Abstract
2D NMR 1H–X (X = 15N or 13C) HSQC spectra contain cross-peaks for all XHn moieties. Multiplicity-edited 1H–13C HSQC pulse sequences generate opposite signs between peaks of CH2 and CH/CH3 at a cost of lower signal-to-noise due to the 13C T2 relaxation during an additional 1/1JCH period. Such CHn-editing experiments are useful in assignment of chemical shifts and have been successfully applied to small molecules and small proteins (e.g. ubiquitin) dissolved in deuterated solvents where, generally, peak overlap is minimal. By contrast, for larger biomolecules, peak overlap in 2D HSQC spectra is unavoidable and peaks with opposite phases cancel each other out in the edited spectra. However, there is an increasing need for using NMR to profile biomolecules at natural abundance dissolved in water (e.g., protein therapeutics) where NMR experiments beyond 2D are impractical. Therefore, the existing 2D multiplicity-edited HSQC methods must be improved to acquire data on nuclei other than 13C (i.e. 15N), to resolve more peaks, to reduce T2 losses and to accommodate water suppression approaches. To meet these needs, a multiplicity-separated 1H–X HSQC (MS-HSQC) experiment was developed and tested on 500 and 700 MHz NMR spectrometers equipped with room temperature probes using RNase A (14 kDa) and retroviral capsid (26 kDa) proteins dissolved in 95% H2O/5% D2O. In this pulse sequence, the 1/1JXH editing- period is incorporated into the semi-constant time (semi-CT) X resonance chemical shift evolution period, which increases sensitivity, and importantly, the sum and the difference of the interleaved 1JXH-active and the 1JXH-inactive HSQC experiments yield two separate spectra for XH2 and XH/XH3. Furthermore we demonstrate improved water suppression using triple xyz-gradients instead of the more widely used z-gradient only water-suppression approach.
Keywords: MS-HSQC, Multiplicity editing, Natural abundance, Triple-axis gradient water suppression
1. Introduction
There is an increasing need to fingerprint therapeutic biomolecules by solution NMR in formulated drug products at natural abundance [1–8]. Two-dimensional hetero-nuclear 1H–X (X = 15N or 13C) spectral patterns are sensitive to chemical structure and therefore can detect structural change at the level of individual nuclei. These methods are superior to homo-nuclear two-dimensional spectra because of their increased chemical shift dispersion, less homo-nuclear J-splitting, and concomitant reduced peak overlap [2]. Two-dimensional methods have become even more powerful with the advent of multiplicity-edited 1H–13C HSQC, HMQC, HMBC and H2BC experiments [9–19]. Multiplicity-edited pulse sequences use a dedicated period of 1/1JCH to edit CH2 and CH/CH3 peaks into the opposite phases in the same spectrum. Most edited experiments were developed for and applied to small molecules at 13C natural abundance dissolved in deuterated solvents and are therefore multiple-quantum based experiments. Additionally, generally, small molecules contain fewer overlapping resonances and have longer T2 values compared to larger protein molecules.
For larger molecules like proteins, HSQC-based experiments have higher sensitivity than HMQC-based experiments, because, due to the transverse 1H magnetization during t1, the HMQC-based experiments have additional T2 decay [20]. Interestingly, among all published 13C multiplicity-edited 2D experiments only the HSQC version was demonstrated on ubiquitin dissolved in D2O [16].
Experimental protein NMR spectra are typically collected in H2O, where some protein backbone amide NH peaks overlap with side-chain NH2 peaks. In addition, CHn peaks also overlap with CHm (where n ≠ m) peaks, especially in spectra where peaks are folded. Finally, XHn peaks in un-folded peptides and proteins may overlap with peaks from un-structured regions of a folded protein. Unresolvable 2D cross-peaks, though edited, will adversely affect chemical shift assignment and, concomitantly, chemometric analysis of 2D-NMR data acquired on biomolecules at natural abundance. Thus, to resolve potentially overlapped XHn peaks, we present a multiplicity-separated (MS) HSQC experiment. Here, the most important feature of multiplicity-separation is achieved by separately collecting the 1JXH-active and the 1JXH-inactive spectra in an interleaved fashion; then, the sum and the difference are calculated directly to yield separation. This new approach absorbs the previously separate editing period of 1/1JXH into a modified semiconstant time (semi-CT) chemical shift evolution period, reducing the total time that X magnetization spends in the transverse plane, and minimizing signal loss due to T2 relaxation. In addition, water suppression can be readily achieved in 95% H2O/5% D2O using either flip-back pulses [21] or triple-axis gradients. Herein, we demonstrate the new experiments on a 14-kDa natural abundant RNase A and a 26-kDa 15N-labeled retroviral capsid within a reasonable amount of spectrometer time (1–2.5 days for the natural abundance sample) using a room-temperature probe-head.
