13C direct detected NMR increases the detectability of residual dipolar couplings

Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center

The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.

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.

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.

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.

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.

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.

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.

The long-standing relationship between paramagnetic NMR and iron-sulfur proteins: the mitoNEET example. An old method for new stories or the other way around?

Paramagnetic NMR spectroscopy and iron-sulfur (Fe-S) proteins have maintained a synergic relationship for decades. Indeed, the hyperfine shifts with their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues have been extensively used as a fingerprint of the type and of the oxidation state of the Fe-S cluster within the protein frame. The identification of NMR signals from residues surrounding the metal cofactor is crucial for understanding the structure-function relationship in Fe-S proteins, but it is generally impaired in standard NMR experiments by paramagnetic relaxation enhancement due to the presence of the paramagnetic cluster(s). On the other hand, the availability of systems of different sizes and stabilities has, over the years, stimulated NMR spectroscopists to exploit iron-sulfur proteins as paradigmatic cases to develop experiments, models, and protocols. Here, the cluster-binding properties of human mitoNEET have been investigated by 1D and 2D 1 H diamagnetic and paramagnetic NMR, in its oxidized and reduced states. The NMR spectra of both oxidation states of mitoNEET appeared to be significantly different from those reported for previously investigated [ Fe 2 S 2 ] 2 + / + proteins. The protocol we have developed in this work conjugates spectroscopic information arising from "classical" paramagnetic NMR with an extended mapping of the signals of residues around the cluster which can be taken, even before the sequence-specific assignment is accomplished, as a fingerprint of the protein region constituting the functional site of the protein. We show how the combined use of 1D NOE experiments, 13 C direct-detected experiments, and double- and triple-resonance experiments tailored using R1 - and/or R2 -based filters significantly reduces the "blind" sphere of the protein around the paramagnetic cluster. This approach provided a detailed description of the unique electronic properties of mitoNEET, which are responsible for its biological function. Indeed, the NMR properties suggested that the specific electronic structure of the cluster possibly drives the functional properties of different [ Fe 2 S 2 ] proteins.

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.

Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra

Paramagnetic metal ions with fast-relaxing electrons generate pseudocontact shifts (PCSs), residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) and cross-correlated relaxation (CCR) in the nuclear magnetic resonance (NMR) spectra of the molecules they bind to. These effects offer long-range structural information in molecules equipped with binding sites for such metal ions. Here we present the new open-source software Paramagpy, which has been written in Python 3 with a graphic user interface. Paramagpy combines the functionalities of different currently available programs to support the fitting of magnetic susceptibility tensors using PCS, RDC, PRE and CCR data and molecular coordinates in Protein Data Bank (PDB) format, including a convenient graphical user interface. Paramagpy uses efficient fitting algorithms to avoid local minima and supports corrections to back-calculated PCS and PRE data arising from cross-correlation effects with chemical shift tensors. The source code is available from 10.5281/zenodo.3594568 .

Both metal-chelating and free radical-scavenging synthetic pentapeptides as efficient inhibitors of reactive oxygen species generation

The very first Fe(iii)-peptide chelators exhibiting antioxidant properties thanks to an unprecedented dual direct/indirect mode of action.

Resonance Assignments of Lowly Populated and Unstable Enzyme Intermediate Complex under Real-Time Conditions

Unstable and low-abundance protein complexes represent a large family of transient protein complexes that are difficult to characterize, even by means of high-resolution NMR spectroscopy. A method to assign the NMR signals of these unstable complexes through a combination of selective isotope labeling of amino acids in a protein and site-specific labeling the protein with a paramagnetic tag is presented herein. By using this method, the resonances of unstable thioester intermediate complex (lifetime <5 h and highest concentration ≈20 μm) generated by Staphylococcus aureus sortase A and its peptide substrate under a real-time reaction have been assigned.

Capturing a dynamically interacting inhibitor by paramagnetic NMR spectroscopy

Transient and fuzzy intermolecular interactions are fundamental to many biological processes. Despite their importance, they are notoriously challenging to characterize. Effects induced by paramagnetic ligands in the NMR spectra of interacting biomolecules provide an opportunity to amplify subtle manifestations of weak intermolecular interactions observed for diamagnetic ligands. Here, we present an approach to characterizing dynamic interactions between a partially flexible dimeric protein, HIV-1 protease, and a metallacarborane-based ligand, a system for which data obtained by standard NMR approaches do not enable detailed structural interpretation. We show that for the case where the experimental data are significantly averaged to values close to zero the standard fitting of pseudocontact shifts cannot provide reliable structural information. We based our approach on generating a large ensemble of full atomic models, for which the experimental data can be predicted, ensemble averaged and finally compared to the experiment. We demonstrate that a combination of paramagnetic NMR experiments, quantum chemical calculations, and molecular dynamics simulations offers a route towards structural characterization of dynamic protein-ligand complexes.

