15 research outputs found
Metabolic Measurements of Nonpermeating Compounds in Live Cells Using Hyperpolarized NMR
Hyperpolarization by dissolution
dynamic nuclear polarization (D-DNP)
has emerged as a technique for enhancing NMR signals by several orders
of magnitude, thereby facilitating the characterization of metabolic
pathways both in vivo and in vitro. Following the introduction of
an externally hyperpolarized compound, real-time NMR enables the measurement
of metabolic flux in the corresponding pathway. Spin relaxation however
limits the maximum experimental time and prevents the use of this
method with compounds exhibiting slow membrane transport rates. Here,
we demonstrate that on-line electroporation can serve as a method
for membrane permeabilization for use with D-DNP in cell cultures.
An electroporation apparatus hyphenated with stopped-flow sample injection
permits the introduction of the hyperpolarized metabolite within 3
s after the electrical pulse. In yeast cells that do not readily take
up pyruvate, the addition of the electroporation pulse to the D-DNP
experiment increases the signals of the downstream metabolic products
CO<sub>2</sub> and HCO<sub>3</sub><sup>–</sup>, which otherwise
are near the detection limit, by 8.2- and 8.6-fold. Modeling of the
time dependence of these signals then permits the determination of
the respective kinetic rate constants. The observed conversion rate
from pyruvate to CO<sub>2</sub> normalized for cell density was found
to increase by a factor of 12 due to the alleviation of the membrane
transport limitation. The use of electroporation therefore extends
the applicability of D-DNP to in vitro studies with a wider range
of metabolites and at the same time reduces the influence of membrane
transport on the observed conversion rates
Metabolic Measurements of Nonpermeating Compounds in Live Cells Using Hyperpolarized NMR
Hyperpolarization by dissolution
dynamic nuclear polarization (D-DNP)
has emerged as a technique for enhancing NMR signals by several orders
of magnitude, thereby facilitating the characterization of metabolic
pathways both in vivo and in vitro. Following the introduction of
an externally hyperpolarized compound, real-time NMR enables the measurement
of metabolic flux in the corresponding pathway. Spin relaxation however
limits the maximum experimental time and prevents the use of this
method with compounds exhibiting slow membrane transport rates. Here,
we demonstrate that on-line electroporation can serve as a method
for membrane permeabilization for use with D-DNP in cell cultures.
An electroporation apparatus hyphenated with stopped-flow sample injection
permits the introduction of the hyperpolarized metabolite within 3
s after the electrical pulse. In yeast cells that do not readily take
up pyruvate, the addition of the electroporation pulse to the D-DNP
experiment increases the signals of the downstream metabolic products
CO<sub>2</sub> and HCO<sub>3</sub><sup>–</sup>, which otherwise
are near the detection limit, by 8.2- and 8.6-fold. Modeling of the
time dependence of these signals then permits the determination of
the respective kinetic rate constants. The observed conversion rate
from pyruvate to CO<sub>2</sub> normalized for cell density was found
to increase by a factor of 12 due to the alleviation of the membrane
transport limitation. The use of electroporation therefore extends
the applicability of D-DNP to in vitro studies with a wider range
of metabolites and at the same time reduces the influence of membrane
transport on the observed conversion rates
Hyperpolarized Hadamard Spectroscopy Using Flow NMR
The
emergence of the dissolution dynamic nuclear polarization (D-DNP)
technique provides an important breakthrough to overcome inherent
sensitivity limitations in nuclear magnetic resonance (NMR) experiments.
In dissolution DNP, only a small amount of frozen sample is polarized,
dissolved, and injected into an NMR spectrometer. Although substantially
enhanced NMR signals can be obtained, the single scan nature of this
technique a priori impedes the use of correlation experiments, which
represent some of the most powerful applications of NMR spectroscopy.
Here, an alternative method for multiscan spectroscopy from D-DNP
samples utilizing a flow NMR probe is described. Multiple hyperpolarized
segments of sample are sequentially injected using a purpose designed
device. Hadamard spectroscopy can then be applied for obtaining chemical
shift correlation information even from a small number of scans. This
capability is demonstrated with a four-scan data set for obtaining
the [<sup>13</sup>C,<sup>1</sup>H] correlations in the test molecule
1-butanol. Because of the effects of spin–lattice relaxation
and concentration gradients in the D-DNP experiment, the subtractive
process for Hadamard reconstruction requires an additional step of
intensity scaling. For this purpose, a reconstruction procedure was
developed that uses entropy maximization and is robust with respect
to noise and signal overlap. In a broader sense, the multiscan NMR
as described here is amenable to various correlation NMR experiments,
and increases the versatility of D-DNP in small-molecule characterization
Characterization of Chemical Exchange Using Relaxation Dispersion of Hyperpolarized Nuclear Spins
Chemical
exchange phenomena are ubiquitous in macromolecules, which
undergo conformational change or ligand complexation. NMR relaxation
dispersion (RD) spectroscopy based on a Carr–Purcell–Meiboom–Gill
pulse sequence is widely applied to identify the exchange and measure
the lifetime of intermediate states on the millisecond time scale.