2. Results and discussion
2.1. The 1JXH-active and the 1JXH-inactive semi-CT HSQC pulse sequences
The original multiplicity-edited 1H–13C HSQC pulse sequence [16,17], commonly found in vendor pulse sequence libraries, has the signature spin chemical shift and 1JCH evolution shown in Eq. (1). Eq. (1) depicts the 13C antiphase HzCy magnetization evolution between the first and the last INEPT periods,
| (1) |
where t1 is the 13C chemical shift evolution period, ωC is the 13C Larmor frequency and n is the number of 1H attached to 13C. Depending on the value of n, the sign of the HzCy magnetization will be positive for CH2 and negative for CH/CH3 cross-peaks. The maximum amount of time that 13C magnetization spends in the transverse plane is t1max + 1/1JCH.
To keep the editing feature and reduce T2 losses, we incorporated an extra 1/1JXH time, 8–11 ms, into the t1 chemical shift evolution period, i.e., t1max of 40–50 ms. The semi-CT method is selected for this purpose. The semi-CT was originally used for 1H chemical shift evolution during INEPT transfers to 13C in order to minimize 1H T2 losses [22,23]. Here, we modify the semi-CT during the hetero-nuclear X chemical shift evolution to generate the multiplicity- separated spectra. Briefly two semi-CT HSQC pulse sequences were run in an interleaved fashion. The difference between the two sequences lies in where the 1H 180° pulse is applied (Fig. 1). In the 1JXH-active experiment, the 1H 180° pulse is applied at the red position and properly decrementing ta and incrementing tb and tc (Table 1), the net 1JXH evolution time is maintained constant as 1/1JXH (Eq. (2)). Therefore, the editing feature is retained and the t1 chemical shift labeling is properly maintained. The maximum time that hetero-nuclear X magnetization spends in the transverse plane is t1max + (1/1JXH)/(N + 1) ≈ t1max, where N is the number of real points in t1 acquisition.
Fig. 1.

The pulse sequences for the 1JXH-active/inactive semi-CT HSQC experiments, which can be either the standard HSQC (A) or the sensitivity-enhanced version (B). Narrow and wide rectangles correspond to hard pulses with flip angles of 90° and 180°, respectively. Filled and open bells are 90° sinc-shaped water-selective pulses with a duration of 1.5–2.0 ms. The pulses in red and blue are only applied for the 1JXH-active and the 1JXH-inactive experiment, respectively. The open rectangles denoted CPD are low power decoupling scheme in either WALTZ-16 for 15N or GARP for 13C. Pulses are x-phase by default. Phase cycles are listed as follows, ϕ1 = x; ϕ2 = x, −x; ϕ3 = (x)4, (−x)4; ϕ4 = (x)2, (−x)2; ϕ5 = (x)8, (−x)8; ϕrec = (x, −x)2, (−x, x)2 for (A) and ϕ1 = x; ϕ2 = y, −y; ϕ3 = (x)4, (−x)4; ϕ4 = (x)2, (−x)2; ϕ5 = (y)2, (−y)2; ϕrec = (x, −x, −x, x, −x, x, x, −x) for (B). The fixed delay durations are listed as follows, τ1 = 1/(41JXH), τ2 = 1.25 ms and τ3 = 1/(81JXH). The varied delays ta–d during the X spin chemical shift evolution are listed in Table 1. All gradient pulses are sine-shaped and along z-axis by default except for the xyz gradient pulses G1, G2, G4 and G5 of (B). The duration and strength for gradient pulses are as follows, G1 = 1 ms, 10 G/cm; G2 = 1 ms, 5 G/cm; G3 = 0.5 ms, 10 G/cm for (A) and G1(xyz) = 5 ms, 12.5 G/cm; G2(xyz) = 1 ms, 40 G/cm; G3 = 0.5 ms, 5 G/cm; G4(xyz) = 1 ms, 20 G/cm; G5(xyz) = 1 ms, 30 G/cm for (B). Quadrature detection in (A) was achieved via States-TPPI method such that phase ϕ1 and ϕ2 of the X pulses were incremented 90° for every FID in t1 acquisition. Quadrature detection in (B) was achieved via the Echo-Antiecho method such that the second FID for each increment of t1 was collected with signs of gradient pulses G2 and phase ϕ5 of the 180° pulse switched simultaneously. The 1H carrier frequency was at water resonance of 4.76 ppm and the 15N and 13C carrier frequencies were at 117 ppm and 57.0 ppm, respectively. The spectral width of 1H was 12 ppm and the number of direct time domain complex points was 1024. The 15N acquisition time was 42.1 ms and the spectral width was 30 ppm. The 13C acquisition time was 50.7 ms and the spectral width was 14 ppm. The 1JXH-active and the 1JXH-inactive spectra were collected in interleaved manner by switching the position of the 180° 1H pulse between the red and the blue. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Table 1.
