Spin-state selection in solid-state NMR

Enantiospecificity in NMR enabled by chirality-induced spin selectivity

Spin polarization in chiral molecules is a magnetic molecular response associated with electron transport and enantioselective bond polarization that occurs even in the absence of an external magnetic field. An unexpected finding by Santos and co-workers reported enantiospecific NMR responses in solid-state cross-polarization (CP) experiments, suggesting a possible additional contribution to the indirect nuclear spin-spin coupling in chiral molecules induced by bond polarization in the presence of spin-orbit coupling. Herein we provide a theoretical treatment for this phenomenon, presenting an effective spin-Hamiltonian for helical molecules like DNA and density functional theory (DFT) results on amino acids that confirm the dependence of J-couplings on the choice of enantiomer. The connection between nuclear spin dynamics and chirality could offer insights for molecular sensing and quantum information sciences. These results establish NMR as a potential tool for chiral discrimination without external agents.

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.

Biomolecular NMR spectroscopy in the era of artificial intelligence

Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in accurately characterizing protein dynamics, allostery, and conformational heterogeneity. We begin by highlighting the unique abilities of biomolecular NMR spectroscopy to complement AI-based structural predictions toward addressing these knowledge gaps. We then highlight the direct integration of deep learning approaches into biomolecular NMR methods. AI-based tools can dramatically improve the acquisition and analysis of NMR spectra, enhancing the accuracy and reliability of NMR measurements, thus streamlining experimental processes. Additionally, deep learning enables the development of novel types of NMR experiments that were previously unattainable, expanding the scope and potential of biomolecular NMR spectroscopy. Ultimately, a combination of AI and NMR promises to further revolutionize structural biology on several levels, advance our understanding of complex biomolecular systems, and accelerate drug discovery efforts.

A direct nuclear magnetic resonance method to investigate lysine acetylation of intrinsically disordered proteins

Intrinsically disordered proteins are frequent targets for functional regulation through post-translational modification due to their high accessibility to modifying enzymes and the strong influence of changes in primary structure on their chemical properties. While lysine Nε-acetylation was first observed as a common modification of histone tails, proteomic data suggest that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, compared with our biophysical understanding of the other common post-translational modifications, mechanistic studies to document how lysine Nε-acetyl marks are placed, utilized to transduce signals, and eliminated when signals need to be turned off, have not kept pace with proteomic discoveries. Herein we report a nuclear magnetic resonance method to monitor Nε-lysine acetylation through enzymatic installation of a13C-acetyl probe on a protein substrate, followed by detection through 13C direct-detect spectroscopy. We demonstrate the ease and utility of this method using histone H3 tail acetylation as a model. The clearest advantage to this method is that it requires no exogenous tags that would otherwise add steric bulk, change the chemical properties of the modified lysine, or generally interfere with downstream biochemical processes. The non-perturbing nature of this tagging method is beneficial for application in any system where changes to local structure and chemical properties beyond those imparted by lysine modification are unacceptable, including intrinsically disordered proteins, bromodomain containing protein complexes, and lysine deacetylase enzyme assays.

Surface Accessibility of an Intrinsically Disordered Protein Probed by 2D Time-Resolved Laser-Assisted NMR Spectroscopy

Probing the protein surface accessibility of different residues is a powerful way of characterizing the overall conformation of intrinsically disordered proteins (IDPs). We present a two-dimensional (2D) time-resolved photo-CIDNP (TR-CIDNP) experiment suitable for IDP analysis. Pulse stretching of high-power laser pulses, band-selective decoupling of ¹³C^α, and simultaneous application of radiofrequency and laser pulses were implemented to quantitatively analyze the IDP surface at ultrahigh resolution. Comparative analysis with other methods that measure protein surface accessibility validated the newly developed method and emphasized the importance of dye charge in photo-CIDNP. Using the neutral riboflavin dye, surface accessibilities were measured to be nearly identical for the four Tyr residues of α-synuclein (α-Syn), whose ¹H^α-¹³C^α correlations were well-resolved in the 2D TR-CIDNP spectrum. Having confirmed the similarity between the time-resolved and steady-state photo-CIDNP results for α-Syn, we used the more sensitive latter method to show that divalent cations induce compaction of the C-terminal region and release of the N-terminal region of α-Syn. The photo-CIDNP method presented herein can be used as an orthogonal and independent method for investigating important biological processes associated with changes in the overall IDP conformation.

