The largest database of trusted experimental protocols

11 protocols using nmrfam sparky

1

Histone peptide binding assay for PfBDP1-BRD

Check if the same lab product or an alternative is used in the 5 most similar protocols
Chemical shift perturbation experiments were performed using 0.3–0.5 mM of uniformly 15N-labeled PfBDP1-BRD (303–488) in NMR buffer containing 20 mM Tris-HCl pH 6.8, 150 mM NaCl, 10 mM DTT and 10% D2O. Titration mixtures of the PfBDP1-BRD (303–488) and each of the modified histone peptides (res 1–24) unmodified H3, H3K9ac, H3K14ac, H3K9acK14ac, unmodified H4, H4K5ac, H4K12ac, H4K5acK8acK12acK16ac, unmodified H2A.Z, H2A.ZK11ac, unmodified H2B.Z, H2B.ZK3acK8acK13acK14acK18ac were prepared at molar ratios of 1:0, 1:0.5, 1:1, 1:2.5, and 1:5 M, in a total volume of 80 μL, The sample mixtures were then transferred into 1.7 mm NMR tubes (Bruker). Two-dimensional 15N−1H HSQC (heteronuclear single quantum coherence) experiments for all samples were acquired on Bruker Avance III spectrometer equipped with a cryogenic 1.7 mm probe. The temperature of the samples was regulated at 25°C throughout data collection. All spectra were processed using TopSpin (Bruker) as described previously [43 (link)] and analyzed using NMRFAM-SPARKY [48 (link)].
+ Open protocol
+ Expand
2

NMR Spectroscopy of GPCR C-Termini

Check if the same lab product or an alternative is used in the 5 most similar protocols
All NMR experiments were performed on a Bruker Bruker Avance III 700 MHz spectrometer, except for the 3D assignment of β2AR-Cter performed on a 800 MHz, and for the 3JHNHA of GHSR-Cter performed on a 500 MHz. The 700 MHz and 800 MHz spectrometers are equipped with a cryogenic triple-resonance (1H, 15N, 13C) probe and shielded z-gradients. All NMR experiments were recorded at 20 °C in a buffer (named NMR buffer) composed of 50 mM Bis-Tris pH 6.7, 150 mM NaCl, 1 mM EDTA, 0.5 mM TCEP, 5% D2O (Eurisotop), and 5 mM DSS-d6 (2,2-dimethyl-2-silapentane-5-sulfonate, Sigma) as internal reference [42 ]. All experiments used the pulse sequences provided by Bruker TOPSPIN 3.2. Squared cosine apodization was used in indirect dimensions, prior to zero-filling and Fourier transformation using TOPSPIN (version 4.0.6, Bruker) and data processing was performed using NMRFAM-SPARKY (version 1.414, [43 (link)]). For each NMR experiments, concentrations of GPCR-Cters were indicated in Table S1. For all NMR experiments, data were measured for all residues of C-terminus regions excepted proline residues, the residue A339 of β2AR-Cter, and the first N-terminal residue.
+ Open protocol
+ Expand
3

NMR Analysis of 15N-labeled α-Synuclein

Check if the same lab product or an alternative is used in the 5 most similar protocols
1H-15N heterogenous single-quantum coherence (HSQC) NMR measurements were performed using 100 µM 15N-labeled ɑSyn dissolved in fibrillation buffer prepared in H2O/D2O (9:1, v/v). The 15N-labeled ɑSyn was expressed in M9 minimal medium containing 15NH4Cl and purified as described for the unlabeled protein. NMR spectra were acquired at 37 °C on a Bruker AVANCE III HD 600 MHz NMR spectrometer equipped with a 5 mm quadruple resonance cryogenic probe (Bruker Biospin). The data size and spectral width were 256 (t1) × 2048 (t2) and 1338 Hz (ω1, 15N) × 9,615 Hz (ω2, 1H), respectively. The carrier frequencies of 1H and 15N were 4.7 and 118 ppm, respectively. The number of scans/FID was 32. The repetition time was 1 s. The peak assignment at pH 7.4 was achieved employing the assignment data reported by El Turk et al. [61 (link)]. The chemical shift perturbation (CSP) is calculated as follows: Δδ=ΔδH2+18ΔδN2, where ΔδH and ΔδN are the chemical shift changes (in ppm) with respect to the H and N axes, respectively. All NMR spectra were processed with Topspin (Bruker Biospin), NMRPipe [15 (link)] and NMRFAM-sparky [30 (link)].
+ Open protocol
+ Expand
4