Advances in hyperpolarization methods improve the applicability of
NMR spectroscopy when rapid acquisitions or low concentrations are
required, through an increase in signal strength by several orders
of magnitude. Here, we demonstrate the measurement of chemical exchange
from a single aliquot of a ligand hyperpolarized by dissolution dynamic
nuclear polarization (D-DNP). Transverse relaxation rates are measured
simultaneously at different pulsing delays by dual-channel <sup>19</sup>F NMR spectroscopy. This two-point measurement is shown to allow
the determination of the exchange term in the relaxation rate expression.
For the ligand 4-(trifluoromethyl)Âbenzene-1-carboximidamide binding
to the protein trypsin, the exchange term is found to be equal within
error limits in neutral and acidic environments from D-DNP NMR spectroscopy,
corresponding to a pre-equilibrium of trypsin deprotonation. This
finding illustrates the capability for determination of binding mechanisms
using D-DNP RD. Taking advantage of hyperpolarization, the ligand
concentration in the exchange measurements can reach on the order
of tens of μM and protein concentration can be below 1 μM,
i.e., conditions typically accessible in drug discovery
Modeling of Polarization Transfer Kinetics in Protein Hydration Using Hyperpolarized Water
Water–protein
interactions play a central role in protein
structure, dynamics, and function. These interactions, traditionally,
have been studied using nuclear magnetic resonance (NMR) by measuring
chemical exchange and nuclear Overhauser effect (NOE). Polarization
transferred from hyperpolarized water can result in substantial transient
signal enhancements of protein resonances due to these processes.
Here, we use dissolution dynamic nuclear polarization and flow-NMR
for measuring the pH dependence of transferred signals to the protein
trypsin. A maximum enhancement of 20 is visible in the amide proton
region of the spectrum at pH 6.0, and of 47 at pH 7.5. The aliphatic
region is enhanced up to 2.3 times at pH 6.0 and up to 2.5 times at
pH 7.5. The time dependence of these observed signals can be modeled
quantitatively using rate equations incorporating chemical exchange
to amide sites and, optionally, intramolecular NOE to aliphatic protons.
On the basis of these two- and three-site models, average exchange
(<i>k</i><sub>ex</sub>) and cross-relaxation rates (σ)
obtained were <i>k</i><sub>ex</sub> = 12 s<sup>–1</sup>, σ = −0.33 s<sup>–1</sup> for pH 7.5 and <i>k</i><sub>ex</sub> = 1.8 s<sup>–1</sup>, σ = −0.72
s<sup>–1</sup> for pH 6.0 at a temperature of 304 K. These
values were validated using conventional EXSY and NOESY measurements.
In general, a rapid measurement of exchange and cross-relaxation rates
may be of interest for the study of structural changes of the protein
occurring on the same time scale. Besides protein–water interactions,
interactions with cosolvent or solutes can further be investigated
using the same methods
Parallelized Ligand Screening Using Dissolution Dynamic Nuclear Polarization
Protein–ligand
interactions are frequently screened using
nuclear magnetic resonance (NMR) spectroscopy. The dissociation constant
(<i>K</i><sub>D</sub>) of a ligand of interest can be determined
via a spin–spin relaxation measurement of a reporter ligand
in a single scan when using hyperpolarization by means of dissolution
dynamic nuclear polarization (D-DNP). Despite nearly instantaneous
signal acquisition, a limitation of D-DNP for the screening of protein–ligand
interactions is the required polarization time on the order of tens
of minutes. Here, we introduce a multiplexed NMR experiment, where
a single hyperpolarized ligand sample is rapidly mixed with protein
injected into two flow cells. NMR detection is achieved simultaneously
on both channels, resulting in a chemical shift resolved spin relaxation
measurement. Spectral resolution allows the use of reference compounds
for accurate quantification of concentrations. Simultaneous use of
two concentration ratios between protein and ligand broadens the range
of <i>K</i><sub>D</sub> that is accurately measurable in
a single experiment to at least an order of magnitude. In a comparison
of inhibitors for the protein trypsin, the average <i>K</i><sub>D</sub> values of benzamidine and benzylamine were found to
be 12.6 ± 1.4 μM and 207 ± 22 μM from three
measurements, based on <i>K</i><sub>D</sub> = 142 μM
assumed known for the reporter ligand 4-(trifluoromethyl)Âbenzene-1-carboximidamide.
