxation of 1H nuclei in the family of complexes investigated here.

Iron oxide nanoparticles as positive T1 contrast agents for low-field magnetic resonance imaging at 64 mT

We have investigated the efficacy of superparamagnetic iron oxide nanoparticles (SPIONs) as positive T₁ contrast agents for low-field magnetic resonance imaging (MRI) at 64 millitesla (mT). Iron oxide-based agents, such as the FDA-approved ferumoxytol, were measured using a variety of techniques to evaluate T₁ contrast at 64 mT. Additionally, we characterized monodispersed carboxylic acid-coated SPIONs with a range of diameters (4.9-15.7 nm) in order to understand size-dependent properties of T₁ contrast at low-field. MRI contrast properties were measured using 64 mT MRI, magnetometry, and nuclear magnetic resonance dispersion (NMRD). We also measured MRI contrast at 3 T to provide comparison to a standard clinical field strength. SPIONs have the capacity to perform well as T₁ contrast agents at 64 mT, with measured longitudinal relaxivity (r₁) values of up to 67 L mmol^-1 s^-1, more than an order of magnitude higher than corresponding r₁ values at 3 T. The particles exhibit size-dependent longitudinal relaxivities and outperform a commercial Gd-based agent (gadobenate dimeglumine) by more than eight-fold at physiological temperatures. Additionally, we characterize the ratio of transverse to longitudinal relaxivity, r₂/r₁ and find that it is ~ 1 for the SPION based agents at 64 mT, indicating a favorable balance of relaxivities for T₁-weighted contrast imaging. We also correlate the magnetic and structural properties of the particles with models of nanoparticle relaxivity to understand generation of T₁ contrast. These experiments show that SPIONs, at low fields being targeted for point-of-care low-field MRI systems, have a unique combination of magnetic and structural properties that produce large T₁ relaxivities.

Paramagnetic NMR restraints for the characterization of protein structural rearrangements

Mobility is a common feature of biomacromolecules, often fundamental for their function. Thus, in many cases, biomacromolecules cannot be described by a single conformation, but rather by a conformational ensemble. NMR paramagnetic data demonstrated quite informative to monitor this conformational variability, especially when used in conjunction with data from different sources. Due to their long-range nature, paramagnetic data can, for instance, i) clearly demonstrate the occurrence of conformational rearrangements, ii) reveal the presence of minor conformational states, sampled only for a short time, iii) indicate the most representative conformations within the conformational ensemble sampled by the molecule, iv) provide an upper limit to the weight of each conformation.

Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase

Many proteins naturally carry metal centers, with a large share of them being in the active sites of several enzymes. Paramagnetic effects are a powerful source of structural information and, therefore, if the native metal is paramagnetic, or it can be functionally substituted with a paramagnetic one, paramagnetic effects can be used to study the metal sites, as well as the overall structure of the protein. One notable example is cobalt(II) substitution for zinc(II) in carbonic anhydrase. In this manuscript we investigate the effects of sodium thiocyanate on the chemical environment of the metal ion of the human carbonic anhydrase II. The electron paramagnetic resonance (EPR) titration of the cobalt(II) protein with thiocyanate shows that the EPR spectrum changes from A-type to C-type on passing from 1:1 to 1:1000-fold ligand excess. This indicates the occurrence of a change in the electronic structure, which may reflect a sizable change in the metal coordination environment in turn caused by a modification of the frozen solvent glass. However, paramagnetic nuclear magnetic resonance (NMR) data indicate that the metal coordination cage remains unperturbed even in 1:1000-fold ligand excess. This result proves that the C-type EPR spectrum observed at large ligand concentration should be ascribed to the low temperature at which EPR measurements are performed, which impacts on the structure of the protein when it is destabilized by a high concentration of a chaotropic agent.