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.

Virtual Homonuclear Decoupling in Direct Detection Nuclear Magnetic Resonance Experiments Using Deep Neural Networks

Nuclear magnetic resonance (NMR) experiments are frequently complicated by the presence of homonuclear scalar couplings. For the growing body of biomolecular 13C-detected NMR methods, one-bond 13C-13C couplings significantly reduce sensitivity and resolution. The solution to this problem has typically been to perform virtual decoupling by recording multiple spectra and taking linear combinations. Here, we propose an alternative method of virtual decoupling using deep neural networks, which only requires a single spectrum and gives a significant boost in resolution while reducing the minimum effective phase cycles of the experiments by at least a factor of 2. We successfully apply this methodology to virtually decouple in-phase CON (13CO-15N) protein NMR spectra, 13C-13C correlation spectra of protein side chains, and 13Cα-detected protein 13Cα-13CO spectra where two large homonuclear couplings are present. The deep neural network approach effectively decouples spectra with a high degree of flexibility, including in cases where existing methods fail, and facilitates the use of simpler pulse sequences.

Residue-specific identification of phase separation hot spots of Alzheimer's-related protein tau

Visualizing liquid–liquid phase separation by NMR spectroscopy: LLPS of the Alzheimer's-related protein tau involves aggregation-prone hexapeptides and activity regulating KXGS motifs.

Liquid–liquid phase separation (LLPS) of proteins enables the formation of non-membrane-bound organelles in cells and is associated with cancer and neurodegeneration. Little is known however about the structure and dynamics of proteins in LLPS conditions, because of the polymorphic nature of liquid-like protein droplets. Using carbon-detected NMR experiments we here show that the conversion of the aggregation-prone repeat region of the Alzheimer's-related protein tau from the dispersed monomeric state to phase-separated liquid-like droplets involves tau's aggregation-prone hexapeptides and regulatory KXGS motifs. Droplet dissolution in presence of 1,6-hexanediol revealed that chemical shift perturbations in the hexapeptide motifs are temperature driven, while those in KXGS motifs report on phase separation. Residue-specific secondary structure analysis further indicated that tau's repeat region exists in extended conformation in the dispersed state and attains transient β-hairpin propensity upon LLPS. Taken together our work shows that NMR spectroscopy can provide high-resolution insights into LLPS-induced changes in intrinsically disordered proteins.

Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations

In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.

Pure shift NMR

Although scalar-coupling provides important structural information, the resulting signal splittings significantly reduce the resolution of NMR spectra. Limited resolution is a particular problem in proton NMR experiments, resulting in part from the limited proton chemical shift range (∼10 ppm) but even more from the splittings due to scalar coupling to nearby protons. "Pure shift" NMR spectroscopy (also known as broadband homonuclear decoupling) has been developed for disentangling overlapped proton NMR spectra. The resulting spectra are considerably simplified as they consist of single lines, reminiscent of proton-decoupled C-13 spectra at natural abundance, with no multiplet structure. The different approaches to obtaining pure shift spectra are reviewed here and several applications presented. Pure shift spectra are especially useful for highly overlapped proton spectra, as found for example in reaction mixtures, natural products and biomacromolecules.

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.

NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines

Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).

Long-observation-window band-selective homonuclear decoupling: increased sensitivity and resolution in solid-state NMR spectroscopy of proteins

Sensitivity and resolution are the two fundamental obstacles to extending solid-state nuclear magnetic resonance to even larger protein systems. Here, a novel long-observation-window band-selective homonuclear decoupling (LOW BASHD) scheme is introduced that increases resolution up to a factor of 3 and sensitivity up to 1.8 by decoupling backbone alpha-carbon (C(α)) and carbonyl (C') nuclei in U-(13)C-labeled proteins during direct (13)C acquisition. This approach introduces short (<200 μs) pulse breaks into much longer (~8 ms) sampling windows to efficiently refocus the J-coupling interaction during detection while avoiding the deleterious effects on sensitivity inherent in rapid stroboscopic band-selective homonuclear decoupling techniques. A significant advantage of LOW-BASHD detection is that it can be directly incorporated into existing correlation methods, as illustrated here for 2D CACO, NCO, and NCA correlation spectroscopy applied to the β1 immunoglobulin binding domain of protein G and 3D CBCACO correlation spectroscopy applied to the α-subunit of tryptophan synthase.

Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of (13)C(α), is proposed.

Radio-frequency magnetometry using a single electron spin

We experimentally demonstrate a simple and robust protocol for the detection of weak radio-frequency magnetic fields using a single electron spin in diamond. Our method relies on spin locking, where the Rabi frequency of the spin is adjusted to match the MHz signal frequency. In a proof-of-principle experiment we detect a 7.5 MHz magnetic probe field of ~40 nT amplitude with <10 kHz spectral resolution. Rotating-frame magnetometry may provide a direct and sensitive route to high-resolution spectroscopy of nanoscale nuclear spin signals.

Backbone assignment and secondary structure of the PsbQ protein from photosystem II

PsbQ is one of the extrinsic proteins situated on the lumenal surface of photosystem II (PSII) in the higher plants and green algae. Its three-dimensional structure was determined by X-ray crystallography with exception of the residues 14-33. To obtain further details about its structure and potentially its dynamics, we approached the problem by NMR. In this paper we report (1)H, (15)N, and (13)C NMR assignments for the PsbQ protein. The very challenging oligo-proline stretches could be assigned using (13)C-detected NMR experiments that enabled the assignments of twelve out of the thirteen proline residues of PsbQ. The identification of PsbQ secondary structure elements on the basis of our NMR data was accomplished with the programs TALOS+, web server CS23D and CS-Rosetta. To obtain additional secondary structure information, three-bond H(N)-H(α) J-coupling constants and deviation of experimental (13)C(α) and (13)C(β) chemical shifts from random coil values were determined. The resulting "consensus" secondary structure of PsbQ compares very well with the resolved regions of the published X-ray crystallographic structure and gives a first estimate of the structure of the "missing link" (i.e. residues 14-33), which will serve as the basis for the further investigation of the structure, dynamics and interactions.

Improved accuracy in measuring one-bond and two-bond (15)N, (13)C (α) coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy

An extension to HN(CO-α/β-N,C(α)-J)-TROSY (Permi and Annila in J Biomol NMR 16:221-227, 2000) is proposed that permits the simultaneous determination of the four coupling constants (1) J (N'(i)Cα(i)), (2) J (HN(i)Cα(i)), (2) J (Cα(i-1)N'(i)), and (3) J (Cα(i-1)HN(i)) in (15)N,(13)C-labeled proteins. Contrasting the original scheme, in which two separate subspectra exhibit the (2) J (CαN') coupling as inphase and antiphase splitting (IPAP), we here record four subspectra that exhibit all combinations of inphase and antiphase splittings possible with respect to both (2) J (CαN') and (1) J (N'Cα) (DIPAP). Complementary sign patterns in the different spectrum constituents overdetermine the coupling constants which can thus be extracted at higher accuracy than is possible with the original experiment. Fully exploiting data redundance, simultaneous 2D lineshape fitting of the E.COSY multiplet tilts in all four subspectra provides all coupling constants at ultimate precision. Cross-correlation and differential-relaxation effects were taken into account in the evaluation procedure. By applying a four-point Fourier transform, the set of spectra is reversibly interconverted between DIPAP and spin-state representations. Methods are exemplified using proteins of various size.

Characteristics of zero-quantum correlation spectroscopy in MAS NMR experiments

Zero-quantum coherence generation and reconversion in magic-angle spinning solid-state NMR is analyzed. Two methods are discussed based on implementations using symmetry-based pulse sequences that utilize either isotropic J couplings or dipolar couplings. In either case, the decoupling of abundant proton spins plays a crucial role for the efficiency of the zero-quantum generation. We present optimized sequences for measuring zero-quantum single-quantum correlation spectra in solids, achieving an efficiency of 50% in ubiquitin. The advantages and disadvantages of zero-quantum single-quantum over single-quantum single-quantum correlation spectroscopy are explored, and similarities and differences with double-quantum single-quantum correlation spectroscopy are discussed. Finally, possible application of zero-quantum single-quantum experiments to polypeptides, where it can lead to better spectral resolution is investigated using ubiquitin, where we find high efficiency and high selectivity, but also increased line widths in the MQ dimension.