Long-range paramagnetic NMR data can provide a closer look on metal coordination in metalloproteins

Paramagnetic NMR data can be profitably incorporated in structural refinement protocols of metalloproteins or metal-substituted proteins, mostly as distance or angle restraints. However, they could in principle provide much more information, because the magnetic susceptibility of a paramagnetic metal ion is largely determined by its coordination sphere. This information can in turn be used to evaluate changes occurring in the coordination sphere of the metal when ligands (e.g.: inhibitors) are bound to the protein. This gives an experimental handle on the molecular structure in the vicinity of the metal which falls in the so-called blind sphere. The magnetic susceptibility anisotropy tensors of cobalt(II) and nickel(II) ions bound to human carbonic anhydrase II in free and inhibited forms have been determined. The change of the magnetic susceptibility anisotropy is directly linked to the binding mode of different ligands in the active site of the enzyme. Indication about the metal coordination sphere in the presence of an inhibitor in pharmaceutically relevant proteins could be important in the design of selective drugs with a structure-based approach.

Perspectives on paramagnetic NMR from a life sciences infrastructure

The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as "paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the exploitation of the Overhauser effect occurring through the contact-driven relaxation mechanism: the very large enhancement of the ¹³C signal observed in a variety of liquid organic compounds at high fields is expected to open up new perspectives for applications of solution NMR.

Towards a protocol for solution structure determination of copper(II) proteins: the case of Cu(II)Zn(II) superoxide dismutase

We have developed an optimized protocol to solve the solution structure of copper(II) proteins. After assignment, proton-proton NOEs are used for the shell where 1H spectra are conveniently observed. In a shell closer to the metal ion, 13C NMR spectra with band-selective homonuclear decoupling provide the assignment of all nuclei except for those of the metal ligands. A convenient method for the measurement of 13C longitudinal-relaxation rates (R1) of carbonyls and carboxylate moieties is proposed. 1H NOEs and 1H and 13C R1 data are sufficient to produce a good/reasonable solution structure, as demonstrated for a monomeric species of superoxide dismutase, a 153-residue protein.

Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR

Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.

Spin-state-selective methods in solution- and solid-state biomolecular 13C NMR

Spin-state-selective methods to achieve homonuclear decoupling in the direct acquisition dimension of (13)C detected NMR experiments have been one of the key contributors to converting (13)C detected NMR experiments into really useful tools for studying biomolecules. We discuss here in detail the various methods that have been proposed, summarize the large array of new experiments that have been developed and present applications to different kinds of proteins in different aggregation states.

FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data

Pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) arising from the presence of paramagnetic metal ions in proteins as well as RDCs due to partial orientation induced by external orienting media are nowadays routinely measured as a part of the NMR characterization of biologically relevant systems. PCSs and RDCs are becoming more and more popular as restraints (1) to determine and/or refine protein structures in solution, (2) to monitor the extent of conformational heterogeneity in systems composed of rigid domains which can reorient with respect to one another, and (3) to obtain structural information in protein-protein complexes. The use of both PCSs and RDCs proceeds through the determination of the anisotropy tensors which are at the origin of these NMR observables. A new user-friendly web tool, called FANTEN (Finding ANisotropy TENsors), has been developed for the determination of the anisotropy tensors related to PCSs and RDCs and has been made freely available through the WeNMR ( http://fanten-enmr.cerm.unifi.it:8080 ) gateway. The program has many new features not available in other existing programs, among which the possibility of a joint analysis of several sets of PCS and RDC data and the possibility to perform rigid body minimizations.

Insights into domain-domain motions in proteins and RNA from solution NMR

Many multidomain proteins and ribonucleic acids consist of domains that autonomously fold and that are linked together by flexible junctions. This architectural design allows domains to sample a wide range of positions with respect to one another, yet do so in a way that retains structural specificity, since the number of sampled conformations remains extremely small compared to the total conformations that would be sampled if the domains were connected by an infinitely long linker. This “tuned” flexibility in interdomain conformation is in turn used in many biochemical processes.