Isotopic Labeling and NMR Analysis of TDP-43 RRM1

Check if the same lab product or an alternative is used in the 5 most similar protocols
The E. coli cells harboring the TDP‐43 expression vector were grown in M9 minimal medium supplemented with 15N‐NH4Cl (1 g/L). The 15N‐labeled proteins were purified in the same way as the un‐labeled proteins. The protein samples were prepared in a buffer containing 25 mM HEPES pH 7.0, 125 mM NaCl, and 1 mM DTT. The proteins at a concentration of 0.7 mM in 10% D2O were centrifuged at 20,000 g for 30 min to remove any insolubilities and potential aggregates. The 2D 15N/1H HSQC data were collected using a 600‐MHz Bruker Avance spectrometer equipped with a 5‐mm TCI CryoProbe at 298 K. The spectra were processed using Topspin 2 (Bruker) and analyzed in NMRFAM Sparky. Backbone assignment for wild‐type RRM1 was reported previously (BMRB accession number 18765). The following formula was used to calculate the CSP shown in Figure 7e: CSP=δH2+0.14×δN22 where δH and δN are the chemical shift changes (in ppm) of 1H and 15N shifts, respectively.
+ Open protocol
+ Expand
5

Structural Characterization of SRC1-Nurr1 Complex

Check if the same lab product or an alternative is used in the 5 most similar protocols
2D 1H-15N heteronuclear single-quantum coherence (HSQC) NMR spectra were acquired on a Bruker Neo 600 MHz spectrometer equipped with a QCI-F cryoprobe at 25 °C sample temperature for SRC1 PAS-B and 30 °C for the SRC1 PAS-B-Nurr1 AF128−51 fusion. NMR spectra were processed using Bruker TopSpin or NMRpipe [16 (link)] and analyzed using NMRFAM-Sparky [17 (link)]. All small-molecule compounds used for the titrations were purchased from vendors in highly pure form and used without further purification. Prostaglandins (PGs) were purchased from Cayman Chemical while all the others were purchased from Sigma. The compounds were dissolved in DMSO or NMR buffer at high concentrations (≥25 mM). Background chemical shift perturbations (CSPs) caused by DMSO were subtracted prior to quantitation of ligand-induced shifts. CSPs were calculated as (0.5[ΔδH2+(0.04(ΔδN2))])1/2 , where δH and δN are the amide proton and nitrogen chemical shifts, respectively.
+ Open protocol
+ Expand
6

NMR Backbone Resonance Assignment Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
NMR spectra were recorded at 298K on 800 MHz Bruker Avance III HD spectrometer with a cryo-probehead, processed with NMRpipe (50 (link)), and analyzed in NMRFAM-SPARKY (51 (link)). Standard triple resonance CBCA(CO)NH, HNCACB, HNCO, and HN(CA)CO experiments were used for backbone assignments. All NMR data for resonance assignment were processed using NMRPipe and analyzed using Sparky software (52 ). Following peak picking of the backbone experimental data in Sparky, the data were assigned by the PINE NMR-server (53 ) and then verified, corrected, and completed manually. All NMR titrations were carried out at 298K in PBS buffer, pH 7.4. NMRFAM-SPARKY was used to calculate the peak intensities. The graphs were plotted using the Origin software package.
+ Open protocol
+ Expand
7