13C-direct detected NMR experiments for the sequential J-based resonance assignment of RNA oligonucleotides

We present here a set of (13)C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose (13)C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4' nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1',H1' ribose signals. The experiments were applied to two RNA hairpin structures. The current set of (13)C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, (13)C-direct detected NMR methods constitute useful complements to the conventional (1)H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs.

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.

NMR structure of the N-terminal domain of capsid protein from the mason-pfizer monkey virus

The high-resolution structure of the N-terminal domain (NTD) of the retroviral capsid protein (CA) of Mason-Pfizer monkey virus (M-PMV), a member of the betaretrovirus family, has been determined by NMR. The M-PMV NTD CA structure is similar to the other retroviral capsid structures and is characterized by a six alpha-helix bundle and an N-terminal beta-hairpin, stabilized by an interaction of highly conserved residues, Pro1 and Asp57. Since the role of the beta-hairpin has been shown to be critical for formation of infectious viral core, we also investigated the functional role of M-PMV beta-hairpin in two mutants (i.e., DeltaP1NTDCA and D57ANTDCA) where the salt bridge stabilizing the wild-type structure was disrupted. NMR data obtained for these mutants were compared with those obtained for the wild type. The main structural changes were observed within the beta-hairpin structure; within helices 2, 3, and 5; and in the loop connecting helices 2 and 3. This observation is supported by biochemical data showing different cleavage patterns of the wild-type and the mutated capsid-nucleocapsid fusion protein (CANC) by M-PMV protease. Despite these structural changes, the mutants with disrupted salt bridge are still able to assemble into immature, spherical particles. This confirms that the mutual interaction and topology within the beta-hairpin and helix 3 might correlate with the changes in interaction between immature and mature lattices.

Discerning the degenerate transitions of scalar coupled 1H NMR spectra: correlation and resolved techniques at higher quantum

The blend of spin topological filtering and the spin state selective detection of single quantum transitions by the two dimensional multiple quantum-single quantum correlation and higher quantum resolved techniques have been employed for simplifying the complexity of scalar coupled (1)H NMR spectra. The conventional two dimensional COSY and TOCSY experiments, though identify the coupled spin networks, fail to differentiate them due to severe overlap of transitions. Non-selective excitation of homonuclear higher quantum of protons results in filtering of spin systems irrespective of their spin topologies. The spin state selection by passive (19)F spins provides fewer transitions in each cross section of the single quantum dimension simplifying the analyses of the complex spectra. The degenerate single quantum transitions are further discerned by spin selective double and/or triple quantum resolved experiments that mimic simultaneous heteronuclear and selective homonuclear decoupling in the higher quantum dimension. The techniques aided the determination of precise values of spectral parameters and relative signs of the couplings.

Spin-selective multiple quantum excitation: relative signs of the couplings and ambiguous situations

Homonuclear higher quantum NMR spectra of heteronuclear spin systems result in fewer transitions aiding the analyses. In such experiments the spin states of the heteronuclei do not get disturbed in both single and multiple quantum dimensions resulting in the separation of active homonuclear and passive heteronuclear couplings in two dimensions. The cross sections of the single-quantum dimension get displaced according to the strengths of the passive couplings. The directions of the displacement of these cross sections provide relative signs among the passive couplings. The present study demonstrates the situations when the displacement vectors, though provide the relative signs, could be ambiguous. The dynamics of the spin systems in homo- and heteronuclear multiple quantum studies have been discussed using polarization operator approach. The experimental results on (13)C- and (15)N-labeled isotopomers of acetonitrile, in both isotropic and thermotropic liquid crystalline phases, are reported.