There is great interest in characterizing the dynamic properties of multidomain systems, and moving beyond conventional descriptions in terms of static structures, toward the characterization of population-weighted ensembles describing a distribution of many conformations sampled in solution. There is also great interest in understanding the design principles and underlying physical and chemical interactions that specify the nature of interdomain flexibility. NMR spectroscopy is one of the most powerful techniques for characterizing motions in complex biomolecules and has contributed greatly toward our basic understanding of dynamics in proteins and nucleic acids and its role in folding, recognition, and signaling.

Here, we review methods that have been developed in our laboratories to address these challenges. Our approaches are based on the ability of one domain of the molecule to self-align in a magnetic field, or to dominate the overall orientation of the molecule, so that the conformational freedom of other domains can be assessed by their degree of alignment induced by the aligned part. In turn, this self-alignment ability can be intrinsic or can be caused by tagging appropriate constructs to the molecule of interest. In general, self-alignment is due to magnetic susceptibility anisotropy. Nucleic acids with elongated helices have this feature, as well as several paramagnetic metal centers that can be found in, or attached to, a protein domain.

Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

Novel methods based on (13)C detection to study intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.

The IR-¹⁵N-HSQC-AP experiment: a new tool for NMR spectroscopy of paramagnetic molecules

A crucial factor for the understanding of structure-function relationships in metalloproteins is the identification of NMR signals from residues surrounding the metal cofactor. When the latter is paramagnetic, the NMR information in the proximity of the metal center may be scarce, because fast nuclear relaxation quenches signal intensity and coherence transfer efficiency. To identify residues at a short distance from a paramagnetic center, we developed a modified version of the ¹⁵N-HSQC experiment where (1) an inversion recovery filter is added prior to HSQC, (2) the INEPT period has been optimized according to fast relaxation of interested spins, (3) the inverse INEPT has been eliminated and signals acquired as antiphase doublets. The experiment has been successfully tested on a human [Fe₂S₂] protein which is involved in the biogenesis of iron-sulfur proteins. Thirteen HN resonances, unobserved with conventional HSQC experiments, could be identified. The structural arrangement of the protein scaffold in the proximity of the Fe/S cluster is fundamental to comprehend the molecular processes responsible for the transfer of Fe/S groups in the iron-sulfur protein assembly machineries.

Structural characterization of intrinsically disordered proteins by NMR spectroscopy

Recent advances in NMR methodology and techniques allow the structural investigation of biomolecules of increasing size with atomic resolution. NMR spectroscopy is especially well-suited for the study of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) which are in general highly flexible and do not have a well-defined secondary or tertiary structure under functional conditions. In the last decade, the important role of IDPs in many essential cellular processes has become more evident as the lack of a stable tertiary structure of many protagonists in signal transduction, transcription regulation and cell-cycle regulation has been discovered. The growing demand for structural data of IDPs required the development and adaption of methods such as ¹³C-direct detected experiments, paramagnetic relaxation enhancements (PREs) or residual dipolar couplings (RDCs) for the study of ‘unstructured’ molecules in vitro and in-cell. The information obtained by NMR can be processed with novel computational tools to generate conformational ensembles that visualize the conformations IDPs sample under functional conditions. Here, we address NMR experiments and strategies that enable the generation of detailed structural models of IDPs.

Electron self-exchange of cytochrome c measured via13C detected protonless NMR

The use of protonless 13C′–13C′ EXSY (COCO-EXSY) is proposed here to measure electron self-exchange rates. The experiment is compared to the commonly employed 1H and 15N EXSY experiments using as a reference system human cytochrome c. In COCO-EXSY, the exchange peaks are stronger than in the other experiments with respect to the self peaks and their intensity is less dependent on the choice of the EXSY mixing time. The use of 13C directed detection may be essential for all those cases where T2 relaxation is detrimental, as in the case of proteins containing highly paramagnetic metal centers, or rotating slowly in solution, or where the amide signals are difficult to detect due to chemical or conformational exchange. The proposed experiment has a general applicability and can be used to monitor exchange phenomena different from electron self-exchange.

