Dariusz Gołowicz1, Alexandra Shchukina2, Krzysztof Kazimierczuk1. 1. Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland. 2. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
Abstract
Chemical analysis based on liquid-state nuclear magnetic resonance spectroscopy exploits numerous observables, mainly chemical shifts, relaxation rates, and internuclear coupling constants. Regarding the latter, the efficiencies of internuclear coherence transfers may be encoded in spectral peak intensities. The dependencies of these intensities on the experimental parameter that influences the transfer, for example, mixing time, are an important source of structural information. Yet, they are costly to measure and difficult to analyze. Here, we show that peak intensity build-up curves in two-dimensional total correlation spectroscopy (2D TOCSY) experiments may be quickly measured by employing nonuniform sampling and that their analysis can be effective if supported by quantum mechanical calculations. Thus, such curves can be used to form a new, third pseudodimension of the TOCSY spectrum. Similarly to the other two frequency dimensions, this one also resolves ambiguities and provides characteristic information. We show how the approach supports the analysis of a fragment of protein Tau Repeat-4 domain. Yet, its potential applications are far broader, including the analysis of complex mixtures or other polymers.
Chemical analysis based on liquid-state nuclear magnetic resonance spectroscopy exploits numerous observables, mainly chemical shifts, relaxation rates, and internuclear coupling constants. Regarding the latter, the efficiencies of internuclear coherence transfers may be encoded in spectral peak intensities. The dependencies of these intensities on the experimental parameter that influences the transfer, for example, mixing time, are an important source of structural information. Yet, they are costly to measure and difficult to analyze. Here, we show that peak intensity build-up curves in two-dimensional total correlation spectroscopy (2D TOCSY) experiments may be quickly measured by employing nonuniform sampling and that their analysis can be effective if supported by quantum mechanical calculations. Thus, such curves can be used to form a new, third pseudodimension of the TOCSY spectrum. Similarly to the other two frequency dimensions, this one also resolves ambiguities and provides characteristic information. We show how the approach supports the analysis of a fragment of protein Tau Repeat-4 domain. Yet, its potential applications are far broader, including the analysis of complex mixtures or other polymers.
Nuclear magnetic resonance (NMR) spectroscopy
is widely used in
many branches of chemical analysis. It manipulates nuclear spins and
measures the response of a sample as a free induction decay (FID)
signal. The FID has the form of oscillations decaying in time, so
its Fourier transform yields a spectrum with resonance peaks described
by Lorentzian functions. The most informative spectral parameters
are peak positions and volumes, the former dependent on a molecular
structure and the latter proportional to the number of nuclei resonating
at a given frequency.Two-dimensional (2D) NMR, in turn, yields
peaks in a spectrum that
are described by two coordinates. They can be related to various types
of spin interactions in a molecule. The spectral peak heights encode
the information about the strength of a coupling. An additional dimension
also enhances peak dispersion: When peaks in a 1D spectrum overlay,
the second dimension will most probably separate them. 2D NMR is extensively
applied in determining molecular structures[1] and in identifying chemical compounds, for example, components of
natural mixtures.[2]In many research
tasks, we acquire a series of spectra varying
certain parameters in-between. Usually, we vary an environmental condition[3−6] or a pulse-sequence parameter.[7−15] Such a series of spectra can be regarded as one object with a higher
dimensionality. A series of 1D spectra thus forms a 2D object; the
most well-known example here is diffusion-ordered spectroscopy (DOSY).[9] A series of 2D spectra constitutes a 3D object,
for example, as in nuclear overhauser effect spectroscopy (NOESY)
with variable mixing times.[14] In both cases,
the varied parameter forms an extra (second or third) pseudodimension.Any additional dimension, be it a “normal” Fourier
one or a pseudodimension, brings in two advantages for the spectral
analysis. First, it enhances the peak dispersion. Second, an additional
dimension helps with the peak assignment. When peak parameters from
a lower-dimensional spectrum are not enough to state which group of
nuclei have yielded a given peak, one more dimension may make up for
the missing information. For example, overlapping resonances in 2D 15N HSQC spectrum of an unfolded protein are often well separated
in the third (CO) dimension of a 3D HNCO spectrum.[7]In this work, we research the possibilities arising
from the incrementation
of isotropic mixing time in total-correlation spectroscopy (TOCSY).