Large Protein Assemblies for High-Relaxivity Contrast Agents: The Case of Gadolinium-Labeled Asparaginase

Biologics are emerging as the most important class of drugs and are used to treat a large variety of pathologies. Most of biologics are proteins administered in large amounts, either by intramuscular injection or by intravenous infusion. Asparaginase is a large tetrameric protein assembly, currently used against acute lymphoblastic leukemia. Here, a gadolinium(III)-DOTA derivative has been conjugated to asparaginase, and its relaxation properties have been investigated to assess its efficiency as a possible theranostic agent. The field-dependent ¹H longitudinal relaxation measurements of water solutions of gadolinium(III)-labeled asparaginase indicate a very large increase in the relaxivity of this paramagnetic protein complex with respect to small gadolinium chelates, opening up the possibility of its use as an MRI contrast agent.

Reweighting methods for elucidation of conformation ensembles of proteins

Proteins are inherently dynamic macromolecules that exist in equilibrium among multiple conformational states, and motions of protein backbone and side chains are fundamental to biological function. The ability to characterize the conformational landscape is particularly important for intrinsically disordered proteins, multidomain proteins, and weakly bound complexes, where single-structure representations are inadequate. As the focus of structural biology shifts from relatively rigid macromolecules toward larger and more complex systems and molecular assemblies, there is a need for structural approaches that can paint a more realistic picture of such conformationally heterogeneous systems. Here, we review reweighting methods for elucidation of structural ensembles based on experimental data, with the focus on applications to multidomain proteins.

Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems

Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.

Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag

Flexibility between the paramagnetic tag and its protein conjugates is a common yet unresolved issue in the applications of paramagnetic NMR spectroscopy in biological systems. The flexibility greatly attenuates the magnetic anisotropy and compromises paramagnetic effects especially for pseudocontact shift and residual dipolar couplings. Great efforts have been made to improve the rigidity of paramagnetic tag in the protein conjugates, however, the effect of local environment vicinal to the protein ligation site on the paramagnetic effects remains poorly understood. In the present work, the stereospecific effect of chiral tether between the protein and a tag on the paramagnetic effects produced by the tag attached via a D- and L-type linker between the protein and paramagnetic metal chelating moiety was assessed. The remarkable chiral effect of the D- and L-type tether between the tag and the protein on the rigidity of paramagnetic tag is disclosed in a number of protein-tag-Ln complexes. The chiral tether formed between the D-type tag and L-type protein surface minimizes the effect of the local environment surrounding the ligation site on the averaging of paramagnetic tag, which is helpful to preserve the rigidity of a paramagnetic tag in the protein conjugates.

The evolution of paramagnetic NMR as a tool in structural biology

Paramagnetic NMR data contain extremely accurate long-range information on metalloprotein structures and, when used in the frame of integrative structural biology approaches, they allow for the retrieval of structural details to a resolution that is not achievable using other techniques. Paramagnetic data thus represent an extremely powerful tool to refine protein models in solution, especially when coupled to X-ray or cryoelectron microscopy data, to monitor the formation of complexes and determine the relative arrangements of their components, and to highlight the presence of conformational heterogeneity. More recently, theoretical and computational advancements in quantum chemical calculations of paramagnetic NMR observables are progressively opening new routes in structural biology, because they allow for the determination of the structure within the coordination sphere of the metal center, thus acting as a loupe on sites that are difficult to observe but very important for protein function.

Paramagnetic NMR Shielding Tensors Based on Scalar Exact Two-Component and Spin-Orbit Perturbation Theory

The temperature-dependent Fermi-contact and pseudocontact terms are important contributions to the paramagnetic NMR shielding tensor. Herein, we augment the scalar-relativistic (local) exact two-component (X2C) framework with spin-orbit perturbation theory including the screened nuclear spin-orbit correction for the EPR hyperfine coupling and g tensor to compute these temperature-dependent terms. The accuracy of this perturbative ansatz is assessed with the self-consistent spin-orbit two-component and four-component treatments serving as reference. This shows that the Fermi-contact and pseudocontact interaction is sufficiently described for paramagnetic NMR shifts; however, larger deviations are found for the EPR spectra and the principle components of the EPR properties of heavy elements. The impact of the perturbative treatment is further compared to that of the density functional approximation and the basis set. Large-scale calculations are routinely possible with the multipole-accelerated resolution of the identity approximation and the seminumerical exchange approximation, as shown for [CeTi₆O₃(OiPr)₉(salicylate)₆].

