Pseudomultidimensional NMR by Spin-State Selective Off-Resonance Decoupling

Confronting the Invisible: Assignment of Protein 1HN Chemical Shifts in Cases of Extreme Broadening

NMR studies of intrinsically disordered proteins (IDPs) at neutral pH values are hampered by the rapid exchange of backbone amide protons with solvent. Although exchange rates can be modulated by changes in pH, interactions between IDPs that lead to phase separation sometimes only occur at neutral pH values or higher, where backbone amide-based experiments fail. Here we describe a simple NMR experiment for measuring amide proton chemical shifts in cases where ¹H^N spectra cannot be obtained. The approach uses a weak ¹H B₁ field, searching for elusive ¹H^N resonance frequencies that become encoded in the intensities of cross-peaks in three-dimensional ¹H^α-detect spectra. Applications to the CAPRIN1 protein in both dilute- and phase-separated states highlight the utility of the method, establishing that accurate ¹H^N chemical shifts can be obtained even in cases where solvent hydrogen exchange rates are on the order of 1500 s^-1.

Measurement of J-couplings between chemically equivalent nuclei using off-resonance decoupling

The method of measuring J-couplings between chemically equivalent nuclei in isotopically/magnetically non-equivalent environment, based on off-resonance decoupling, is described. The approach uses intensities, rather than frequencies of the spectral peaks and, therefore, the accuracy of measurement is not limited by spectral resolution.

Multidimensional J-driven NMR correlations by single-scan offset-encoded recoupling

Two-dimensional (2D) correlations between bonded heteroatoms, lie at the cornerstone of many uses given to contemporary nuclear magnetic resonance (NMR). Improving the efficiency with which these correlations are established is an important topic in modern NMR, with potential applications in rapid chemical analysis and dynamic biophysical studies. Alternatives have been developed over the last decade to speed up these experiments, based among others on reducing the number of data points that need to be sampled, and/or shortening the inter-scan delays. Approaches have also been proposed to forfeit multi-scan schemes altogether, and complete full 2D correlations in a single shot. Here we explore and discuss a new alternative enabling the collection of such very fast - in principle, single-scan - acquisitions of 2D heteronuclear correlations among bonded species, which operates on the basis of a partial reintroduction of J couplings. Similar approaches had been proposed in the past based on collecting coupled spectra for arrays of off-resonance decoupling values; the proposal that is here introduced operates on the basis of suitably incorporating frequency-swept pulses, into spin-echo sequences. Thanks to the offset-dependent amplitude modulations of the in- and anti-phase components that such sequences impart, chemical shifts of coupled but otherwise unobserved nuclear species, can be extracted from the relative intensities and phases of J-coupled multiplets observed in one-dimensional acquisitions. A description of the steps needed to implement this rapid acquisition approach in a quantitative fashion, as well as applications of the ensuing sequences, are presented.

SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition

Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.

Chemical shift correlations from hyperpolarized NMR using a single SHOT

A significant challenge in realizing the promise of the dissolution dynamic nuclear polarization technique for signal enhancement in high-resolution NMR lies in the nonrenewability of the hyperpolarized spin state. This property prevents the application of traditional two-dimensional correlation spectroscopy, which relies on regeneration of spin polarization before each successive increment of the indirect dimension. Since correlation spectroscopy is one of the most important approaches for the identification and structural characterization of molecules by NMR, it is important to find easily applicable methods that circumvent this problem. Here, we introduce the application of scaling of heteronuclear couplings by optimal tracking (SHOT) to achieve this goal. SHOT decoupling pulses have been numerically optimized on the basis of optimal control algorithms to obtain chemical shift correlations in C-H groups, either by acquiring a single one-dimensional (13)C spectrum with (1)H off-resonance decoupling or vice versa. Vanillin, which contains a number of functional groups, was used as a test molecule, allowing the demonstration of SHOT decoupling tailored toward simplified and accurate data analysis. This strategy was demonstrated for two cases: First, a linear response to chemical shift offset in the correlated dimension was optimized. Second, a pulse with alternating linear responses in the correlated dimension was chosen as a goal to increase the sensitivity of the decoupling response to the chemical shift offset. In these measurements, error ranges of ±0.03 ppm for the indirectly determined (1)H chemical shifts and of ±0.4 ppm for the indirectly determined (13)C chemical shifts were found. In all cases, we show that chemical shift correlations can be obtained from information contained in a single scan, which maximizes the ratio of signal to stochastic noise. Furthermore, a comprehensive discussion of the robustness of the method toward nonideal conditions is included based on experimental and simulated data. Unique features of this technique include the abilities to control the accuracy of chemical shift determination in spectral regions of interest and to acquire such chemical shift correlations rapidly-the latter being of interest for potential application in real-time spectroscopy.