We show that it can be used to form a spectral dimension providing
both the mentioned benefits: higher resolution and a unique peak-characteristic
profile.TOCSY spectra are widely used in chemical analysis
as they present
(at least theoretically) the correlations between all the coupled
nuclei within the entire spin system. In the case of peptides, the
amino acid residues form separate spins systems and thus TOCSY crosspeaks
usually form amino-acid-specific patterns.[16,17] The key element of a TOCSY pulse sequence is an isotropic mixing
block, implemented with multipulse decoupling sequences (e.g., DIPSI[18] or MLEV type[19]).
During this block, the system (ideally) evolves under a strong coupling
Hamiltonian alone, and the transfer proceeds through the whole scalar
coupling network.In practice, however, the coherence transfer
under isotropic mixing
depends on the J-couplings present in the particular
spin system as well as on its topology. Such transfer dependencies
can be determined by measuring a series of TOCSY experiments with
incremented isotropic mixing times, keeping in mind possible distortions
caused by a rotating frame nuclear Overhauser effect,[20] unwanted coherences,[21] and the
signal loss due to T1ρ relaxation.
TOCSY–transfer curves have already found many interesting applications.
For instance, their analysis made it possible to estimate J-coupling values in sugar rings[22] and small biomolecules,[23,24] identify polyaromatic
spin systems in crude gas–oil mixtures,[25] and assign resonances of small molecules in complex mixtures[26] and monosacharide units in oligo- and polysaccharides.[27,28]Knowing the spin-system topology and assuming the J-coupling constants, one may calculate the magnetization
evolution
during the isotropic mixing conditions. For the simple spin systems,
the analytical equations have been delivered[29−31] and used for
isotropic transfer optimization.[32] For
the “mechanics” of TOCSY transfer, see also ref (33). However, simulating TOCSY
transfer for complex spin systems requires numerical calculations
based on a density matrix evolution. Although these calculations are
computationally demanding, nowadays they can be carried out efficiently,
even for big spin systems using dedicated software, for example, Spinach.[34]The measurement of intensity build-up
curves in a series of 2D
TOCSY spectra is lengthy. This is caused by the conventional time-domain
sampling strategy based on the Nyquist-Shannon theorem,[35] which requires the sampling rate to be equal
to the spectral bandwidth. For typical bandwidths of ca. 7–10
kHz (1H dimension on our 700 MHz spectrometer), thousands
of sampling points are needed to reach evolution times, that provide
natural, relaxation-determined line widths. High spectral resolution
is particularly necessary for spectra of complex molecules, such as
the peptide studied in this work. Since every point in the indirect
dimension takes several seconds to acquire, the measurement of a single
high-resolution 2D spectrum sometimes lasts for tens of hours,[36] making the serial acquisition of several 2D
spectra merely impossible. Fortunately, the approach known as nonuniform
sampling (NUS) is a well-established method to accelerate a measurement
by omitting major parts of data during the acquisition and reconstructing
them afterward using sophisticated mathematical algorithms.[37]One of the most commonly used NUS methods
is compressed sensing
(CS). It reconstructs the missing data points by assuming that the
resulting spectrum is sparse, that is, that the number of significant
spectral points (peaks) is relatively low. This can be done by convex
optimization of a simple loss function by taking into account two
assumptions about the resulting spectrum: accordance with the experimental
data and maximum compressibility.[38,39] The most commonly
applied CS algorithms are iterative soft thresholding[38,40] and iteratively reweighted least squares.[38,41]In this article, we apply the NUS/CS approach to accelerate
the
measurement of transfer curves in 2D TOCSY spectra, effectively creating
a pseudo-3D experiment. The shapes of these curves are nuclei-specific
and can be used to identify peaks or detect peak overlap. To match
curves with the nuclei, the TOCSY transfer has to be effectively simulated.