Incorporation of residual chemical shift anisotropy into the treatment of 15N pseudocontact shifts for structural refinement

Paramagnetic NMR experiments, including the pseudocontact shift experiment, have seen increasing use due to recently developed probes and labeling strategies. The pseudocontact shift experiment can provide valuable intra- or inter-molecular distance and orientation information. However, the use of 1H/13C or 1H/15N PCS data in structure calculations is currently complicated by the contribution of residual chemical shift anisotropy to the 13C or 15N datasets. Here, we present a corrected PCS energy term for the software package Xplor-NIH with the appropriate residual chemical shift anisotropy correction and show its suitability for model refinements of ubiquitin labeled at residue 57 with a Tm-M8-SPy tag. For data taken at 800 MHz, the improvement with the corrected energy term is sufficient to make the quality of the fit for the 15N dataset comparable to that of the 1H dataset, for which no correction is needed. The corrected energy term is expected to become more relevant with increased use of higher field instruments and as new paramagnetic probes with larger magnetic susceptibility tensors continue to be developed.

Paramagnetic encoding of molecules

Contactless digital tags are increasingly penetrating into many areas of human activities. Digitalization of our environment requires an ever growing number of objects to be identified and tracked with machine-readable labels. Molecules offer immense potential to serve for this purpose, but our ability to write, read, and communicate molecular code with current technology remains limited. Here we show that magnetic patterns can be synthetically encoded into stable molecular scaffolds with paramagnetic lanthanide ions to write digital code into molecules and their mixtures. Owing to the directional character of magnetic susceptibility tensors, each sequence of lanthanides built into one molecule produces a unique magnetic outcome. Multiplexing of the encoded molecules provides a high number of codes that grows double-exponentially with the number of available paramagnetic ions. The codes are readable by nuclear magnetic resonance in the radiofrequency (RF) spectrum, analogously to the macroscopic technology of RF identification. A prototype molecular system capable of 16-bit (65,535 codes) encoding is presented. Future optimized systems can conceivably provide 64-bit (~10^19 codes) or higher encoding to cover the labelling needs in drug discovery, anti-counterfeiting and other areas.

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.

A dysprosium single molecule magnet outperforming current pseudocontact shift agents

A common criterion for designing performant single molecule magnets and pseudocontact shift tags is a large magnetic anisotropy. In this article we present a dysprosium complex chemically designed to exhibit strong easy-axis type magnetic anisotropy that is preserved in dichloromethane solution at room temperature. Our detailed theoretical and experimental studies on the magnetic properties allowed explaining several features typical of highly performant SMMs. Moreover, the NMR characterization shows remarkably large chemical shifts, outperforming the current state-of-the art PCS tags.

13C Direct Detected NMR for Challenging Systems

Thanks to recent improvements in NMR spectrometer hardware and pulse sequence design, modern 13C NMR has become a useful tool for biomolecular applications. The complete assignment of a protein can be accomplished by using 13C detected multinuclear experiments and it can provide unique information relevant for the study of a variety of different biomolecules including paramagnetic proteins and intrinsically disordered proteins. A wide range of NMR observables can be measured, concurring to the structural and dynamic characterization of a protein in isolation, as part of a larger complex, or even inside a living cell. We present the different properties of 13C with respect to 1H, which provide the rationale for the experiments developed and their application, the technical aspects that need to be faced, and the many experimental variants designed to address different cases. Application areas where these experiments successfully complement proton NMR are also described.