High-resolution characterization of intrinsic disorder in proteins: expanding the suite of (13)C-detected NMR spectroscopy experiments to determine key observables

Order in disorder: The characterization of intrinsically disordered proteins by NMR spectroscopy is a necessity on the one hand and a continuous challenge on the other. We propose two experiments that provide diagnostic parameters to monitor the degree of unfolding of a polypeptide. The test was performed on the yeast Cox17 protein, known to gain its function through maturation from an intrinsically disordered state (see figure).

Solid-state NMR crystallography through paramagnetic restraints

Pseudocontact shifts (PCSs) measured by solid-state NMR spectroscopy (SS-NMR) on microcrystalline powders of a paramagnetic metalloprotein permit NMR crystallography. Along with other restraints for SS-NMR experiments, the protein molecular structure as well as the correct crystal packing are obtained.

Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains

Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramagnetism-based restraints. These restraints were measured after inclusion of a lanthanide binding tag in the C-terminal domain to supplement the data obtained by substitution of three paramagnetic lanthanide ions to the calcium ion in the second calcium binding loop of the N-terminal domain. The analysis shows that the availability of paramagnetic restraints arising from metal ions placed on both domains, reduces the MO of the conformations to different extents, thereby helping to identify those conformations that can be mostly sampled by the protein.

High-resolution solid-state NMR structure of a 17.6 kDa protein

The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.

Perspectives in paramagnetic NMR of metalloproteins

NMR experiments and tools for the characterization of the structure and dynamics of paramagnetic proteins are presented here. The focus is on the importance of (13)C direct-detection NMR for the assignment of paramagnetic systems in solution, on the information contained in paramagnetic effects observed both in solution and in the solid state, and on novel paramagnetism-based tools for the investigation of conformational heterogeneity in protein-protein complexes or in multi-domain proteins.

13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases

The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

Spin-state selective carbon-detected HNCO with TROSY optimization in all dimensions and double echo-antiecho sensitivity enhancement in both indirect dimensions

A carbon-detected TROSY-optimized experiment correlating 1HN, 15N, and 13C' resonances, referred to as c-TROSY-HNCO is presented, in which the 1HN and 15N TROSY effects are maintained in both indirect dimensions, while the directly detected 13C' is doubly TROSY-optimized with respect to 1HN and 15N. A new strategy for sensitivity enhancement, the so-called double echo-antiecho (dEA), is described and implemented in the c-TROSY-HNCO experiment. dEA offers sensitivity enhancement of square root of 2 in both indirect dimensions and is generally applicable to many multidimensional experiments. A carbon-detected HNCO experiment, c-HNCO, without TROSY optimization and sensitivity enhancement is also designed for comparison purposes. Relaxation simulations show that for a protein with a rotational correlation time of 10 ns or larger, the c-TROSY-HNCO experiment displays comparable or higher signal-to-noise (S/N) ratios than the c-HNCO experiment, although the former selects only 1/4 of the initial magnetization relative to the later. The high resolution afforded in the directly detected carbon dimension allows direct measurement of the doublet splitting to extract 1JCalphaC' scalar and 1DCalphaC' residual dipolar couplings. Simulations indicate that the c-TROSY-HNCO experiment offers higher precision (lower uncertainty) compared to the c-HNCO experiment for larger proteins. The experiments are applied to 15N/13C/2H/[Leu,Val]-methyl-protonated IIBMannose, a protein of molecular mass 18.6 kDa with a correlation time of approximately 10 ns at 30 degrees C. The experimental pairwise root-mean-square deviation for the measured 1JCalphaC' couplings obtained from duplicate experiments is 0.77 Hz. By directly measuring the doublet splitting, the experiments described here are expected to be much more tolerant to nonuniform values of 1JCalphaC' (or 1JCalphaC' + 1DCalphaC' for aligned samples) and pulse imperfections due to the smaller number of applied pulses in the "out-and-stay" coherence transfer in the c-HNCO-TROSY experiment relative to conventional 1H-detected "out-and-back" quantitative J correlation experiments. A carbon-detected TROSY-optimized experiment correlating 1HN, 15N, and 13C' resonances, referred to as c-TROSY-HNCO is presented, in which the 1HN and 15N TROSY effects are maintained in both indirect dimensions, while the directly detected 13C' is doubly TROSY-optimized with respect to 1HN and 15N. A new strategy for sensitivity enhancement, the so-called double echo-antiecho (dEA), is described and implemented in the c-TROSY-HNCO experiment. dEA offers sensitivity enhancement of in both indirect dimensions and is generally applicable to many multidimensional experiments.