We demonstrate that it can be done using Spinach software[34] and numerous protein structures deposited in
the Protein Data Bank (PDB).[42] We show
the application of the method in assisting the assignment of 1H side-chain peaks in an unlabeled, 32-residues long peptide
(Tau protein 4-repeat domain).
Experimental Section
Sample Preparation
We prepared the sample by dissolving
Tau Repeat-4 domain peptide (unlabeled, trifluoroacetate salt form,
CPC Scientific) in phosphate-buffered saline (10% D2O,
pH 6.5) to the concentration of 1 mM.
Data Acquisition
We acquired a series of 21 zero-quantum
filtered 1H–1H z-TOCSY
spectra with varied DIPSI-2 mixing sequence[18] time. The duration of a single supercycle of DIPSI-2 was 3.425 ms.
To extend the isotropic mixing time in consecutive spectra, we incremented
the number of supercycles in the range from 2 to 22, which corresponded
to the mixing time from 6.85 to 75.35 ms. We acquired each 2D TOCSY
spectrum with a spectral width of 16.38 ppm in the direct dimension
and 10.00 ppm in the indirect dimension, 512 increments in the indirect
dimension, 4 scans per increment (8 scans including quadrature detection),
and the direct acquisition time of 0.5 s. The total acquisition time
of 21 spectra was ca. 40 h. We acquired the data using an Agilent
700 MHz DirectDrive2 NMR spectrometer equipped with a room-temperature
HCN probe at 298 K. Raw experimental data and processing scripts are
available at DOIs 10.5281/zenodo.6412801 and 10.5281/zenodo.6563108, respectively.
Data Processing
We subsampled all
the acquired 2D TOCSY
FIDs down to 75%, 50%, 37.5%, 25%, 18.75%, 12.5%, and 6.25% of the
full Nyquist grid in the indirect dimension using exponentially weighted
sampling schedules generated with the nussampler program
from the MddNMR package.[43] The subsampled
signals corresponded to ca. 30 h (75%), 20 h (50%), 15 h (37.5%),
10 h (25%), 7.5 h (18.75%), 5 h (12.5%), and 2.5 h (6.25%) acquisition
time. Then we reconstructed the missing points in each subsampled
data set using Iterative Soft Thresholding (IST) algorithm (1000 iterations).
We applied a Virtual Echo preprocessing[44] step to increase the signal sparsity before the reconstruction.
We performed the preprocessing and data reconstruction with the MddNMR
software[43] on NMRbox.[45] Finally, we obtained the TOCSY-transfer curves from the
original and reconstructed TOCSY spectra by measuring 2D peak volumes
with Peakipy software.[46]
Simulations
In our analysis of the TOCSY-transfer curves,
we compared the experimental and simulated data to improve the side-chain
assignment in a Tau-R4 peptide. We simulated the TOCSY-transfer curves
for side chains in 1188 peptides and small proteins deposited in the
Protein Data Bank[42] (PDB) using the Spinach
simulation library for MATLAB (ver. 2.4.5157).[34] We took PDB entries that had NMR experimental data, had
sequence lengths between 5 and 120 residues, were not complexed or
assembled into bigger structures, and were deposited between 2010-01-01
and 2021-12-15.From the PDB coordinates of all models within
the entry, we estimated the vicinal 3JHH couplings for side-chain spin systems using Karplus
equations[47,48] and assumed 2JHH = −12 Hz for the geminal couplings.
