Exchangeable deuterons introduce artifacts in amide 15N CEST experiments used to study protein conformational exchange

Using the amide 15N CEST NMR experiment to study slow exchange between 'visible' protein states

Slow exchange between 'visible' protein states is often studied using the two-dimensional ZZ exchange class of magnetisation transfer experiments. However, the cross-peaks that arise due to magnetisation transfer between different states can lead to additional overlap in the two-dimensional ZZ exchange NMR spectrum. To overcome this overlap problem, here we have explored the utility of the 15N CEST experiment as an alternative to the 1HN-15N ZZ exchange experiment to study exchange between 'visible' protein states. In the case of two-state exchange, the 1HN-15N correlation map contains two correlations for each exchanging site, one arising from each state. Thus, two 15N CEST profiles can be recorded for each of these sites using a single 15N CEST experiment. We find that site-specific exchange parameters can then be obtained by simultaneously analysing both these 15N CEST profiles recorded at a single 'high' B1 field supplemented with experimentally derived information regarding the initial magnetisation or as in the case of the ZZ exchange experiment, the minor state population. The utility of the 15N CEST based approach to characterise exchange between visible protein states is demonstrated by studying the interconversion of the ∼18 kDa T34A mutant of T4 lysozyme between its native state and a minor state populated to ∼21 % (exchange rate ∼5 s-1) at 40 °C.

Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch

Over 40% of eukaryotic proteomes and 15% of bacterial proteomes are predicted to be intrinsically disordered based on their amino acid sequence. Intrinsically disordered proteins (IDPs) exist as heterogeneous ensembles of interconverting conformations and pose a challenge to the structure-function paradigm by apparently functioning without possessing stable structural elements. IDPs play a prominent role in biological processes involving extensive intermolecular interaction networks and their inherently dynamic nature facilitates their promiscuous interaction with multiple structurally diverse partner molecules. NMR spectroscopy has made pivotal contributions to our understanding of IDPs because of its unique ability to characterize heterogeneity at atomic resolution. NMR methods such as Chemical Exchange Saturation Transfer (CEST) and relaxation dispersion have enabled the detection of 'invisible' excited states in biomolecules which are transiently and sparsely populated, yet central for function. Here, we develop a 1Hα CEST pulse sequence which overcomes the resonance overlap problem in the 1Hα-13Cα plane of IDPs by taking advantage of the superior resolution in the 1H-15N correlation spectrum. In this sequence, magnetization is transferred after 1H CEST using a triple resonance coherence transfer pathway from 1Hα (i) to 1HN(i + 1) during which the 15N(t1) and 1HN(t2) are frequency labelled. This approach is integrated with spin state-selective CEST for eliminating spurious dips in CEST profiles resulting from dipolar cross-relaxation. We apply this sequence to determine the excited state 1Hα chemical shifts of the intrinsically disordered DNA binding domain (CytRN) of the bacterial cytidine repressor (CytR), which transiently acquires a functional globally folded conformation. The structure of the excited state, calculated using 1Hα chemical shifts in conjunction with other excited state NMR restraints, is a three-helix bundle incorporating a helix-turn-helix motif that is vital for binding DNA.

Studying micro to millisecond protein dynamics using simple amide 15N CEST experiments supplemented with major-state R2 and visible peak-position constraints

