Published: March 9th, 2021
This protocol describes the setup of an NMR bioreactor to keep encapsulated human cells viable for up to 72 h, followed by time-resolved in-cell NMR data acquisition and analysis. The methodology is applied to monitor intracellular protein-ligand interactions in real time.
In-cell NMR is a unique approach to observe the structural and dynamic properties of biological macromolecules at atomic resolution directly in living cells. Protein folding, chemical modifications, and conformational changes induced by ligand binding can be observed. Therefore, this method has great potential in the context of drug development. However, the short lifetime of human cells confined in the NMR spectrometer limits the application range of in-cell NMR. To overcome this issue, NMR bioreactors are employed that can greatly improve the cell sample stability over time and, importantly, enable the real-time recording of in-cell NMR spectra. In this way, the evolution of processes such as ligand penetration and binding to the intracellular protein target can be monitored in real time. Bioreactors are often limited by low cell viability at high cell numbers, which results in a trade-off between the overall sensitivity of the experiment and cell viability. We recently reported an NMR bioreactor that maintains a high number of human cells metabolically active for extended periods of time, up to 72 h. This setup was applied to monitor protein-ligand interactions and protein chemical modification. We also introduced a workflow for quantitative analysis of the real-time NMR data, based on multivariate curve resolution. The method provides concentration profiles of the chemical species present in the cells as a function of time, which can be further analyzed to obtain relevant kinetic parameters. Here we provide a detailed description of the NMR bioreactor setup and its application to monitoring protein-ligand interactions in human cells.
In-cell Nuclear Magnetic Resonance (NMR) spectroscopy has recently emerged as a powerful approach to investigate structural and dynamical properties of macromolecules within the cellular environment1,2,3,4,5,6. In-cell NMR succeeded in the investigation of functionally relevant processes such as protein folding/misfolding7,8,9, metal binding7,10, disulfide bond formation11,12, and protein−protein interaction13, protein-ligand interaction14,15,16, and nucleic acid-ligand interaction17,18 in living human cells. One of the limiting factors of in-cell NMR applications is the short lifetime of the cells during the experiment. The solution to this problem involves the use of NMR bioreactors. In these devices, a constant flow of growth medium is applied to the cells, which are kept confined within the NMR spectrometer, in order to provide oxygen and nutrients and to remove toxic byproducts. Following the advent of in-cell NMR, several NMR bioreactors designs have been developed to improve cell viability for longer periods of time, in which either bacteria or mammalian cells are encapsulated in a hydrogel19,20,21,22 or kept in suspension and perfused through the use of a microdialysis membrane23. Such bioreactors have allowed the acquisition of longer NMR experiments with increased signal-to-noise ratio (S/N)5 and, even more importantly, could be employed to investigate cellular processes in real time22,23,24. Thanks to the high chemical and conformational sensitivity of NMR, the latter application can provide precious insights on the kinetics of functional processes within living cells at atomic resolution.
In this protocol, we show how to set up and operate an improved bioreactor recently reported25, which was obtained by combining an existing modular bioreactor design23 with the approach relying on cell encapsulation in hydrogel that were pioneered by other groups19,20,21,22,26,27. We describe the application of the bioreactor to real-time in-cell NMR studies of intracellular protein-observe ligand binding in HEK293T cells. In the bioreactor, cells are encapsulated at high density in agarose gel threads and are maintained highly viable and metabolically active for up to 72 h, during which real-time in-cell NMR experiments are recorded. The bioreactor is composed of a glass tube that fits standard 5 mm NMR probes that is watertight and connected to a tube holder so that the internal sample chamber has 4.2 mm internal diameter, 38 mm height, and a volume of 526 µL. The inlet is a 7-meter-long PEEK capillary (o.d. = 1/32", i.d. = 0.5 mm) inserted in the sample chamber down to ~6 mm from the bottom, while the outlet is a 7-meter-long PTFE capillary (o.d. = 1/32", i.d. = 0.5 mm) attached at the top of the tube holder (Figure 1). The tubing is coaxially inserted in a temperature-controlled line connected to a water bath. The inlet and outlet are connected through PEEK tubing to a 4-way, 2-position valve attached to an FPLC pump for controlling the medium flow and a waste container.