This was done in Spinach by calling read_pd1b_pro and guess_j_pro functions. Although geminal
couplings for methylene groups within amino acid residue spin systems
may differ,[49] setting a single arbitrary
value for 2JHH should not impact
simulated TOCSY-transfer curves in our study. For each residue, we
simulated the TOCSY transfer by defining the initial state of the
spin system as HN in-phase magnetization and tracking its
evolution in the Liouville space, assuming scalar coupling interactions
only. Because the peptide used in our study is disordered, we narrowed
down the simulated data to residues not involved in the formation
of secondary structure elements (26,766 residues). After such a filtering,
we prepared reference TOCSY-transfer curves for each residue type
by averaging out simulated data. Then we compared them to the experimental
data. Although in most of cases such a straightforward approach was
sufficient, a more sophisticated procedure is also possible and we
found it necessary for several residues in our peptide. Namely, we
searched for the simulated TOCSY curve for a given residue type that
was the closest to the experimental one (in terms of the least residual
of their subtraction). In a real spectrum, the peak overlap may lead
to unusual TOCSY crosspeak patterns; therefore, we tested various
combinations of simulated nucleus-specific transfer curves to recognize
such patterns and assign overlapped peaks.
Results and Discussion
The key benefits of the proposed technique include nuclei identification
based on the shape of the build-up curve and peak overlap detection.
To make the method feasible, we accelerate it by the application of
NUS. These crucial aspects of signal processing and analysis are discussed
below.
Application to Tau-R4 Peptide
Resonances of all amide
protons in the studied peptide fall within a 0.7 ppm range, as Figure shows. Such a low 1H chemical shift dispersion is typical for unstructured peptides
and requires extraordinary spectral resolution. On the positive side,
the spins in unfolded peptides relax more slowly than those in the
structured ones; thus, the TOCSY-transfer curves can be sampled for
higher mixing times.[50] The assignment of 1H peaks to particular side-chain protons can be a challenging
task, even with a relatively high field spectrometer, such as the
one at our disposal. Typically, for unlabeled peptides, the choice
of two-dimensional techniques is limited. The combination of homonuclear
techniques (TOCSY, COSY, and NOESY) is the only feasible approach[16] because the heteronuclear methods (e.g., HCCH-TOCSY)
are too insensitive. In the current study, we found the extra TOCSY
dimension useful to confirm the assignment of side-chain 1H NMR signals in several residues of Tau-R4 peptide.
Figure 1
Amide 1H TOCSY
spectral region for Tau-R4 peptide. The
spectrum was obtained by adding 21 TOCSY spectra acquired for different
isotropic mixing times (6.85–75.35 ms). Dashed lines indicate
HN chemical shifts of the observed residues and their crosspeak
patterns.
Amide 1H TOCSY
spectral region for Tau-R4 peptide. The
spectrum was obtained by adding 21 TOCSY spectra acquired for different
isotropic mixing times (6.85–75.35 ms). Dashed lines indicate
HN chemical shifts of the observed residues and their crosspeak
patterns.It is often observed that crosspeak
patterns for leucine and lysine
residues vary significantly: Their crosspeaks may overlay in different
combinations or exchange positions. It happens because their β,
γ, and δ protons appear at very similar chemical shifts.[51] In particular, these residues revealed unusual
crosspeak patterns in the studied Tau-R4 peptide. We employed TOCSY-transfer
curves to detect a potential peak overlap and confirm the peak assignment
of these residues.Using different combinations of nucleus-specific
TOCSY-transfer
curves for leucine allowed us to reproduce experimental data and confirm
that the signal of one of the β protons is overlapped with the
signal of γ proton (see Figure ) and exclude the possibility of Hβ2 and Hβ3 overlap. However, the configurational assignment
of leucine’s methylene protons with the analysis of TOCSY transfer
is difficult as the build-ups of Hβ signals show
only subtle differences for gauche and trans configurations.[52]
Figure 2
Five-peaks TOCSY pattern (A) for leucine residue in Tau-R4
peptide
and the corresponding experimental (B) and simulated (C) TOCSY-transfer
curves. The chemical shifts of the analyzed peaks are shown at the
top of panel B. Panel C shows the combination of the simulated nucleus-specific
TOCSY-transfer curves that matches experimental data. The information
on the co-added nucleus-specific curves is in the upper-left corner
of each window in panel C. The reference simulated curves were obtained
by averaging simulated curves for 1758 leucine residues not involved
in secondary structure elements, according to the PDB library.