Measurement of proton chemical shifts in invisible states of slowly exchanging protein systems by chemical exchange saturation transfer

Chemical exchange saturation transfer (CEST) NMR spectroscopy has emerged as a powerful technique for studies of transiently formed, sparsely populated (excited) conformational states of protein molecules in slow exchange with a dominant structure. The most popular form of the experiment, and the version originally developed, uses a weak (1)H radio frequency field to perturb longitudinal magnetization of one state with the effect transferred to magnetization in the second conformation via chemical exchange. A significant limitation of the method for protein applications emerges from (1)H magnetization transfer via dipolar relaxation (NOE effect) that can severely complicate analysis of the resulting CEST profile. This is particularly an issue since the (1)H chemical shifts of the excited state, critical for structural studies of these elusive conformers, become difficult to extract. Here we present a method for measurement of these shifts via CEST experiments in which the NOE effect is not an issue. The methodology is illustrated through applications to a pair of exchanging systems where the results are cross-validated.

Tailored real-time scaling of heteronuclear couplings

Heteronuclear couplings are a valuable source of molecular information, which is measured from the multiplet splittings of an NMR spectrum. Radiofrequency irradiation on one coupled nuclear spin allows to modify the effective coupling constant, scaling down the multiplet splittings in the spectrum observed at the resonance frequency of the other nuclear spin. Such decoupling sequences are often used to collapse a multiplet into a singlet and can therefore simplify NMR spectra significantly. Continuous-wave (cw) decoupling has an intrinsic non-linear offset dependence of the scaling of the effective J-coupling constant. Using optimal control pulse optimization, we show that virtually arbitrary off-resonance scaling of the J-coupling constant can be achieved. The new class of tailored decoupling pulses is named SHOT (Scaling of Heteronuclear couplings by Optimal Tracking). Complementing cw irradiation, SHOT pulses offer an alternative approach of encoding chemical shift information indirectly through off-resonance decoupling, which however makes it possible for the first time to achieve linear J scaling as a function of offset frequency. For a simple mixture of eight aromatic compounds, it is demonstrated experimentally that a 1D-SHOT {(1)H}-(13)C experiment yields comparable information to a 2D-HSQC and can give full assignment of all coupled spins.

Multi-dimensional NMR without coherence transfer: minimizing losses in large systems

Most multi-dimensional solution NMR experiments connect one dimension to another using coherence transfer steps that involve evolution under scalar couplings. While experiments of this type have been a boon to biomolecular NMR the need to work on ever larger systems pushes the limits of these procedures. Spin relaxation during transfer periods for even the most efficient (15)N-(1)H HSQC experiments can result in more than an order of magnitude loss in sensitivity for molecules in the 100 kDa range. A relatively unexploited approach to preventing signal loss is to avoid coherence transfer steps entirely. Here we describe a scheme for multi-dimensional NMR spectroscopy that relies on direct frequency encoding of a second dimension by multi-frequency decoupling during acquisition, a technique that we call MD-DIRECT. A substantial improvement in sensitivity of (15)N-(1)H correlation spectra is illustrated with application to the 21 kDa ADP ribosylation factor (ARF) labeled with (15)N in all alanine residues. Operation at 4°C mimics observation of a 50 kDa protein at 35°C.

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.

Indirect determination of chemical shift by coupling evolution during adiabatic pulses

The use of adiabatic 180 degrees X-pulses within INEPT refocusing periods results in chemical shift-dependent evolution of J-couplings. This has been viewed as a disadvantage and several methods of overcoming it have been suggested. This article shows that there is the potential to use this chemical shift dependence to determine heteronuclear chemical shift without a heteronuclear evolution time. In this way, it possible to estimate heteronuclear chemical shift indirectly from a single one-dimensional proton-observe spectrum and determine it with high accuracy from a extensively-folded two-dimensional proton-observe spectrum.

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.

Fast multidimensional NMR spectroscopy by spin-state selective off-resonance decoupling (SITAR)

Spin-state selective off-resonance decoupling (SITAR) is applied to the amide proton-to-nitrogen-to-alpha-carbon correlation (HNCA) triple-resonance experiment by measuring the 15N chemical shift during the acquisition simultaneously with the 1H chemical shift. The simultaneous detection of both 1H and 15N chemical shifts in SITAR reduces the dimensionality of the HNCA-type experiment from three dimensions to two dimensions with a 15N chemical shift resolution of approximately 0.4 ppm. This enables the recording of triple-resonance experiments in several minutes. SITAR is furthermore applied to the amide proton-to-nitrogen-to-alpha-carbon-and-beta-carbon correlation (HNCACB) triple-resonance experiment and the 15N-resolved [1H,1H]-nuclear Overhauser enhancement spectroscopy (NOESY) experiment with similar success. The accompanied peak crowding and chemical shift degeneracy of the amide protons in the SITAR two-dimensional (2D) spectra, which are inherent properties of pseudo-dimensional experiments, are resolved by local correlation of the two sub-spectra. With this procedure a 13C--1H strip for each 15N--1H moiety is generated resulting in a three-dimensional (3D) strip list known from the conventional 3D spectra. The quality of the strip list in terms of peak crowding and chemical shift degeneracy is comparable to their corresponding 3D counterparts. An analysis-software within the CARA package is presented, which generates, visualizes and manages the SITAR spectra, the corresponding strip lists and the assignment process.