Resolution enhancement by homonuclear J-decoupling: application to three-dimensional solid-state magic angle spinning NMR spectroscopy

We describe a simple protocol to achieve homonuclear J-decoupling in the indirect dimensions of multidimensional experiments, and to enhance spectral resolution of the backbone Calpha carbons in the 3D NCACX experiment. In the proposed protocol, the refocusing of the Calpha-CO homonuclear J-couplings is achieved by applying an off-resonance selective pi pulse to the CO spectral region in the middle of Calpha chemical shift evolution. As is commonly used in solution NMR, a compensatory echo period is used to refocus the unwanted chemical shift evolution of Calpha spins, which takes place during the off-resonance selective pulse. The experiments were carried out on the beta1 immunoglobulin binding domain of protein G (GB1). In GB1, such implementation results in significantly reduced line widths, and leads to an overall sensitivity enhancement.

Spin state selective coherence transfer: a method for discrimination and complete analyses of the overlapped and unresolved 1H NMR spectra of enantiomers

In general, the proton NMR spectra of chiral molecules aligned in the chiral liquid crystalline media are broad and featureless. The analyses of such intricate NMR spectra and their routine use for spectral discrimination of R and S optical enantiomers are hindered. A method is developed in the present study which involves spin state selective two dimensional correlation of higher quantum coherence to its single quantum coherence of a chemically isolated group of coupled protons. This enables the spin state selective detection of proton single quantum transitions based on the spin states of the passive nuclei. The technique provides the relative signs and magnitudes of the couplings by overcoming the problems of enantiomer discrimination, spectral complexity and poor resolution, permitting the complete analyses of the otherwise broad and featureless spectra. A non-selective 180 degrees pulse in the middle of MQ dimension retains all the remote passive couplings. This accompanied by spin selective MQ-SQ conversion leads to spin state selective coherence transfer. The removal of field inhomogeneity contributes to dramatically enhanced resolution. The difference in the cumulative additive values of chemical shift anisotropies and the passive couplings, between the enantiomers, achieved by detecting Nth quantum coherence of N magnetically equivalent spins provides enhanced separation of enantiomer peaks. The developed methodology has been demonstrated on four different chiral molecules with varied number of interacting spins, each having a chiral centre.

13C-detection in RNA bases: revealing structure-chemical shift relationships

The chemical shifts of the unprotonated carbons in the proton-deficient nucleobases of RNA are rarely reported, despite the valuable information that they contain about base-pairing and base-stacking. We have developed 13C-detected 2D-experiments to identify the unprotonated 13C in the RNA bases and have assigned all the base nuclei of uniformly 13C,15N-labeled HIV-2 TAR-RNA. The 13C chemical shift distributions revealed perturbations correlated with the base-pairing and base-stacking properties of all four base-types. From this work, we conclude that the information contained in the chemical shift perturbations within the base rings can provide valuable restraint information for solving RNA structures, especially in conformational averaged regions, where NOE-based information is not available.

J-based 2D homonuclear and heteronuclear correlation in solid-state proteins

Scalar-based two-dimensional heteronuclear experiments are reported for NCO and NCA chemical shift correlation in the solid state. In conjunction with homonuclear CACO correlation, these experiments form a useful set for tracing connectivities and assigning backbone resonances in solid-state proteins. The applicability of this approach is demonstrated on two proteins, the β 1 immunoglobulin binding domain of protein G at 9.4 T and reassembled thioredoxin at 14.1 T, using different decoupling conditions and MAS frequencies. These constant-time J-based correlation experiments exhibit increased resolution in the indirect dimension owing to homonuclear and heteronuclear decoupling, and because the indirect evolution and transfer periods are combined into a single constant time interval, this increased resolution is not obtained at the cost of sensitivity. These experiments are also shown to be compatible with in-phase anti-phase (IPAP) selection, giving increased resolution in the directly detected dimension.

A method for C(alpha) direct-detection in protonless NMR

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.

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.