Five-peaks TOCSY pattern (A) for leucine residue in Tau-R4
peptide
and the corresponding experimental (B) and simulated (C) TOCSY-transfer
curves. The chemical shifts of the analyzed peaks are shown at the
top of panel B. Panel C shows the combination of the simulated nucleus-specific
TOCSY-transfer curves that matches experimental data. The information
on the co-added nucleus-specific curves is in the upper-left corner
of each window in panel C. The reference simulated curves were obtained
by averaging simulated curves for 1758 leucine residues not involved
in secondary structure elements, according to the PDB library.Another leucine showed a different crosspeak pattern
with one broad
peak in a 1–3 ppm region. An isotropic mixing dimension confirms
that two Hβ and one Hγ protons contribute
to this peak. Summing nucleus-specific curves for Hβ and Hγ protons nicely reproduced TOCSY buildup
of the broadened peak at 1.63 ppm, as shown in Figure ).
Figure 3
Four-peaks TOCSY pattern (A) for leucine residue
in Tau-R4 peptide
and the corresponding experimental (B) and simulated (C) TOCSY-transfer
curves. The chemical shifts of the analyzed peaks are shown at the
top of panel B. The simulation assumed the overlap of Hβ and Hγ protons as indicated in the upper-left corner
of the second (from left to right) window in C. The simulated curves
were obtained based on 1758 leucine spin systems not involved in secondary
structure elements from the PDB library.
Four-peaks TOCSY pattern (A) for leucine residue
in Tau-R4 peptide
and the corresponding experimental (B) and simulated (C) TOCSY-transfer
curves. The chemical shifts of the analyzed peaks are shown at the
top of panel B. The simulation assumed the overlap of Hβ and Hγ protons as indicated in the upper-left corner
of the second (from left to right) window in C. The simulated curves
were obtained based on 1758 leucine spin systems not involved in secondary
structure elements from the PDB library.Another example of residue where side-chain 1H NMR peaks
appear within a relatively narrow spectral range is lysine. Among
four lysine residues present in Tau-R4 peptide, three of them showed
a typical crosspeak pattern with unique chemical shifts for each of
the Hβ and Hγ protons. The other
one showed the number of crosspeaks reduced by two. We assigned the
signals in both lysine crosspeak patterns by analyzing the new pseudodimension.
The experimental and simulated TOCSY buildups showed that, for lysine
with a reduced number of peaks, two Hβ, two Hγ, and two Hδ protons yield three peaks
caused by overlap, as indicated in Figure .
Figure 4
Four-peaks TOCSY pattern (A) for lysine residue
and the corresponding
experimental (B) and simulated (C) TOCSY-transfer curves. The chemical
shifts of the analyzed peaks are shown at the top of panel B. The
simulated data assumed the overlap of Hβ2 and Hβ3, Hγ2 and Hγ3, and
Hδ2 and Hδ3 protons, as indicated
in panel C. The set of curves matching the experimental data was selected
from the library of TOCSY curves containing 2031 lysine spin systems
not involved in secondary structure elements.
Four-peaks TOCSY pattern (A) for lysine residue
and the corresponding
experimental (B) and simulated (C) TOCSY-transfer curves. The chemical
shifts of the analyzed peaks are shown at the top of panel B. The
simulated data assumed the overlap of Hβ2 and Hβ3, Hγ2 and Hγ3, and
Hδ2 and Hδ3 protons, as indicated
in panel C. The set of curves matching the experimental data was selected
from the library of TOCSY curves containing 2031 lysine spin systems
not involved in secondary structure elements.We performed a similar analysis for one of the lysines with a typical
crosspeak pattern to further demonstrate that the simulated TOCSY
curves match the experimental data well and can increase assignment
reliability (see Figure ). In this case simulations confirmed that each of the four peaks
correspond to one of the Hβ and Hγ protons.