Theoretical analysis of the long-distance limit of NMR chemical shieldings

After some years of controversy, it was recently demonstrated how to obtain the correct long-distance limit [point-dipole approximation (PDA)] of pseudo-contact nuclear magnetic resonance chemical shifts from rigorous first-principles quantum mechanics [Lang et al., J. Phys. Chem. Lett. 11, 8735 (2020)]. This result confirmed the classical Kurland-McGarvey theory. In the present contribution, we elaborate on these results. In particular, we provide a detailed derivation of the PDA both from the Van den Heuvel-Soncini equation for the chemical shielding tensor and from a spin Hamiltonian approximation. Furthermore, we discuss in detail the PDA within the approximate density functional theory and Hartree-Fock theories. In our previous work, we assumed a relatively crude effective nuclear charge approximation for the spin-orbit coupling operator. Here, we overcome this assumption by demonstrating that the derivation is also possible within the fully relativistic Dirac equation and even without the assumption of a specific form for the Hamiltonian. Crucial ingredients for the general derivation are a Hamiltonian that respects gauge invariance, the multipolar gauge, and functional derivatives of the Hamiltonian, where it is possible to identify the first functional derivative with the electron number current density operator. The present work forms an important foundation for future extensions of the Kurland-McGarvey theory beyond the PDA, including induced magnetic quadrupole and higher moments to describe the magnetic hyperfine field.

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.

Not only manganese, but fruit component effects dictate the efficiency of fruit juice as an oral magnetic resonance imaging contrast agent

Several fruit juices are used as oral contrast agents to improve the quality of images in magnetic resonance cholangiopancreatography. They are often preferred to conventional synthetic contrast agents because of their very low cost, natural origin, intrinsic safety, and comparable image qualities. Pineapple and blueberry juices are the most employed in clinical practice due to their higher content of manganese(II) ions. The interest of pharmaceutical companies in these products is testified by the appearance in the market of fruit juice derivatives with improved contrast efficacy. Here, we investigate the origin of the contrast of blueberry juice, analyze the parameters that can effect it, and elucidate the differences with pineapple juice and manganese(II) solutions. It appears that, although manganese(II) is the paramagnetic ion responsible for the contrast, it is the interaction of manganese(II) with other juice components that modulates the efficiency of the juice as a magnetic resonance contrast agent. On these grounds, we conclude that blueberry juice concentrated to the same manganese concentration of pineapple juice would prove a more efficient contrast agent than pineapple juice.

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

Ultrasonic Imaging of Carotid Inflammatory Plaque with Superparamagnetic Nanoparticles

Chronic inflammation can stimulate the formation and progression of atherosclerotic plaques and increase the vulnerability of plaques. However, there are few studies on the changes of carotid inflammatory plaques during treatment. Our study attempted to investigate the use of superparamagnetic iron oxide nanoparticle (SPION) ultrasound imaging to detect the expression of vascular cell adhesion molecule-1 (VCAM-1) in patients with carotid plaques and analyze the effects of SPION ultrasound imaging in inflammatory plaque visualization effect. SPION microbubble contrast agents have good imaging effects both in vivo and in vitro. We conjugated the VCAM-1 protein to the microbubbles wrapped in SPIONs to form SPIONs carrying VCAM-1 antibodies. Observe the signal intensity of SPIONs carrying VCAM-1 antibody to arteritis plaque. The results showed that the SPION contrast agent carrying VCAM-1 antibody had higher peak gray-scale video intensity than the other two groups of contrast agents not carrying VCAM-1 antibody. It shows that SPIONs have excellent imaging effects in ultrasound imaging, can evaluate the inflammatory response of arterial plaque lesions, and are of great significance for the study of carotid inflammatory plaque changes.

Sorting Phenomena and Chirality Transfer in Fluoride-Bridged Macrocyclic Rare Earth Complexes