The bioreactor is applied to study the kinetics of the interaction, previously reported14,25, between two drugs, acetazolamide (AAZ) and methazolamide (MZA), in human cells with the second isoform of human carbonic anhydrase (CA II), a pharmacologically relevant target28,29,30, and the kinetics of the formation of the intramolecular disulfide bond, promoted by the small molecule ebselen25,31, of the copper-free, zinc-bound form of human copper, zinc superoxide dismutase (SOD1), an antioxidant enzyme implicated in the onset of amyotrophic lateral sclerosis7,8,32. Finally, quantitative analysis of the real-time NMR data is performed in MATLAB using the Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) algorithm33, through which the pure spectral components and the concentration profiles as a function of time are obtained for the species observed, that can be further analyzed to obtain relevant kinetic parameters.
The protocol starts from a T75 flask of HEK293T cells (~3 x 107 cells per flask) transiently overexpressing either human CA II (unlabeled) or human SOD1 (15N-labeled). The cells were grown and maintained in T75 flasks with DMEM high glucose by 1:10 passages every 3-4 days and transfected with the cDNA encoding the protein of interest 48 h prior to the experiment. The steps involved in this phase are reported in detail elsewhere34.
1. Reagent and solution setup
2. Bioreactor setup
3. Preparation of the cell sample
4. Bioreactor operation and cleaning
5. NMR experiments
6. MCR-ALS analysis
7. Trypan blue test
The above protocol allows the encapsulation of cells in threads of hydrogel to maximize cell viability for long periods of time, necessary to investigate in real time intracellular processes. In the bioreactor, the cells are maintained alive and metabolically active up to 72 h, as confirmed by Trypan blue test (Figure 2a-c). In principle, this protocol can be applied to observe an intracellular protein of interest undergoing any conformational or chemical changes. In the first application described above, the bioreactor is applied to monitor in real time the binding of two inhibitors, AAZ and MZA, to CA II overexpressed in the cytosol of HEK293T cells. The first 1H excitation sculpting spectrum (zgesgp) recorded is used to assess the overall signal intensity (which is proportional to the number of cells), the presence of signals from the overexpressed protein and the field homogeneity (Figure 2d). In the case of CA II, the intracellular binding of the two inhibitors can be monitored by WATERGATE 3-9-1935 1D 1H NMR spectra (p3919gp), by observing 1H signals in the region between 11 and 16 ppm. These signals arise from the zinc-coordinating histidines and other aromatic residues of CA II36 and are perturbed upon ligand binding14,15. Ligand concentrations can be chosen based on the diffusion rate or, if available, from previously determined permeability values14. Successful binding is confirmed visually by the appearance of an additional set of signals in the spectral region of interest, that gradually replaces the original signals (Figure 3). Time-dependent binding curves are obtained by MCR-ALS analysis, which separates the two sets of NMR signals arising from free and bound CA II (Figure 4a) and simultaneously provides the relative concentration profiles of the two species (Figure 4b). In the second application, the bioreactor is applied to monitor the formation of zinc-bound SOD1 intramolecular disulfide bond promoted by ebselen, a glutathione peroxidase mimetic, in human cells. This process is monitored by observing changes in 1H-15N 2D SOFAST-HMQC37 spectra (which provides a fingerprint of the protein backbone conformation) caused by perturbations of the protein structure induced by the disulfide bond formation. Additional signals arising from disulfide-oxidized SOD1 appear in the 1H-15N spectrum and gradually replace those from disulfide-reduced SOD1. MCR-ALS analysis on selected regions of the 2D spectrum separates the signals arising from the two species (Figure 5a) and provides their relative concentration profiles (Figure 5b). The obtained concentration curves can be further analyzed by non-linear fitting to provide information on the kinetics of the processes under study25.
Figure 1: Scheme of the bioreactor. Left: cross-section view of the empty flow unit. Right: scheme of the bioreactor setup. The PEEK inlet tubing is shown in green; the PTFE outlet tubing is shown in blue. The left panel is reproduced with permission from Luchinat et al.25. Please click here to view a larger version of this figure.