Figure 5
Common six-peaks TOCSY pattern (A) for lysine residue and the corresponding
experimental (B) and simulated (C) TOCSY-transfer curves. The chemical
shifts of the analyzed peaks are shown at the top of panel B. The
simulated data assumed overlap of Hδ2 and Hδ3 protons, as indicated in panel C. The set of curves matching experimental
data was selected from the library of TOCSY curves containing 2031
lysine spin systems not involved in secondary structure elements.
Common six-peaks TOCSY pattern (A) for lysine residue and the corresponding
experimental (B) and simulated (C) TOCSY-transfer curves. The chemical
shifts of the analyzed peaks are shown at the top of panel B. The
simulated data assumed overlap of Hδ2 and Hδ3 protons, as indicated in panel C. The set of curves matching experimental
data was selected from the library of TOCSY curves containing 2031
lysine spin systems not involved in secondary structure elements.Importantly, all these examples do not take the
relaxation or the
coherence loss into account for the simulations and still provide
a good agreement with the experimental data. Furthermore, one may
potentially combine the acquisition of the TOCSY-transfer dimension
with multiplet collapsing methods[53,54] for easier
identification of overlapping peaks.
Accelerated Measurement
of TOCSY-Transfer Curves
As
demonstrated, matching the experimental and simulated TOCSY-transfer
curves significantly supports the spectral analysis and the resonance
assignment. However, collecting a long series of 2D spectra to obtain
precisely described TOCSY-transfer profiles takes tens of hours. For
example, a pseudo-3D TOCSY experiment for Tau-R4 peptide costed us
about 40 h of experimental time. Thus, to accelerate the acquisition,
we propose to employ NUS, followed by the signal reconstruction using
the CS method.The nonlinearity of the CS reconstruction, particularly
pronounced for low sampling levels, is a known problem.[55] This unwanted effect has to be minimized because
the unbiased shapes of build-up curves are necessary for the feasibility
of the method. Thus, we evaluated the reconstruction of TOCSY buildups
at different subsampling levels by comparing peak volumes in the reconstructed
spectra to those from the uniformly sampled spectra. The results of
this test are shown in Figure .
Figure 6
Correlations between normalized cross-peak volumes in conventional
spectra (512/512 sampling) and reconstructed spectra (384/512, 256/512,
192/512, 128/512, 96/512, 64/512, and 32/512 sampling levels) plotted
for each residue type (row-wise). Subplots contain cross-peak volumes
for each residue type in the 21 TOCSY spectra acquired for different
isotropic mixing times. The horizontal axis in each subplot corresponds
to the cross-peak volumes measured in conventional, fully sampled
spectra, whereas the vertical axis shows peak volumes in reconstructed
NUS spectra.
Correlations between normalized cross-peak volumes in conventional
spectra (512/512 sampling) and reconstructed spectra (384/512, 256/512,
192/512, 128/512, 96/512, 64/512, and 32/512 sampling levels) plotted
for each residue type (row-wise). Subplots contain cross-peak volumes
for each residue type in the 21 TOCSY spectra acquired for different
isotropic mixing times. The horizontal axis in each subplot corresponds
to the cross-peak volumes measured in conventional, fully sampled
spectra, whereas the vertical axis shows peak volumes in reconstructed
NUS spectra.We observed that TOCSY-transfer
curves can be reliably reproduced
at sampling levels as low as 18.75% of the Nyquist grid (see the “96/512”
column in Figure ).
It means that the acquisition can be accelerated about fivefold. In
our study, it corresponds to shortening the experimental time from
≈40 to ≈7.5 h. This significant reduction of acquisition
time allows for collecting data overnight and makes the experiment
practical to use, even for difficult samples such as our peptide.
Because the total time required to collect the series of spectra for
the peptide resonance assignment (15N HSQC, 13C HSQC, COSY, TOCSY, and NOESY) reaches several days, an extra few
hours seem to be a reasonable price for the amount of information
gained.Figure also indicates
that TOCSY buildups for smaller spin systems (e.g., glycine) were
reproduced well, even at the lowest tested sampling level, that is,
32/512, whereas the reconstruction for bigger spin systems, such as
Arg, Ile, Leu, or Lys, failed. This is in agreement with the CS theory,
which states that the minimum number of points required for successful
reconstruction is proportional to K log(N). Here, K is the number of significant spectral
points and N is the length of the vector (here, N = 512 t1 points; see ref (55) for detailed examples).