The reaction of fluoride anions with mononuclear lanthanide(III) and yttrium(III) hexaaza-macrocyclic complexes results in the formation of dinuclear fluoride-bridged complexes. As indicated by X-ray crystal structures, in these complexes two metal ions bound by the macrocycles are linked by two or three bridging fluoride anions, depending on the type of the macrocycle. In the case of the chiral hexaaza-macrocycle L1 derived from trans-1,2-diaminocyclohexane, the formation of these μ2-fluorido dinuclear complexes is accompanied by enantiomeric self-recognition of macrocyclic units. In contrast, this kind of recognition is not observed in the case of complexes of the chiral macrocycle L2 derived from 1,2-diphenylethylenediamine. The reaction of fluoride with a mixture of mononuclear complexes of L1 and L2, containing two different Ln(III) ions, results in narcissistic sorting of macrocyclic units. Conversely, a similar reaction involving mononuclear complexes of L1 and complexes of achiral macrocycle L3 based on ethylenediamine results in sociable sorting of macrocyclic units and preferable formation of heterodinuclear complexes. In addition, formation of these heterodinuclear complexes is accompanied by chirality transfer from the chiral macrocycle L1 to the achiral macrocycle L3 as indicated by CPL and CD spectra.

Unravelling of a [High Spin-Low Spin] ↔ [Low Spin-High Spin] Equilibrium in Spin-Crossover Iron(II) Dinuclear Helicates Using Paramagnetic NMR Spectroscopy

Spin-crossover between high-spin (HS) and low-spin (LS) states of selected transition metal ions in polynuclear and polymeric compounds is behind their use as multistep switchable materials in breakthrough electronic and spintronic devices. We report the first successful attempt to observe the dynamics of a rarely found broken-symmetry spin state in binuclear complexes, which mixes the states [HS-LS] and [LS-HS] on a millisecond timescale. The slow exchange between these two states, which was identified by paramagnetic NMR spectroscopy in solutions of two spin-crossover iron(II) binuclear helicates that are amenable to molecular design, opens a path to double quantum dot cellular automata for information storage and processing.

An automated iterative approach for protein structure refinement using pseudocontact shifts

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.

NMR for Single Ion Magnets

Nuclear Magnetic Resonance is particularly sensitive to the electronic structure of matter and is thus a powerful tool to characterize in-depth the magnetic properties of a system. NMR is indeed increasingly recognized as an ideal tool to add precious structural information for the development of Single Ion Magnets, small complexes that are recently gaining much popularity due to their quantum computing and spintronics applications. In this review, we recall the theoretical principles of paramagnetic NMR, with particular attention to lanthanoids, and we give an overview of the recent advances in this field.

Unveiling protein dynamics in solution with field-cycling NMR relaxometry

Field-cycling NMR relaxometry is a well-established technique that can give information on molecular structure and dynamics of biological systems. It provides the nuclear relaxation rates as a function of the applied magnetic field, starting from fields as low as ~ 10^-4 T up to about 1-3 T. The profiles so collected, called nuclear magnetic relaxation dispersion (NMRD) profiles, can be extended to include the relaxation rates at the largest fields achievable with high resolution NMR spectrometers. By exploiting this wide range of frequencies, the NMRD profiles can provide information on motions occurring on time scales from 10^-6 to 10^-9 s. ¹H NMRD measurements have proved very useful also for the characterization of paramagnetic proteins, because they can help characterise a number of parameters including the number, distance and residence time of water molecules coordinated to the paramagnetic center, the reorientation correlation times and the electron spin relaxation time, and the electronic structure at the metal site.

A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties

Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.

Assessing multiple conformations of lanthanide binding tags for proteins using a sensitive 19F-reporter

Quantifying the isomeric species of metal complexes in solution is difficult. 19F NMR herein was used to determine the abundance of isomeric species and dynamic properties of lanthanide binding tags. The results suggest that 19F is an efficient reporter in assessing and screening paramagnetic tags suitable for protein NMR analysis.

Characterization of lanthanoid-binding proteins using NMR spectroscopy

The variety of magnetic properties exhibited by paramagnetic lanthanoids provides outstanding information in NMR-based structural biology and therefore can be a very useful tool for characterizing lanthanoid-binding proteins. Because of their dependence on the relative positions of the protein nuclei and of the lanthanoid ion, the paramagnetic restraints (PCS, PRDC and PRE) provide information on structure and dynamics of proteins. In this Chapter, we cover the use of lanthanoids in structural biology including protein sample preparation, NMR experiments and data interpretation.