The varied delays in the 1JXH-active/inactive semi-CT HSQC experiments.
| Varied delay | In-/de-crement value | Resulting value |
|---|---|---|
| ta | Δta = (1/21JXH)/(N + 1)a | 1/(21JXH) − Δta |
| tb | Δtb = Δt1/2 + Δtab | Δtb |
| tc | Δtc = Δt1/2 | 1/(21JXH) + Δtc |
| td | Δtd = Δt1/2 | Δtd |
N is the number of real points in the indirect t1 dimension.
Δt1 = 1/SW, where SW is the spectral width of the X (15N or 13C) spin.
| (2) |
In parallel the 1JXH-inactive experiment has the 1H 180° pulse being applied at the blue position (Fig. 1) with a new introduction of variable delay td, which is incremented within the tc period (Table 1). The modification results in the net 1JXH evolution time of 0 (Eq. (3)), ensuring the 1H-decoupling throughout the full t1 period. The 1JXH-inactive spectrum yields the same sign for all XHn cross-peaks. The t1 chemical shift labeling is identical to the 1JXH-active spectrum.
| (3) |
2.2. MS-HSQC spectra
Since both the 1JXH-active and the 1JXH-inactive experiments have the identical pulse execution time or T2 loss, the post-acquisition sum and difference of the two at a 1:1 ratio yields the XH2 only and the XH/XH3 only spectrum (Figs. 2–4 and S2) without any need to scale relative intensities or further correct phases. The approach of directly adding and subtracting to obtain the desired spectra is similar to the in-phase-anti-phase (IPAP) HSQC experiments for residual dipolar coupling (RDC) measurement [24].
Fig. 2.
The sub-region of the 1H–15N MS-HSQC spectra of RNase A at natural abundance dissolved in 95% H2O/5% D2O. The positive and the negative peaks are shown in black and red, respectively. The spectra of the 1JNH-active (A) and the 1JNH-inactive (B) were collected using the pulse sequence in Fig. 1A. The post-acquisition difference (C) and sum (D) spectra showed multiplicity separation between peaks of NH and NH2, e.g., peaks a and b within the dashed box. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 4.
The 1H–13C MS-HSQC spectra for moieties of CH/CH3 of RNase A at natural abundance dissolved in 95% H2O/5% D2O. The positive and the negative peaks are shown in black and red, respectively. The two spectra were collected with identical experimental parameters except for the use of the xyz-axis gradient pulses (A) and the z-axis only ones (B). The red dashed-circles indicate CH2 cross-peaks that were not completely removed due to 1JCH mis-match. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
For experiments on proteins at natural abundance the current multiplicity-separation is an efficient and practical choice because chemical shift assignments from MS-HSQC spectra are more interpretable than those from multiplicity-edited spectra and an improved S/N is obtained relative to the standard multiplicity edited HSQC sequence. We tested both 1H–15N (Figs. 1A and 2) and 1H–13C (Figs. 1B, 4A and S2) MS-HSQC experiments on an RNase A sample at natural abundance dissolved in 95% H2O/5% D2O. For example, the NH peak a of RNase A, would commonly be treated as a minor impurity peak in the 1JNH-active (edited) spectrum (Fig. 2A) or as a tail of peak b in the 1JNH-inactive (regular) spectrum (Fig. 2B). Only under the separation method we can confidently identify peak a as an NH peak (Fig. 2C) and peak b as an NH2 peak with correct intensity (Fig. 2D).