Histone peptide binding assay for PfBDP1-BRD

Check if the same lab product or an alternative is used in the 5 most similar protocols
Chemical shift perturbation experiments were performed using 0.3–0.5 mM of uniformly 15N-labeled PfBDP1-BRD (303–488) in NMR buffer containing 20 mM Tris-HCl pH 6.8, 150 mM NaCl, 10 mM DTT and 10% D2O. Titration mixtures of the PfBDP1-BRD (303–488) and each of the modified histone peptides (res 1–24) unmodified H3, H3K9ac, H3K14ac, H3K9acK14ac, unmodified H4, H4K5ac, H4K12ac, H4K5acK8acK12acK16ac, unmodified H2A.Z, H2A.ZK11ac, unmodified H2B.Z, H2B.ZK3acK8acK13acK14acK18ac were prepared at molar ratios of 1:0, 1:0.5, 1:1, 1:2.5, and 1:5 M, in a total volume of 80 μL, The sample mixtures were then transferred into 1.7 mm NMR tubes (Bruker). Two-dimensional 15N−1H HSQC (heteronuclear single quantum coherence) experiments for all samples were acquired on Bruker Avance III spectrometer equipped with a cryogenic 1.7 mm probe. The temperature of the samples was regulated at 25°C throughout data collection. All spectra were processed using TopSpin (Bruker) as described previously [43 (link)] and analyzed using NMRFAM-SPARKY [48 (link)].
+ Open protocol
+ Expand
8

NMR Spectroscopy Analysis of Histone Tails

Check if the same lab product or an alternative is used in the 5 most similar protocols
All NMR data were processed in Bruker Topspin and analyzed in NMRFAM-Sparky (Lee et al., 2015). Assignments of the histone H2A and H3 tail resonances were taken from
Xiang et al. (2018). Chemical shift perturbations (CSPs) were calculated as the 2D peak displacement in ppm using a weighting factor of
the 15 N chemical shift differences (in ppm) of 0.154 (Williamson,
2013). For the calculation of peak intensity ratios, peak intensities in
individual spectra were scaled by the number of scans, receiver gain
setting, Bruker nc_proc parameter and, for solution NMR experiments, dilution factor. Errors in peak intensities were based on
the spectral noise level.
+ Open protocol
+ Expand
9

NMR Backbone Assignment of CEACAM1-LF

Check if the same lab product or an alternative is used in the 5 most similar protocols
All experiments were carried out at 25 °C on a 700 MHz Bruker Ascend with a TXI-triple resonance cryoprobe. For the backbone assignment of CEACAM1-LF cytoplasmic domain peptide, 2D 1H-15N-HSQC, 1H-13C-HSQC, 3D 15N-TOCSY-HSQC, 3D 15N-NOESY-HSQC, HCC(CO)NH, (H)CC(CO)NH, HNCO, HNCACO, HNCACB, HNCOCACB data were acquired. The sample concentration used for backbone assignment experiment is 0.4 mM for 15N, 13C-CEACAM1-LF, and 0.9 mM for 15N-CEACAM1-LF. The data were processed and analyzed using NMRPipe (56 (link)), NMRView (57 (link)), NMRFAM-SPARKY (58 (link)), and Bruker Topspin. The CEACAM1-LF amide assignment at pH 6.6 was obtained from that at pH 5.5 through monitoring 1H-15N-HSQC spectra at different pH titrated from pH 5.5 to pH 6.6. The longitudinal 1H-15N spectra was acquired using sofast HMQC (59 (link)) to monitor the enzyme kinetics.
+ Open protocol
+ Expand
10

NMR Data Processing and Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
All NMR data were processed in Bruker Topspin and analyzed in NMRFAM-Sparky (Lee et al., 2015 (link)). Assignments of the histone H2A and H3 tail resonances were taken from Xiang et al. (2018) (link). Chemical shift perturbations (CSPs) were calculated as the 2D peak displacement in ppm using a weighting factor of the 15N chemical shift differences (in ppm) of 0.154 (Williamson, 2013 (link)). For the calculation of peak intensity ratios, peak intensities in individual spectra were scaled by the number of scans, receiver gain setting, Bruker nc_proc parameter and, for solution NMR experiments, dilution factor. Errors in peak intensities were based on the spectral noise level.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!