Figure 2: Trypan Blue Test on encapsulated cells and sample check by 1H NMR. Representative slices of agarose containing embedded cells and stained with Trypan blue (a) immediately after casting and (b) after 72 h in the bioreactor; (c) cell viability as a function of time in the NMR bioreactor under active flow (black) and under static conditions (red), measured by Trypan Blue Test. (d) zgesgp 1H NMR spectra recorded on agarose-embedded cells overexpressing CA II in the absence (black) and in the presence (red) of gas bubbles in the bioreactor. In the latter case, decreased field homogeneity causes line broadening and the appearance of solvent suppression artifacts. Interesting spectral features are labeled. Panels (a-c) are reproduced with permission from Luchinat et al.25. Please click here to view a larger version of this figure.
Figure 3: Representative real-time in-cell 1H NMR data obtained on agarose-encapsulated cells in the bioreactor. Waterfall plots of 1D 1H NMR spectra (region between 15.6 and 11.1 ppm) of HEK293T cells overexpressing CA II and subsequently treated with (a) 25 µM AAZ and (b) 10 µM MZA, recorded as a function of time in the NMR bioreactor. The time of ligand treatment is shown with an arrow. Spectral intensity (a.u.) is color-coded from blue (lowest) to yellow (highest). This figure is reproduced with permission from Luchinat et al.25. Please click here to view a larger version of this figure.
Figure 4: Representative MCR-ALS output from 1D NMR spectra. (a) 1H NMR spectra of the pure components reconstructed by MCR-ALS: CA II in the absence of ligands (black) and in the complex with AAZ (red) or MZA (magenta); (b) relative concentration profiles of free (black) and bound CA II as a function of time upon addition of AAZ (red) or MZA (magenta) obtained by MCR-ALS. Times of ligand treatment are marked with arrows. This figure is reproduced with permission from Luchinat et al.25. Please click here to view a larger version of this figure.
Figure 5: Representative MCR-ALS output from 2D NMR spectra. (a) 1H-15N spectral regions (labeled I-IV) of the pure components reconstructed by MCR-ALS: disulfide-reduced SOD1 (black) and disulfide-oxidized SOD1 (red); (b) relative concentration profile of the pure components as a function of time upon addition of ebselen (marked with an arrow) obtained by MCR-ALS. This figure is reproduced with permission from Luchinat et al.25. Please click here to view a larger version of this figure.
The aim of using a bioreactor for in-cell NMR experiment is to keep cells alive and metabolically active for a prolonged period of time. A number of critical aspects must be taken into consideration to achieve this aim. First, it is paramount to avoid bacterial contamination when preparing the cell sample and during the NMR data acquisition. If strains of E. coli or other bacteria commonly used for gene cloning and recombinant protein expression are used in the laboratory, they may contaminate the cells during sample preparation. Once in the bioreactor, the bacteria will grow quickly exploiting the fresh growth medium and will cause cell death due to the production of endotoxins. Bacterial contamination is only spotted at an advanced stage, when it turns the growth medium yellow and turbid. Furthermore, incomplete cleaning of the bioreactor could cause contamination of the pump or the tubing with bacteria, yeasts, or common molds.
A requirement for the success of the experiment is the avoidance of gas bubble formation. Gas bubbles trapped between the agarose threads in the active volume of the NMR coil would introduce large magnetic field inhomogeneities, causing incomplete suppression of the H2O signal and severe loss of spectral quality (Figure 2d). Bubbles may be caused by air trapped in the system or by the formation of gaseous CO2. The former can be easily avoided by flushing the system with medium prior to inserting the cell sample, while to avoid the latter it is recommended to decrease the concentration of NaHCO3 in the growth medium, and to keep all parts of the system at a constant temperature to minimize differences in the CO2 solubility. Cellular aerobic metabolism may also cause the formation of gaseous CO2, which can be prevented by increasing the flow rate.