The 1H–15N MS-HSQC experiments were also demonstrated on a larger 15N-labeled 26-kDa retroviral capsid protein (Fig. 3). The capsid protein shape is highly asymmetric, with an anisotropy of 1.8. Indeed, its averaged 15N T2 relaxation rate and Stokes radius correspond to that of a 32 kDa symmetric protein [25]. Table 2 shows sensitivity comparisons of the standard HSQC, the standard multiplicity-edited HSQC and the new semi-CT HSQC (Table 2). Due to the reduction in the time that 15N magnetization spends in the transverse plane, the MS-HSQC yielded an average of 10% increase in peak S/N from the standard edited HSQC (Table 2 and Fig. S1). The MS-HSQC is at 85% of the S/N of the standard HSQC spectra, indicating a protein sample should be roughly 15% more concentrated to obtain S/N similar to a standard HSQC, if an MS-HSQC spectrum is desired. Based on the comparison we expect the MS-HSQC is generally applicable to a similar molecular mass range as the standard HSQC.
Fig. 3.
The 1H–15N MS-HSQC spectra of a 15N-labeled 26 kDa retroviral capsid protein dissolved in 95% H2O/5% D2O. The post-acquisition difference (A) and sum (B) spectra showed multiplicity separation between peaks of NH and NH2.
Table 2.
Feature comparison among the three 1H–15N HSQC spectra collected on a 26 kDa 15N-labeled protein.
| Type | Pulse program | Cross-peak sign | Averaged S/Na | Experimental timeb | ||
|---|---|---|---|---|---|---|
|
| ||||||
| NH | NH2 | Separation | ||||
| Standard | Bruker hsqcfpf3gpphwg | + | + | No | 32.4 | 3 h 18 min |
| Standard multiplicity-edited | hsqcfpf3gpphwg with an extra 1/1JNH period after t1 | + | − | No | 24.6 | 3 h 21 min |
| Semi-CT | The 1JNH-active version in Fig. 1A | + | − | Yes | 27.1 | 3 h 12 min |
A total of 137 isolated cross-peaks were picked on all spectra and peak S/N were calculated using Sparky (T.D. Goddard and D.G. Kneller, University of California, San Francisco). The averaged S/N are shown.
The sample is a 0.1 mM 15N-labeled retroviral capsid protein (26 kDa). All HSQC spectra were collected on a Bruker 500 MHz spectrometer equipped with a room-temperature probe.
Natural abundance 1H–13C MS-HSQC experiments were performed on the RNase A sample. The 1JCH-active and the 1JCH-inactive 1H–13C HSQC spectra were collected with CH2/CH3 peaks folded (Figs. S2A and S2B). The difference and sum yielded the CH/CH3 only (Figs. S2C and 4A) and the CH2 only spectra (Fig. S2D). Importantly, the 1JCH values vary among CHn moieties, i.e., the 1JCH values of the sp2 ring CH are 220–155 Hz, the 1JCH of the sp3 groups are 140–150 Hz for CH, 135–145 Hz for CH2 and 125–135 Hz for CH3, and are directly correlated to their respective 13C chemical shifts [26]. Since all amino acid aromatic groups have CH only, a standard HSQC can be collected for them without any need of multiplicity separation. For aliphatic CHn moieties, we have used the value of 125 Hz to match CH3 peaks. Notably, the CH2 only spectra contain undetectable CH/CH3 peaks at a S/N threshold of 7.8 (Fig. S2D). However, there are still 3 CH2 clusters/peaks with attenuated intensity in CH/CH3 sub-spectra (red-dashed circles in Figs. 4 and S2C). In practice the 1JCH value might be set higher to 135 Hz, closer to the CH2 1JCH values to minimize the imperfect cancelation. Another alternative approach demonstrated by Heikkinen et al. is to add several MS-HSQC spectra with varied 1JCH values, because the sum of these spectra are less sensitive to 1JCH variations [27].
2.3. Water suppression
The MS-HSQC methods developed here (Fig. 1) also minimize sample manipulation steps, (e.g., freeze-drying a biomolecule sample and re-dissolving in D2O for 1H–13C HSQC data) because all NMR experiments can be performed in 95% H2O/5% D2O. Water suppression was demonstrated on two general versions of HSQC, the standard HSQC [28] (Fig. 1A) and the sensitivity-enhanced version [29,30] (Fig. 1B). For the standard HSQC experiment, we used low-power shaped pulses to achieve a more complete water flip-back scenario, where water magnetization has been kept along +z throughout the pulse sequence except for the first INEPT transfer, where water magnetization was along the y-axis. The complete +z-flip-back is more robust than the typical flip-back pulse used in vendor libraries. Specifically, in typical flip-back experiments, the water magnetization is aligned along the –z-axis for a period of t1/2, which increases the likelihood of radiation damping, especially at longer t1 acquisition times.