Typical confidence ranges at 95% evaluated for single experiments
were (8.3 μM, 20 μM) and (151 μM, 328 μM).
The multiplexed detection of two or more hyperpolarized samples increases
throughput of D-DNP by the same factor, improving the applicability
to most multipoint measurements that would traditionally be achieved
using titrations
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 <sup>13</sup>C spectrum
with <sup>1</sup>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 <sup>1</sup>H chemical shifts and of ±0.4 ppm for the indirectly
determined <sup>13</sup>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 rapidlyî—¸the latter being of interest for potential
application in real-time spectroscopy
Determination of Intermolecular Interactions Using Polarization Compensated Heteronuclear Overhauser Effect of Hyperpolarized Spins
The nuclear Overhauser effect (NOE)
has long been used as a selective
indicator for intermolecular interactions. Due to relatively small
changes of signal intensity, often on the order of several percent,
quantitative NOE measurements can be challenging. Hyperpolarization
of nuclear spins can dramatically increase the NOE intensity by increasing
population differences, but poses its own challenge in quantifying
the original polarization level. Here, we demonstrate a method for
the accurate measurement of intermolecular heteronuclear cross-relaxation
rates by simultaneous acquisition of signals from both nuclei. Using
this method, we measure cross-relaxation rates between water protons
and <sup>19</sup>F of trifluoroacetic acid at concentrations ranging
from 23 to 72 mM. A concentration-independent value of 2.46 ×
10<sup>–4</sup> ± 1.02 × 10<sup>–5</sup> s<sup>–1</sup> M<sup>–1</sup> is obtained at a temperature
of 301 K and validated using a nonhyperpolarized measurement. In a
broader context, accurate measurement of heteronuclear cross-relaxation
rates may enable the study of intermolecular interactions including
those involving macromolecules where <sup>19</sup>F atoms can be introduced
as site-selective labels
Multinuclear Detection of Nuclear Spin Optical Rotation at Low Field
We
describe the multinuclear detection of nuclear spin optical
rotation (NSOR), an effect dependent on the hyperfine interaction
between nuclear spins and electrons. Signals of <sup>1</sup>H and <sup>19</sup>F are discriminated by frequency in a single spectrum acquired
at sub-millitesla field. The simultaneously acquired optical signal
along with the nuclear magnetic resonance signal allows the calculation
of the relative magnitude of the NSOR constants corresponding to different
nuclei within the sample molecules. This is illustrated by a larger
NSOR signal measured at the <sup>19</sup>F frequency despite a smaller
corresponding spin concentration. Second, it is shown that heteronuclear <i>J</i>-coupling is observable in the NSOR signal, which can be
used to retrieve chemical information. Multinuclear frequency and <i>J</i> resolution can localize optical signals in the molecule.
Properties of electronic states at multiple sites in a molecule may
therefore ultimately be determined by frequency-resolved NSOR spectroscopy
at low field
Measurement of Kinetics and Active Site Distances in Metalloenzymes Using Paramagnetic NMR with <sup>13</sup>C Hyperpolarization
Paramagnetic
relaxation enhancement (PRE) conjoint with hyperpolarized
NMR reveals structural information on the enzyme–product complex
in an ongoing metalloenzyme-catalyzed reaction. Substrates of pseudouridine
monophosphate glycosidase are hyperpolarized using the dynamic nuclear
polarization (DNP) method. Time series of <sup>13</sup>C NMR spectra
are subsequently measured with the enzyme containing diamagnetic Mg<sup>2+</sup> or paramagnetic Mn<sup>2+</sup> ions in the active site.
The differences of the signal evolution and line widths in the Mg<sup>2+</sup> vs Mn<sup>2+</sup> reactions are explained through PRE in
the enzyme-bound product, which is in fast exchange with its free
form. Here, a strong distance dependence of the paramagnetically enhanced
relaxation rates enables the calculation of distances from product
atoms to the metal center in the complexed structure. The same method
can be used to add structural information to real-time characterizations
of chemical processes involving compounds with naturally present or
artificially introduced paramagnetic sites