Over the last decade amide 15N CEST experiments have emerged as a popular tool to study protein dynamics that involves exchange between a 'visible' major state and sparsely populated 'invisible' minor states. Although initially introduced to study exchange between states that are in slow exchange with each other (typical exchange rates of, 10 to 400 s-1), they are now used to study interconversion between states on the intermediate to fast exchange timescale while still using low to moderate (5 to 350 Hz) 'saturating' B1 fields. The 15N CEST experiment is very sensitive to exchange as the exchange delay TEX can be quite long (~0.5 s) allowing for a large number of exchange events to occur making it a very powerful tool to detect minor sates populated ([Formula: see text]) to as low as 1%. When systems are in fast exchange and the 15N CEST data has to be described using a model that contains exchange, the exchange parameters are often poorly defined because the [Formula: see text] versus [Formula: see text] and [Formula: see text] versus exchange rate ([Formula: see text]) plots can be quite flat with shallow or no minima and the analysis of such 15N CEST data can lead to wrong estimates of the exchange parameters due to the presence of 'spurious' minima. Here we show that the inclusion of experimentally derived constraints on the intrinsic transverse relaxation rates and the inclusion of visible state peak-positions during the analysis of amide 15N CEST data acquired with moderate B1 values (~50 to ~350 Hz) results in convincing minima in the [Formula: see text] versus [Formula: see text] and the [Formula: see text] versus [Formula: see text] plots even when exchange occurs on the 100 μs timescale. The utility of this strategy is demonstrated on the fast-folding Bacillus stearothermophilus peripheral subunit binding domain that folds with a rate constant ~104 s-1. Here the analysis of 15N CEST data alone results in [Formula: see text] versus [Formula: see text] and [Formula: see text] versus [Formula: see text] plots that contain shallow minima, but the inclusion of visible-state peak positions and restraints on the intrinsic transverse relaxation rates of both states during the analysis of the 15N CEST data results in pronounced minima in the [Formula: see text] versus [Formula: see text] and [Formula: see text] versus [Formula: see text] plots and precise exchange parameters even in the fast exchange regime ([Formula: see text]~5). Using this strategy we find that the folding rate constant of PSBD is invariant (~10,500 s-1) from 33.2 to 42.9 °C while the unfolding rates (~70 to ~500 s-1) and unfolded state populations (~0.7 to ~4.3%) increase with temperature. The results presented here show that protein dynamics occurring on the 10 to 104 s-1 timescale can be studied using amide 15N CEST experiments.

Measuring radiofrequency fields in NMR spectroscopy using offset-dependent nutation profiles

The application of NMR spectroscopy for studying molecular and reaction dynamics relies crucially on the measurement of the magnitude of radiofrequency (RF) fields that are used to nutate or lock the nuclear magnetization. Here, we report a method for measuring RF field amplitudes that leverages the intrinsic modulations observed in offset-dependent NMR nutation profiles of small molecules. Such nutation profiles are exquisitely sensitive to the magnitude of the RF field, and B₁ values ranging from 1 to 2000 Hz, as well the inhomogeneity in B₁ distributions, can be determined with high accuracy and precision using this approach. In order to measure B₁ fields associated with NMR experiments carried out on protein or nucleic acids, where these modulations are obscured by the large transverse relaxation rate constants of the analyte, our approach can be used in conjunction with a suitable external small molecule standard, expanding the scope of the method for large biomolecules.

Elucidating dissociation activation energies in host-guest assemblies featuring fast exchange dynamics

The ability to mediate the kinetic properties and dissociation activation energies (E _a) of bound guests by controlling the characteristics of "supramolecular lids" in host-guest molecular systems is essential for both their design and performance. While the synthesis of such systems is well advanced, the experimental quantification of their kinetic parameters, particularly in systems experiencing fast association and dissociation dynamics, has been very difficult or impossible with the established methods at hand. Here, we demonstrate the utility of the NMR-based guest exchange saturation transfer (GEST) approach for quantifying the dissociation exchange rates (k _out) and activation energy (E _a,out) in host-guest systems featuring fast dissociation dynamics. Our assessment of the effect of different monovalent cations on the extracted E _a,out in cucurbit[7]uril:guest systems with very fast k _out highlights their role as "supramolecular lids" in mediating a guest's dissociation E _a. We envision that GEST could be further extended to study kinetic parameters in other supramolecular systems characterized by fast kinetic properties and to design novel switchable host-guest assemblies.

A Double-Resonance CEST Experiment To Study Multistate Protein Conformational Exchange: An Application to Protein Folding

Despite the importance of protein dynamics to function, studying exchange between multiple conformational states remains a challenge because sparsely populated states are invisible to conventional techniques. CEST NMR experiments can detect minor states with lifetimes between 5 and 200 ms populated to a level of just ∼1%. However, CEST often cannot provide the exchange mechanism for processes involving three or more states, leaving the role of the detected minor states unknown. Here a double-resonance CEST experiment to determine the kinetics of multistate exchange is presented. The approach that involves irradiating resonances from two minor states simultaneously is used to study the exchange of T4 lysozyme (T4L) between the dominant native state and two minor states, the unfolded state and a second minor state (B), each populated to only ∼4%. Regular CEST does not provide the folding mechanism, but double-resonance CEST clearly shows that T4L can fold directly without going through B.