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71 protocols using spectrometers

1

NMR Spectroscopy of Polyubiquitin Complexes

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Proteins used for NMR studies were buffer exchanged into 20 mM 4‐(2‐hydroxyethyl)‐1‐piperazineethanesulfonic acid (HEPES), 120 mM NaCl, 2 mM DTT, pH 7.4. For pUb titration, 100 μM unlabeled human R0RBR/pUb was added to 50 μM 15N‐labeled pUb. For pUbl titration, 120 μM unlabeled rat R0RBR/pUb was initially added to 60 μM 15N‐labeled pUbl. Then, 60 μM and 120 μM of pUb were added to the protein mixture. 1H‐15N heteronuclear single quantum coherence (HSQC) correlation spectra were acquired at field strengths of 600 MHz using Bruker spectrometers equipped with a triple‐resonance (1H, 13C, 15N) cryoprobe. Spectra were processed using NMRpipe and analyzed with SPARKY (Delaglio et al, 1995 (link); Lee et al, 2015 (link)).
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2

NMR Spectroscopy of Organic Compounds

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1H and 13C NMR
spectra were recorded on Bruker spectrometers operating at 400 and
500 MHz dissolving the compounds in the DMSO-d6 solvent. The chemical shift data are reported in units of
δ (ppm) relative to tetramethylsilane and referenced with residual
DMSO.
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3

NMR Spectroscopy Analysis of Organic Compounds

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NMR spectra were recorded at 300 or 500 MHz (1H) and 75 or 125 MHz (13C) using Bruker spectrometers. Chemical shifts are reported in parts per million (ppm, δ) relative to residual deuterated solvent peaks. The NMR spectra were assigned with the help of 2D NMR analyses (COSY, HSQC, and HMBC). The multiplicities reported are as follows: bs = broad singlet, m = multiplet, s = singlet, d = doublet, t = triplet, q = quadruplet, qt = quintuplet, or combinations thereof. For the peak assignments, the following abbreviations were used: Ar = aromatic, TIPS = triisopropylsilyl, CH=CH = aliphatic alkene, tBu = tert-butyl. Proton numbering was assigned according to IUPAC nomenclature.
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4

Solid-state NMR Characterization of M2 Protein

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Solid-state NMR spectra were measured on Bruker spectrometers at 1H Larmor frequencies of 400 MHz (9.4 Tesla), 600 MHz (14.1 Tesla), and 900 MHz (21.1 Tesla). 4 mm and 3.2 mm MAS probes were used. All 13C chemical shifts were referenced externally to the adamantane CH2 chemical shift at 38.48 ppm on the TMS scale 35 (link). 15N chemical shifts were referenced to the 15N peak of N-acetylvaline at 122.0 ppm on the liquid ammonia scale 36 . Sample temperatures are thermocouple-reported values.
1D 13C and 15N cross-polarization (CP) spectra were measured under 7–16 kHz MAS at 308 K and 243 K. The high-temperature spectra detect conformational dynamics and proton exchange dynamics, while the low-temperature spectra provide information on the rigid-limit tautomeric structure and protonation state of His37. 1D 13C double-quantum (DQ) filtered spectra were measured to suppress the natural-abundance lipid 13C signals and give protein-only 13C spectra. The SPC5 sequence was used for 13C-13C dipolar recoupling 37 . The measured dipolar recoupling efficiency was 10–20% at the MAS frequency of 7 kHz. 2D 13C-13C DARR correlation spectra 38 of VM+ bound M2(21-97) were measured at 600 MHz using mixing times of 30 – 40 ms between 243 K and 249 K. 2D 13C-13C PDSD spectra of DMPC-bound M2(21–97) were measured at 253 K using a 100 ms mixing time on the 900 MHz spectrometer.
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5

NMR Spectroscopy in Aqueous Buffer

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All NMR samples were prepared in aqueous
buffer containing 25 mM phosphate, pH 6.7, and 150 mM NaCl. Spectra
were recorded on one of several Bruker spectrometers operating at
500–800 MHz 1H frequency and equipped with cryogenic
inverse probes. Spectra were processed with TopSpin (Bruker) and analyzed
using Sparky version 3.110 (Goddard and Kneller, UCSF).
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6

