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21 protocols using qci f cryoprobe

1

OTUB1 Binding Interactions by NMR

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We recorded all NMR spectra on a Bruker 600 MHz spectrometer, equipped with a 5 mm QCI-F cryo probe with z-gradient, and kept the temperature constant at 298K during all experiments. To probe compound and E2 ligase binding to OTUB1, we recorded 1H-1D and 13C-SOFAST-HMQC experiments. We used 3 mm NMR tubes filled with 160 μL of 50 μM {U}-2H,1H/13C-methyl-Ile/Leu/Val/Ala(ILVA),{U}-15N labeled OTUB1, 25 mM d-Tris, pH 7.5, 150 mM NaCl, 5% D2O (to lock), 100 μM DSS (internal standard), 75 μM EN-523 (dissolved in 100% d6-DMSO; for compound binding study) and/or 100 μM E2 D2 / Ub-E2 D2 (for ligase binding studies). To allow for complete binding of the compound to OTUB1, we chose an incubation period of ~40 hours. We also recorded reference spectra with the adequate volumes of pure d6-DMSO and/or E2 buffer to compensate for solvent induced effects, and repeated experiments after 40 hours to make sure that any spectral changes were not related to protein oxidation.
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2

NMR Metabolomics Profiling Protocol

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Experiments were performed at 298 K on a Bruker AVANCE 3 600 MHz spectrometer, equipped with a QCI-F cryoprobe. Data sets were acquired with 64k points and a proton window size of 16 ppm. Spectra were referenced against an internal standard of DSS. Excitation sculpting was used to suppress the water peak using pulsed field gradients. Analysis of data was performed using Bruker TopSpin and AMIX data analysis software. Identification of metabolites was performed by comparison to previously published data on the Madison Metabolomics Consortium Database and by reference to internal standards. We utilised Bruker TopSpin to quantify peak intensity with reference to a DSS standard of known concentration. Absolute concentrations were calculated using Concentration (μM)=peak X intensity/((DSS peak intensity/9 protons)×peak X protons)×50.
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3

NMR Characterization of Protein Samples

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NMR spectroscopy
was performed using a 700 MHz Bruker Avance NEO spectrometer fitted
with a Bruker AEON refrigerated magnet and QCI-F cryoprobe. The 15N–1H HSQC spectroscopy experiments were
performed using the hsqcetfpf3gpsi pulse sequence,
while 1H NMR spectra were collected using the zgesgp pulse sequence. Spectra were recorded in the temperature range of
295–323 K at incremental steps of 2 K. To control for thermal
drift of signals, 5 μL of 2,2,3,3-tetradeutero-3-trimethylsilylpropionic
acid (TSP) was added to the protein sample.
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4

Detailed NMR Experimental Protocols for Structural Analysis

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All NMR experiments were carried out on a Bruker Avance NEO 700 MHz spectrometer equipped with a QCI-F cryoprobe (Bruker, Coventry, UK). Water suppression was achieved using excitation sculpting with gradients.22 (link) Phase sensitive 2D-HSQC spectra were acquired using Echo/Antiecho-TPPI gradient selection (Bruker pulse sequences – hsqcetgpsisp.2 and hsqcetfpf3gpsi for 13C and 15N, respectively). Total Correlation Spectroscopy (TOCSY) spectra were acquired using the DIPSY2 sequence, with a mixing time of 80 ms (Bruker pulse sequence – dipsi2esgpph), while Nuclear Overhauser Effect Spectroscopy (NOESY) spectra were collected with a mixing time of 200 ms (Bruker pulse sequence – noesyesgpph). Typical carrier positions used in all experiments were 117 ppm for 15N, 75 ppm for 13C and 4.7 ppm for 1H. Experiments were carried out at a range of temperatures as noted in the text. Titration experiments were carried out at 280 K and hydroxyl NMR investigation were performed at 258.5 K. Data were processed and analysed using Topspin 4.0.3 (Bruker, Karlsruhe, Germany) software.
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5

Intracellular NMR Monitoring of Prodrug

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K562 cells were maintained in IMDM media supplemented with 10% FBS. For NMR measurements cells were harvested by centrifugation, washed, and resuspended in Opti-MEM serum-free media to obtain a suspension with 65% v/v cell content. 10% D2O and 500 µM prodrug in DMSO-d6 were added (0.5% final DMSO concentration) and incubated on a spinning wheel for 5 min. A 200 µl suspension was transferred into a 3 mm Shigemi tube (without insert) matched to the magnetic susceptibility of water. 1D 19F spectra with inverse-gated decoupling of protons were collected at 37 °C with 2048 scans (experiment time 37 min) on a Bruker AVANCE III spectrometer with an 11.7 T magnet using a QCI-F cryoprobe at 470 MHz Lamour frequency. After 4 h the sample was lysed by freeze-thawing and a further spectrum of the lysate was collected. To confirm the identity of the observed species, the lysate was sequentially spiked with 500 µM MN551 and prodrug and measured again. For comparison, 1D 19F spectra of pure MN551 and prodrugs were collected in Opti-MEM media with 10% D2O and 0.5% DMSO-d6. All spectra were processed and analyzed using Topspin 4.1.1.
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6