Cell viability should be checked after each run by Trypan Blue Test. However, that does not provide insights on the metabolic activity. To obtain a more complete picture of the metabolic state of the cells during the bioreactor operation, 31P NMR spectra can be performed to assess the production of ATP as a function of time23,25. However, a dedicated probe is often necessary for this measurement, which may allow simultaneous recording with 1H NMR.
In the case of CA II, the presence of well-resolved reporter signals in an unusual region of the 1H spectrum facilitates the analysis from simple 1D NMR spectra and does not require isotope enrichment during protein expression. In general, other proteins could give rise to 1H signals useful for monitoring spectral changes in other regions, such as that typical of the protein hydrophobic core between 0 and -1 ppm11; however, these regions tend to be crowded for folded proteins larger than ~10 kDa. In this case, as shown for SOD1, it is preferable to enrich the protein with 15N, by providing uniformly 15N-enriched growth medium during protein expression, and to monitor real-time changes in 2D 1H-15N NMR spectra. 2D spectra are imported as a 2D arrays in MATLAB, rearranged to 1D arrays and stacked prior to MCR-ALS analysis. The latter approach is generally applicable to any intracellular protein that gives rise to detectable signals, and provides information on protein conformational changes at the single residue level. In principle, the latter approach can be generalized to nD spectra and to other isotope-labeling schemes.
Concerning the application to different types of cells, the protocol should be easily adapted to different cell lines and does not require that the protein of interest is directly expressed in the cells. Therefore, other approaches to in-cell NMR can be combined with this protocol, in which the macromolecule of interest is produced recombinantly, or synthesized, and subsequently inserted into the cells by electroporation or by other delivery methods1,9,38. When working with different cell lines or sample preparation protocols, parameters such as the agarose concentration, the thread thickness, and the final cell density in the agarose threads may need to be optimized empirically. Furthermore, the applicability of the protocol described here is limited to cells that tolerate agarose encapsulation. Other cell types may require different hydrogel formulations, whereas a different setup is recommended when analyzing cells that natively grow in suspension, for example, making use of a coaxial microdialysis membrane to ensure nutrient diffusion while keeping suspended cells confined in the NMR tube23.
Compared to other NMR bioreactor designs19,20,21,22, the device described here relies on a commercially available flow-unit, adapted with minor modifications. Therefore, the device can be easily replicated in different laboratories with high reproducibility. Furthermore, it allows standardized operation and full compliance with strict laboratory safety regulations, if needed. Overall, the flexibility and ease of operation of the bioreactor should allow many other applications of solution NMR, both in cells and in vitro, in addition to those as already reported23,25. Eventually, the same bioreactor design could be applied to samples that resemble more of the physiological environment of a tissue, such as spheroids or organoids, provided that appropriate scaffolds are found for keeping such samples alive-or even sustaining their growth-in the NMR spectrometer.
The authors declare that there is no conflict of interest.
This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 programme of the European Commission, by Instruct-ULTRA, grant number 731005, an EU H2020 project to further develop the services of Instruct-ERIC, and by Ministero dell'Istruzione, dell'Università e della Ricerca PRIN grant 20177XJCHX. The authors acknowledge the support of Instruct-ERIC, a Landmark ESFRI project, through the JRA Award number 815 and the use of resources of the CERM/CIRMMP Italy Centre. We thank Matteo Pennestri (Bruker, UK) for providing support for the InsightMR flow unit operation.
|DMEM, high glucose
|DMEM, high glucose, powder
|L-glutamine (200 mM)
|Low-gelling agarose, powder
|Penicillin–streptomycin (10,000 U/ml)
|Trypan Blue solution (0.4% (wt/vol)
|Hazard statement(s): H350 may cause cancer.
|Trypsin–EDTA (0.05% (wt/vol))
|Avance III Spectrometer equipped with a 5 mm CryoProbe
|All modern spectrometers and narrow-bore magnets equipped with 5 mm probes are compatible.
|InsightMR flow unit
|P-920 pump module from ÄKTA FPLC
|Any FPLC, HPLC peristaltic or syringe pump should be compatible with the flow unit.
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