NMR Experiments of Biomolecules in D2O and H2O

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Samples for NMR experiments were dissolved (in Na+ form) in either D2O or 9:1 H2O/D2O (25 mM sodium phosphate buffer) in presence of 100 mM NaCl. Experiments were carried out at different pH values, ranging from 3.5 to 7. The pH was adjusted by adding aliquots of concentrated solution of either DCl or NaOD. All NMR spectra were acquired in Bruker spectrometers operating at 600 and 800 MHz, equipped with cryoprobes and processed with the TOPSPIN software. In the experiments in D2O, presaturation was used to suppress the residual H2O signal. A jump-and-return pulse sequence35 (link) was employed to observe the rapidly exchanging protons in 1D H2O experiments. NOESY36 (link) spectra in D2O and 9:1 H2O/D2O were acquired with mixing times of 150, 250 and 300 ms. TOCSY37 spectra were recorded with the standard MLEV-17 spin-lock sequence and a mixing time of 80 ms. In most of the experiments in H2O, water suppression was achieved by including a WATERGATE38 (link) module in the pulse sequence prior to acquisition. The spectral analysis program SPARKY was used for semiautomatic assignment of the NOESY cross-peaks and quantitative evaluation of the NOE intensities.
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7

Comprehensive Analytical Methods for Biomolecular Characterization

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Absorbance data were acquired with an Agilent Cary 60 UV-vis spectrometer. Hydrolysis kinetics were measured with a Tecan Infinite M1000 plate reader. All other fluorescence data were acquired with a PTI QuantaMaster spectrofluorometer. 1H and 13C NMR spectra were acquired on Bruker Spectrometers at the National Magnetic Resonance Facility at Madison (NMRFAM) operating at 500 MHz for 1H and 125 MHz for 13C. Mass spectrometry was performed with a Q Exactive Plus electrospray ionization quadrupole-ion trap (ESI–QIT-MS) mass spectrometer at the Mass Spectrometry Facility in the Department of Chemistry at the University of Wisconsin–Madison. IR spectra were acquired with a Micro FT-IR spectrometer at the Materials Science Center of the University of Wisconsin–Madison. Microscopy images were acquired with a Nikon Eclipse Ti inverted confocal microscope at the Biochemistry Optical Core of the University of Wisconsin–Madison.
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8

NMR Spectroscopy Protocol with Bruker Spectrometers

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The NMR measurements were performed either at 25 or 37 °C, on Bruker spectrometers operating at 400 MHz, 600 MHz, 700 MHz, 800 MHz and 950 MHz and equipped with 5 mm TCI cryoprobes or with a broadband SmartProbe (400 MHz) as detailed in figure captions of each spectrum. 1H-NMR spectra were recorded using either a 1D NOESY sequence or a 1D sequence with presaturation. Spectra were processed and analysed using Bruker TopSpin3.6 or MestReNova 12.
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9

Proton NMR Spectroscopy in CDCl3

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1H (400 and 500 MHz) NMR spectra were recorded using Bruker spectrometers in CDCl3 and calibrated to the solvent peak of δ 7.26 ppm.
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10

NMR Characterization of N-SH2 Binding

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Standard triple resonance experiments [CBCA(CO)NH, HNCACB, HNCO, HN(CA)CO spectra] and HSQC were recorded at 10°C on Bruker spectrometers operating at 1H frequencies of 600 MHz. Solution NMR experiments were carried out in buffer 50 mM Hepes pH 7.4 300 mM NaCl using a 100 μM sample of labeled N-SH2. For the full assignment of the bound N-SH2 we performed titrations of 1H-15N HSQC spectra of a 100 μM sample of N-SH2 with both Gab2448460 and Gab2448460 M457A, which were recorded using progressive concentration of the ligand until 1:1 molar ratio.
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