Dynamic Exchange of the Metal Chelating Moiety: A Key Factor in Determining the Rigidity of Protein-Tag Conjugates in Paramagnetic NMR

Site-specific labeling of proteins with a paramagnetic tag is an efficient way to provide atomic-resolution information about the dynamics, interactions, and structures of the proteins and protein-ligand complexes. The paramagnetic effects manifested in NMR spectroscopy generally contain paramagnetic relaxation enhancement, pseudocontact shifts (PCSs), and residual dipolar coupling (RDC), and these effects correlate closely with the flexibility of protein-tag conjugates. The rigidity of the paramagnetic tag is greatly important in decoding the structural details of macromolecular complexes, because paramagnetic averaging reduces the PCSs and RDCs. Here we show that the dynamic exchange of the metal chelating moiety is a key factor in determining the rigidity of the paramagnetic tag in the protein conjugates. Decreasing the conformational exchange rates in the metal chelating moiety greatly minimizes the paramagnetic averaging and thus increases PCSs and RDCs. This effect has been demonstrated in an open-chain tag, Py-l-Cys-DTPA, which generates large PCSs and RDCs that are comparable to those of the reported cyclic DOTA-like tags. The proposed route offers a unique way to design suitable paramagnetic tags for applications in biological systems.

Solution of a Puzzle: High-Level Quantum-Chemical Treatment of Pseudocontact Chemical Shifts Confirms Classic Semiempirical Theory

A recently popularized approach for the calculation of pseudocontact shifts (PCSs) based on first-principles quantum chemistry (QC) leads to different results than the classic "semiempirical" equation involving the susceptibility tensor. Studies that attempted a comparison of theory and experiment led to conflicting conclusions with respect to the preferred theoretical approach. In this Letter, we show that after inclusion of previously neglected terms in the full Hamiltonian, one can deduce the semiempirical equations from a rigorous QC-based treatment. It also turns out that in the long-distance limit, one can approximate the complete A tensor in terms of the g tensor. By means of Kohn-Sham density functional theory calculations, we numerically confirm the long-distance expression for the A tensor and the theoretically predicted scaling behavior of the different terms. Our derivation suggests a computational strategy in which one calculates the susceptibility tensor and inserts it into the classic equation for the PCS.

Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins

The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.

Measuring transverse relaxation in highly paramagnetic systems

The enhancement of nuclear relaxation rates due to the interaction with a paramagnetic center (known as Paramagnetic Relaxation Enhancement) is a powerful source of structural and dynamics information, widely used in structural biology. However, many signals affected by the hyperfine interaction relax faster than the evolution periods of common NMR experiments and therefore they are broadened beyond detection. This gives rise to a so-called blind sphere around the paramagnetic center, which is a major limitation in the use of PREs. Reducing the blind sphere is extremely important in paramagnetic metalloproteins. The identification, characterization, and proper structural restraining of the first coordination sphere of the metal ion(s) and its immediate neighboring regions is key to understand their biological function. The novel HSQC scheme we propose here, that we termed R2-weighted, HSQC-AP, achieves this aim by detecting signals that escaped detection in a conventional HSQC experiment and provides fully reliable R2 values in the range of 1H R2 rates ca. 50-400 s-1. Independently on the type of paramagnetic center and on the size of the molecule, this experiment decreases the radius of the blind sphere and increases the number of detectable PREs. Here, we report the validation of this approach for the case of PioC, a small protein containing a high potential 4Fe-4S cluster in the reduced [Fe4S4]2+ form. The blind sphere was contracted to a minimal extent, enabling the measurement of R2 rates for the cluster coordinating residues.