At low sampling levels, the reconstruction often fails for weak signals
of bigger spin systems. This usually refers to (Hγ and Hδ) protons as the coherence transfer from
HN to these distant protons is generally weak for isotropic
mixing times under 100 ms.[52] An example
of correct and bad TOCSY-curves reconstruction at a low sampling level
for small and big spin systems is shown in Figure .
Figure 7
TOCSY-transfer curves for glycine at HN chemical shift
of 8.57 ppm (A) and arginine at HN chemical shift of 8.05
ppm (B) obtained from spectra reconstructed at different subsampling
levels (32/512, 64/512, 96/512, 128/512, 192/512, 256/512, and 384/512)
and from conventional (512/512) spectra. The chemical shifts of the
analyzed peaks are shown at the top of each subplot. The red arrows
indicate the regions of the curves where the reconstruction was poor
at low sampling levels.
TOCSY-transfer curves for glycine at HN chemical shift
of 8.57 ppm (A) and arginine at HN chemical shift of 8.05
ppm (B) obtained from spectra reconstructed at different subsampling
levels (32/512, 64/512, 96/512, 128/512, 192/512, 256/512, and 384/512)
and from conventional (512/512) spectra. The chemical shifts of the
analyzed peaks are shown at the top of each subplot. The red arrows
indicate the regions of the curves where the reconstruction was poor
at low sampling levels.The reconstruction of
TOCSY curves for glycine (see Figure A) at a 32/512 sampling level
matches almost perfectly with the results from the conventional 512/512
sampling. On the other hand, at the same sampling level, CS failed
to reconstruct weak Hγ (1.62 and 1.52 ppm) and Hδ (3.15 ppm) signals of arginine (see red arrows in Figure B). As shown previously,[55] at low sampling levels, CS reconstructs only
the most intense Hα and Hβ signals.
As the CS reconstruction is performed trace by trace in the indirect
dimension, the performance of CS is generally worse when the number
of peaks grows, for example, because of similar HN chemical
shifts of two different residues.An interesting feature of
pseudo-3D TOCSY acquisition in terms
of CS reconstruction is that the spectral sparsity decreases with
the length of the isotropic mixing block. We realized that, for a
given total experimental time, it is beneficial to decrease the number
of NUS points for lower mixing times and collect more samples for
longer mixing times. We demonstrate the benefits of this approach
on a weak arginine crosspeak at 3.15 ppm (Hδ) from Figure B. Notably, in such
a “sparsity-matched” approach, we incremented the number
of NUS samples per mixing time from 24/512 to 104/512 with the step
of 4. As can be seen in Figure , the shape of the curve for the arginine crosspeak is reproduced
better from the sparsity-matched sampled data (24–104)/512
than from the data with constant 64/512 sampling, although both data
sets contained the same total amount of NUS samples (1344).
Figure 8
Experimental
TOCSY build-up curves for a Hδ crosspeak
of arginine (8.05, 3.15 ppm) obtained at different NUS levels. The
applied subsampling levels are shown at the top of the corresponding
subplots. The subplot labeled 512/512 corresponds to a series of conventional
2D TOCSY spectra, whereas the subplot labeled (24–104)/512
refers to the sparsity-matched approach. In the sparsity-matched sampling,
the first point of the build-up curve corresponds to 24/512 NUS samples
and the last point to 104/512 NUS samples.