Here, for the sensitivity-enhanced HSQC (Fig. 1B) water suppression was achieved by using xyz-axis gradients after the first INEPT and during the coherence selection without using any shaped pulses. This allows the observation of Cα–Hα correlation in the 1H–13C MS-HSQC spectrum (Fig. 4A), which can be obscured by poor water suppression. The xyz-axis gradient is essential since the same HSQC experiment, when performed without using xy-gradient but otherwise identical experimental parameters, yielded poor water suppression spectrum which precluded the observation of Cα–Hα correlations (Fig. 4B).
3. Conclusion
Here, the application of a new MS-HSQC experiment on biomolecules at natural abundance dissolved in 95% H2O/5% D2O was demonstrated. The new experiment generates separated spectra containing XH2 peaks only or XH/XH3 peaks only with higher sensitivity than the multiplicity-edited HSQC [14–16]. The separation feature is not an issue for 15N/13C-labeled proteins, e.g., a 3D HNCO spectrum can be used to separate the side-chain NH2 peaks and reveal any backbone NH peaks that may be hidden underneath them. However, for proteins at natural abundance, the simplified 2D MS-HSQC can improve the accuracy of comparisons between molecules made by chemometric analysis of specific chemical structures (e.g., backbone NH vs. side-chain NH2) of biomolecules in their native state [31]. This is crucial when profiling protein therapeutics for backbone structure as the side-chain NH2 peaks add no information to such an evaluation and are more susceptible to formulation differences. Thus, the separated HSQC spectra with good water suppression should be amenable to NMR analysis of biotherapeutics in their formulation buffers.
The experiment described here will also work on isotope-labeled molecules for collecting 1H–15N HSQC spectra (with the decoupling of Cα/C′ if 13C-enriched). Similar to protein spectra in natural abundance, this approach can resolve the ambiguities in chemical shift assignments and serve to improve resolution in 2D spectra, which in turn will guide 3D assignments with higher confidence. Finally, the MS-HSQC can reveal more interacting NH peaks in titration studies if such peaks happen to be buried by the NH2 resonances, and when combined with spin relaxation HSQC, allow a more complete set of measurements on the structure and dynamics of a biomolecule.
4. Materials and methods
4.1. Protein sample preparation
The RNase A powder at natural abundance (GE Healthcare Bio- Sciences, Pittsburgh, PA) was dissolved in 2− diluted PBS buffer (Quality Biological, Gaithersburg, MD) to the desired concentration of 1.7 mM. The 15N-labeled retroviral capsid protein, 0.1 mM in PBS buffer, was prepared as described [32]. For both samples, 570 μl protein solution was mixed with 30 μl D2O (Cambridge Isotope Laboratories, Tewksbury, MA) then 550 μl of these solutions were loaded into 5-mm Wilmad 535-pp tubes (Wilmad-LabGlass, Vineland, NJ).
4.2. NMR spectroscopy
All NMR experiments were performed at 25 °C. The experimental temperature was calibrated using pure methanol. The pulse sequence details and acquisition parameters are in Fig. 1 caption and Table 1. We include the pulse sequence codes (Supplementary material) of Fig. 1A and B using the templates of the Bruker pulse programs hsqcfpf3gpphwg and hsqcetgpsi, respectively. For the 1H–15N HSQC experiment, which was performed on a Bruker Avance III, 500 MHz spectrometer, equipped with a room temperature QXI probe and a z-axis gradient, the total experimental time is 63 h using the pulse sequence in Fig. 1A. For the 1H–13C HSQC experiment, which was performed on a Bruker Avance II 700 MHz spectrometer, equipped with a room temperature QXI probe and a xyz-axis gradient, the total experimental time is 21 h using the pulse sequence in Fig. 1B.
4.3. Data processing
The interleaved raw FID file was separated then added and subtracted using NMRPipe [33] scripts (Supplementary material). The resulting time domain FID were polynomial filtered, apodized with a cosine function and zero-filled to 4 k data points before Fourier transform along both dimensions. The both frequency domain were baseline corrected with a polynomial function.
Supplementary Material
Acknowledgments
We thank Hugo Azurmendi, Marcos Battistel and Jinfa Ying for helpful discussions. Support for this work from the US FDA Critical Path funds is gratefully acknowledged.
Appendix A. Supplementary material
Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.jmr.2014.11.011.
Footnotes
5. Disclaimer
The findings and conclusions in this article have not been formally disseminated by the Food and Drug Administration and should not be construed to represent any Agency determination or policy.
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