Rare earth elements (REE) in biology and medicine

This survey reports on topics that were presented at the workshop on “Challenges with Rare Earth Elements. The Periodic Table at work for new Science & Technology” hold at the Academia dei Lincei in November 2019. The herein reported materials refer to presentations dealing with studies and applications of rare earth elements (REE) in several areas of Biology and Medicine. All together they show the tremendous impact REE have in relevant fields of living systems and highlight, on one hand, the still existing knowledge gap for an in-depth understanding of their function in natural systems as well as the very important role they already have in providing innovative scientific and technological solutions in a number of bio-medical areas and in fields related to the assessment of the origin of food and on their manufacturing processes. On the basis of the to-date achievements one expects that new initiatives will bring, in a not too far future, to a dramatic increase of our understanding of the REE involvement in living organisms as well as a ramp-up in the exploitation of the peculiar properties of REE for the design of novel applications in diagnostic procedures and in the set-up of powerful medical devices. This scenario calls the governmental authorities for new responsibilities to guarantee a continuous availability of REE to industry and research labs together with providing support to activities devoted to their recovery/recycling.

Paramagnetic NMR in drug discovery

The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.

Experimental Determination of Magnetic Anisotropy in Exchange-Bias Dysprosium Metallocene Single-Molecule Magnets

We investigate a family of dinuclear dysprosium metallocene single-molecule magnets (SMMs) bridged by methyl and halogen groups [Cp'₂ Dy(μ-X)]₂ (Cp'=cyclopentadienyltrimethylsilane anion; 1: X=CH₃ ^- ; 2: X=Cl^- ; 3: X=Br^- ; 4: X=I^- ). For the first time, the magnetic easy axes of dysprosium metallocene SMMs are experimentally determined, confirming that the orientation of them are perpendicular to the equatorial plane which is made up of dysprosium and bridging atoms. The orientation of the magnetic easy axis for 1 deviates from the normal direction (by 10.3°) due to the stronger equatorial interactions between Dy^III and methyl groups. Moreover, its magnetic axes show a temperature-dependent shifting, which is caused by the competition between exchange interactions and Zeeman interactions. Studies of fluorescence and specific heat as well as ab initio calculations reveal the significant influences of the bridging ligands on their low-lying exchange-based energy levels and, consequently, low-temperature magnetic properties.

The Photocatalyzed Thiol-ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins

Paramagnetic restraints have been used in biomolecular NMR for the last three decades to elucidate and refine biomolecular structures, but also to characterize protein-ligand interactions. A common technique to generate such restraints in proteins, which do not naturally contain a (paramagnetic) metal, consists in the attachment to the protein of a lanthanide-binding-tag (LBT). In order to design such LBTs, it is important to consider the efficiency and stability of the conjugation, the geometry of the complex (conformational exchanges and coordination) and the chemical inertness of the ligand. Here we describe a photo-catalyzed thiol-ene reaction for the cysteine-selective paramagnetic tagging of proteins. As a model, we designed an LBT with a vinyl-pyridine moiety which was used to attach our tag to the protein GB1 in fast and irreversible fashion. Our tag T1 yields magnetic susceptibility tensors of significant size with different lanthanides and has been characterized using NMR and relaxometry measurements.

What are the methodological and theoretical prospects for paramagnetic NMR in structural biology? A glimpse into the crystal ball

NMR spectroscopy is very sensitive to the presence of unpaired electrons, which perturb the NMR chemical shifts, J splittings and nuclear relaxation rates. These paramagnetic effects have attracted increasing attention over the last decades, and their use is expected to increase further in the future because they can provide structural information not easily achievable with other techniques. In fact, paramagnetic data provide long range structural restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements with the X-ray data. They are also precious for obtaining information on the conformational variability of biomolecular systems, possibly in conjunction with SAXS and/or DEER data. We foresee that new tools will be developed in the next years for the simultaneous analysis of the paramagnetic data with data obtained from different techniques, in order to take advantage synergistically of the information content of all of them. Of course, the use of the paramagnetic data for structural purposes requires the knowledge of the relationship between these data and the molecular coordinates. Recently, the equations commonly used, dating back to half a century ago, have been questioned by first principle quantum chemistry calculations. Our prediction is that further theoretical/computational improvements will essentially confirm the validity of the old semi-empirical equations for the analysis of the experimental paramagnetic data.