Experimental
TOCSY build-up curves for a Hδ crosspeak
of arginine (8.05, 3.15 ppm) obtained at different NUS levels. The
applied subsampling levels are shown at the top of the corresponding
subplots. The subplot labeled 512/512 corresponds to a series of conventional
2D TOCSY spectra, whereas the subplot labeled (24–104)/512
refers to the sparsity-matched approach. In the sparsity-matched sampling,
the first point of the build-up curve corresponds to 24/512 NUS samples
and the last point to 104/512 NUS samples.Additional to resolution and spectral information gains, the presented
method also provides sensitivity benefits, similar to the previously
published swept-coherence transfer (SCoT) method.[56] Namely, a dense sampling of mixing times in pseudo-3D TOCSY
prevents the potential missing of crosspeaks, which often occurs in
single-2D TOCSY spectra acquired with too short or too long mixing
times. On the other hand, because many spectra are needed to describe
the shape of the intensity build-up curve, the sensitivity of each
spectrum in a series is accordingly smaller than that in a single
spectrum acquired over the same time.The NOESY variant of an
approach presented here deserves a comment.
Such a method has been proposed in the past by our group.[15] Contrary to the TOCSY case, the NOESY mixing
time can be set to a different value for each t1 point, allowing for the use of time-resolved NUS.[57] In this way, one obtains a “continuous”
intensity build-up curve with a well-described linear part that can
be used to calculate internuclear distances. Yet, significant differences
between the magnitudes of the diagonal and off-diagonal peaks make
NOESY very challenging for NUS.[58] Moreover,
the shape of the intensity build-up curves in NOESY is not as “sophisticated”
as that in TOCSY and thus does not require a dense sampling. Actually,
two well-placed points (mixing time values) provide sufficient information,
making it possible to determine internuclear distances.[14]Finally, we would like to make a remark
on the possibility of using
methods other than CS. Some NUS algorithms allow the co-processing
of 2D spectra in a series by gathering them into one pseudo-3D object
and applying 3D processing. Such methods employ extra assumptions
about the model of changes in the third pseudodimension. For example,
the recently introduced methods based on the Radon transform and its
variants assume simple models of changes of peak positions.[4,59] If peaks do not move between spectra, the method of multidimensional
decomposition (MDD) is applicable. Apparently, this would be the case
of a series of 2D TOCSY spectra. Unfortunately, however, the procedure
that greatly enhances the efficiency of MDD for a single 3D spectrum,
that is, gathering all off-diagonal peaks into one component,[60] is not possible for such cases of serial 2Ds
when different off-diagonal peaks change their intensities independently.
In our hands, the MDD processing of a series of 2D TOCSYs did not
give optimal results. Thus, we decided to process our 2D spectra separately
using the compressed sensing (CS) method.[38,39]
Conclusions
Our results show that the TOCSY-transfer
curves can be used to
form a spectral pseudodimension, providing benefits similar to those
of extra Fourier dimensions, that is, the resolution boost and the
complement of nucleus-specific information. However, to take full
advantage of the concept, we need to sample the mixing time densely
and be able to simulate the shape of the build-up curve with high
fidelity. The former can be obtained with NUS and effective signal
reconstruction methods and the latter requires simulations of strongly
coupled spin systems. Both are possible with modern software—MddNMR
and Spinach—and open a way to a new type of multidimensional
NMR spectroscopy. Although the calculations may take several days,
they have to be performed only once, and the obtained library is general
for all unstructured peptides. The usability of the isotropic mixing
pseudodimensions and the analysis supported by quantum-mechanical
simulations reaches far beyond the peptide research discussed in this
work. We envisage applications to other complex macromolecules and
mixtures where the resolution is an issue. It is worth noting that
the build-up curves can be used as a “fingerprint”.
For example, when we expect a limited set of compounds in the sample
(e.g., in metabolomics), the library of experimentally measured curves
can be created and used for compound identification.[26] Moreover, an extra pseudodimension can be potentially used
to enhance the resolution in NMR spectrometers operating at low magnetic
fields, for example, benchtop NMR spectrometers.
Authors: Sven G Hyberts; Alexander G Milbradt; Andreas B Wagner; Haribabu Arthanari; Gerhard Wagner Journal: J Biomol NMR Date: 2012-02-14 Impact factor: 2.835