TEM and NMR Analysis of PA-Losartan Complex

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Samples for transmission electron microscopy (TEM) were resuspended at a PA concentration of 10 mg/mL and then diluted 10-fold–1 mg/mL immediately before 10 µL of sample solution was transferred to plasma-cleaned 300-mesh copper grids with lacey carbon support (Electron Microscopy Science). Samples were stained with 2% uranyl acetate. Imaging was performed using a FEI Spirit G2 TEM working at 120 kV accelerating voltage.
Nuclear magnetic resonance (NMR) spectroscopy was performed on a Bruker Neo 600 MHz system with QCI-F cryoprobe at 298 K. The lyophilized powders from the sample preparation protocol above were resuspended in D2O at 10 mg/mL PA concentration and 5 mg/mL losartan concentration. This corresponds to 8.7 mM E-PA, 8.7 mM K-PA, and 10.8 mM losartan.
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7

NMR Spectroscopy for Metabolite Profiling

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Nuclear magnetic resonance (NMR) spectroscopy was used to analyse metabolite extracts. All experiments were carried out at 298 K on a Bruker Avance 3 600 MHz spectrometer, equipped with a QCI-F cryoprobe. Datasets were acquired with 64,000 points and a proton window size of 16 ppm. Spectra were referenced against an internal standard of DSS. The excitation sculpting method was used to suppress the water peak using pulsed field gradients.
Bruker TopSpin™ and AMIX data analysis software were used to analyse the NMR spectroscopy spectrum for each sample. The Madison Metabolomics Consortium Database was also used for the identification and quantification of metabolites using NMR spectroscopy (www.mmcd.nmrfam.wisc.edu/).
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8

NMR Experiments Using Bruker Avance III

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NMR experiments were performed on a Bruker 500 MHz Avance III spectrometer using a QCI-F cryoprobe with cooled 1H and 19F channels and sample temperature control unit. Spectra were initially processed and analysed using Topspin 4.1 and Dynamics Centre 2.7 (both Bruker), and plotted in GraphPad Prism 9.
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9

Quantifying BRD7087 Binding to SpCas9:gRNA

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All samples were prepared with 50 μM of BRD7087 in a 20 mM Tris buffer (pH 7.4) with varying concentrations of SpCas9:gRNA in a 3 mm NMR tube. Experiments were performed on a 600 MHz (19F: 564.71 MHz) Bruker AVANCE III NMR spectrometer equipped with a 5 mm QCI-F CryoProbe and a SampleJet for automated sample handling. To acquire the spectra, a standard one-pulse 19F experiment with WALTZ-16 for proton decoupling during acquisition, a 5 second recycle delay, and 256 scans were used. All spectra were recorded at 280 K. NMR data were apodized with a 1-Hz exponential function prior to Fourier transformation. All spectra were baseline corrected, and peak widths and intensities were extracted using the automated line-fitting feature provided with the MNova software package.
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10

STD NMR Screening of FcRn-Ligand Interactions

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STD NMR samples were prepared with a ligand to protein ratio of 50:1 (500 μM ligand, 10 μM FcRnECD) in 500 μL phosphate buffered saline, pH 7.4 (90% H2O, 10% D2O) with 5% d6-DMSO to help solubilize the ligand. STD NMR spectra were recorded using a Bruker Avance III HD 600 MHz spectrometer equipped with a 5 mm QCI-F Cryoprobe. Data were acquired and processed using the standard Bruker software and were collected at 298 K. The protein was saturated in the methyl region of the spectrum at 0 ppm, and off-resonance saturation was performed at 33 ppm. A series of 120 EBurp2 pulses (50 ms each) were applied with a 4-μs delay between each pulse, resulting in total saturation time of 6 s. Protein signals were removed by applying a spinlock of 100 ms. Interleaved on- and off-resonance data were recorded, processed separately, and then the difference spectra obtained by subtracting the on- from the off-resonance spectra. Data were zero filled once and an exponential multiplication window function applied (LB 2 Hz).
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