J-Deconvolution Using Maximum Entropy Reconstruction Applied to 13C−13C Solid-State Cross-Polarization Magic-Angle-Spinning NMR of Proteins

Scalar couplings between 13C spins can impair both resolution and sensitivity in 13C-labeled preparations. It is demonstrated that deconvolution of magic-angle-spinning NMR data with maximum entropy (MaxEnt) reconstruction allows the removal of splittings due to J-couplings without expenses in sensitivity. A combination of MaxEnt reconstruction in t2 with selective pulses in t1 produces fully J-resolved data in both dimensions. The possibility to obtain J-resolved 13C-13C data without compromising the sensitivity is particularly important for solid-state NMR of "difficult" biological samples, like membrane proteins, where sacrifices in signal-to-noise are fatal. The method is demonstrated using preparations of alpha-spectrin SH3 domain (62 residues) as small test system and of outermembrane protein G as example of a membrane protein with higher molecular weight (281 residues). Both preparations were obtained using [2-13C]-glycerol as the carbon source during the bacterial growth.

Improved resolution in (13)C solid-state spectra through spin-state-selection

The application of a spin-state-selective coherence transfer experiment (INADEQUATE-SSS) to solid-state NMR spectroscopy is described. Two-dimensional (13)C double-quantum/single-quantum spectra without J splittings in both dimensions lead to enhanced spectral resolution. The method is demonstrated to significantly improve the spectral resolution of the crowded C'-C(alpha) region of two proteins.

Selective NMR Measurements of Homonuclear Scalar Couplings in Isotopically Enriched Solids

Scalar (J) couplings in solid-state NMR spectroscopy are sensitive to covalent through-bond interactions that make them informative structural probes for a wide range of complex materials. Until now, however, they have been generally unsuitable for use in isotopically enriched solids, such as proteins or many inorganic solids, because of the complications presented by multiple coupled but nonisolated spins. Such difficulties are overcome by incorporating a z-filter that results in a robust method for measuring pure J-coupling modulations between selected pairs of nuclei in an isotopically enriched spin system. The reliability of the new experimental approach is established by using numerical simulations and tested on fully (13)C-labeled polycrystalline L-alanine. It is furthermore shown to be applicable to partially enriched systems, when used in combination with a selective double-quantum (DQ) filter, as demonstrated for the measurement of (2)J((29)Si-O-(29)Si) couplings in a 50% (29)Si-enriched surfactant-templated layered silicate lacking long-range 3D crystallinity. J-coupling constants are obtained with sufficient accuracy to distinguish between different (29)Si-O-(29)Si pairs, shedding insight on the local structure of the silicate framework. The new experiment is appropriate for fully or partially enriched liquid or solid samples.

Band-selective 13C homonuclear 3D spectroscopy for solid proteins at high field with rotor-synchronized soft pulses

We demonstrate improved 3D 13C-13C-13C chemical shift correlation experiments for solid proteins, utilizing band-selective coherence transfer, scalar decoupling and homonuclear zero-quantum polarization transfer. Judicious use of selective pulses and a z-filter period suppress artifacts with a two-step phase cycle, allowing higher digital resolution in a fixed measurement time. The novel correlation of C(ali)-C(ali)-CX (C(ali) for aliphatic carbons, CX for any carbon) reduces measurement time by an order of magnitude without sacrificing digital resolution. The experiment retains intensity from side-chain carbon resonances whose chemical shift dispersion is critical to minimize spectral degeneracy for large proteins with a predominance of secondary structure, such as beta-sheet rich fibrillar proteins and alpha-helical membrane proteins. We demonstrate the experiment for the beta1 immunoglobulin binding domain of protein G (GB1) and fibrils of the A30P mutant of alpha-synuclein, which is implicated in Parkinson's disease. Selective pulses of duration comparable the rotor period give optimal performance, but must be synchronized with the spinning in non-trivial ways to minimize chemical shift anisotropy recoupling effects. Soft pulses with a small bandwidth-duration product are best for exciting the approximately 70 ppm bandwidth required for aliphatic-only dimensions.

Selective refocusing pulses in magic-angle spinning NMR: characterization and applications to multi-dimensional protein spectroscopy

Band-selective pulses are frequently used in multi-dimensional NMR in solution, but have been used relatively less often in solid-state NMR applications because of the complications imposed by magic-angle spinning. In this work, we examine the frequency profiles and the refocusing efficiency of several commonly employed selective general rotation pi pulses through experiments and numerical simulations. We demonstrate that highly efficient refocusing of transverse magnetization can be achieved, with experiments that agree well with numerical simulations. We also show that the rotational echo is shifted by a half rotor period if a selective pulse is applied over an integer number of rotor periods. Appropriately synchronizing indirect evolution periods with selective pulses ensures proper phasing of cross peaks in 2D spectra. The improved performance of selective pulses in multi-dimensional protein spectroscopy is demonstrated on the 56-residue beta1 immunoglobulin binding domain of protein G (GB1).

Novel 13C direct detection experiments, including extension to the third dimension, to perform the complete assignment of proteins

Carbon-13 direct detection NMR methods are feasible thanks to the improvements in probehead technology and to the development of new NMR experiments. We present here a complete set of experiments, based on C' direct detection, developed to perform protein complete assignment of backbone and side-chains (except for aromatic rings). This strategy offers alternative solutions for demanding situations (paramagnetic and/or large molecules) and can be useful in general in conjunction with conventional experiments.

Homo-nuclear 13C J-decoupling in uniformly 13C-enriched solid proteins

Recently, we reported an analysis of carbon lineshapes in high resolution solid-state NMR spectra of uniformly 13C-enriched amino acids. Application of a 13C J-decoupling protocol during the carbon chemical shift evolution period allowed us to separate the contribution of the second-order dipolar shift from that of the 13C-13C J-coupling interactions to carbon linewidths. In this work, we have extended this approach to microcrystalline proteins. We describe the performance of the J-decoupling sequence applied to remove homo-nuclear 13C J-couplings in the 13C spectra of ubiquitin. Analysis of the J-decoupling efficiency for C(alpha) and carbonyl protein sites showed that a significant gain in resolution can be achieved.

Resolution enhancement in MAS solid-state NMR by application of 13C homonuclear scalar decoupling during acquisition

Spectral resolution imposes a major problem on the evaluation of MAS solid-state NMR experiments as larger biomolecular systems are concerned. We show in this communication that decoupling of the (13)C-(13)C homonuclear scalar couplings during stroboscopic detection can be successfully applied to increase the spectral resolution up to a factor of 2-2.5 and sensitivity up to a factor of 1.2. We expect that this approach will be useful for the study of large biomolecular systems like membrane proteins and amyloidogenic peptides and proteins where spectral overlap is critical. The experiments are demonstrated on a uniformly (13)C,(15)N-labelled sample of Nac-Val-Leu-OH and applied to a uniformly (13)C,(15)N-enriched sample of a hexameric amyloidogenic peptide.

(13)C-(13)C NOESY: a constructive use of (13)C-(13)C spin-diffusion

(13)C-(13)C NOESY experiments were performed under long mixing time conditions on reduced human superoxide dismutase (32 kDa, (15)N, (13C) and 70% (2)H labeled). (13)C-(13)C couplings were successfully eliminated through post-processing of in-phase-anti-phase (IPAP) data. It appears that at mixing time tau(m) of 3.0 s the spin diffusion mechanism allows the detection of 96% of the two-bond correlations involving C' and C(beta). The interpretation was confirmed by simulations. This approach broadens the range of applicability of (13)C-(13)C NOESY spectroscopy.

Resolution Enhancement in Multidimensional Solid-State NMR Spectroscopy of Proteins Using Spin-State Selection

We show that the resolution of homonuclear multidimensional solid-state NMR correlation experiments can be significantly improved using transition selection and spin-state-selective polarization transfer techniques. The selection and transfer of single states allow the removal of the J-coupling contribution from the line width in both the direct and indirect spectral dimensions. This is demonstrated with a new spin-state-selective CO-Calpha correlation experiment, applied to a microcrystalline 85-residue protein. With this new sequence, all four components of the CO-Calpha cross-peaks are separated into different spectra, obtained by linear combination of four recorded data sets. Line narrowing of up to 44% was obtained on the protein sample for the spin-state-selective CO-Calpha spectrum compared to a standard spin-diffusion experiment. The new technique also allows an easy distinction between "direct" and "relayed" transfer cross-peaks.