The largest database of trusted experimental protocols

Topspin version 4

Manufactured by Bruker
Sourced in Germany

TopSpin version 4.0.7 is a software package for the acquisition, processing, and analysis of nuclear magnetic resonance (NMR) data. It provides a comprehensive suite of tools for the management and interpretation of NMR experiments.

Automatically generated - may contain errors

6 protocols using topspin version 4

1

Protein BLAST and Sequence Alignment Workflow

Check if the same lab product or an alternative is used in the 5 most similar protocols
BLASTP (63 (link)) (protein-protein BLAST) searches were performed against the nonredundant protein sequence database. The sequence alignment was performed with Clustal Omega (64 (link)) using the UniProt website (http://www.uniprot.org/align/) (65 (link)) and annotated with Jalview (66 (link)). Bruker TopSpin version 4.0.7 was used to process NMR data. Sparky (T. D. Goddard and D. G. Kneller, SPARKY 3; University of California, San Francisco) was used to analyze and assign NMR data.
+ Open protocol
+ Expand
2

High-Resolution Solid-State 7Li NMR Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
7Li magic-angle spinning (MAS) NMR experiments were performed with a Bruker Avance 200 MHz (4.7 T) spectrometer operating at a 7Li Larmor frequency of 77.8 MHz at room temperature with a single channel 1.3 mm Bruker probe. Samples were packed into a 1.3 mm ZrO2 rotor inside the glove box and spun at speeds between 35–60 KHz. A rotor-synchronised Hahn echo sequence (90°-τ−180°-τ-acquisition) with a π/2 pulse length of 1.0 μs and recycle delay of 0.1 s was used. The spectra were referenced to a standard LiF at −1 ppm. Bruker Topspin (version 4.0.7) was used for raw data processing.
+ Open protocol
+ Expand
3

NMR Characterization of Yersiniabactin

Check if the same lab product or an alternative is used in the 5 most similar protocols
All NMR experiments were performed on a Varian 500 MHz spectrometer equipped with a 1H channel cold-probe. The yersiniabactin (Ybt, 0.25 mg) sample was dissolved in deuterated acetonitrile (CD3CN, 300 µl). The NMR spectra were acquired at 298 K in 3-mm NMR tubes and raw data were processed using Bruker Topspin version 4.0.7. The 1H peaks resonance assignments were made using a combination of 2D COSY (Supplementary Fig. 2b), 2D ROESY with a mixing time of 300 ms (Supplementary Fig. 2c). The assignments were made with the assistance of NMRFAM-SPARKY. The 1D experiments were acquired with a relaxation delay of 1 s, 90° 1H pulses of about 9.0 µs, and a spectral width of 8000 Hz. 2D ROESY spectra were acquired with a spinlock of 200–300 ms, using 128 transients per FID, and 128 points in the indirect dimension.
+ Open protocol
+ Expand
4

NMR Spectroscopic Analysis of Deuterated Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
1D and 2D NMR spectra were acquired in deuterated water (Deutero, Kastellaun, Germany) on a Bruker Avance Neo 500 spectrometer equipped with a 5 mm TXI prodigy cryoprobe (Bruker BioSpin GmbH, Rheinstetten, Germany) at 298 K. NMR chemical shifts were reported in parts per million (ppm) relative to the residual solvent signal D2O at δ 4.79. NMR data were analyzed using Topspin, version 4.06 (Bruker, Biospin GmbH, Rheinstetten, Germany) and ACD/Spectrus Processor 2020.2.1 (ACD/Labs, Toronto, Canada).
+ Open protocol
+ Expand
5

NMR Characterization of CYP121A1 Binding

Check if the same lab product or an alternative is used in the 5 most similar protocols
Spectra of CYP121A1 were acquired at 25 °C on an Agilent 400 MHz spectrometer with a 30° pulse angle, 1-s delay, and −84 ppm transmitter offset frequency for 10,000 scans per experiment. The temperature was increased in 5 °C increments for the temperature titration experiment, with 2500 scans collected for each sample. The data were processed and analyzed in Bruker, TopSpin, version 4.0.6, with 6-Hz line broadening applied. The binding constants were approximated from NMR titration data with cYY using an equation (Equation 1) adapted from the analysis of chemical-shift perturbations (39 (link)) to instead measure changes in peak intensity for an interaction occurring at a slow chemical exchange. Briefly, observed and maximum chemical-shift perturbations are substituted by observed (ΔIobs) and maximum (ΔImax) intensity measurements. Relative peak intensity data were quantified for each titration point at the saturated peak values of −84.22 ppm (dimer) and −85.97 ppm (monomer). The intensity data were plotted against cYY concentrations and the resulting plot fit to Equation 1 in Prism v7.05. ΔIobs= ΔImax{([P]t+[cYY]t+Kd)[([P]t+[cYY]t+Kd)2 4[P]t[cYY]t]1/2}/2[P]t
+ Open protocol
+ Expand
6

Fluorine NMR Characterization of CYP121A1

Check if the same lab product or an alternative is used in the 5 most similar protocols
CYP121A1 eluted from the Ni–NTA column was diluted to 2 µM in 50 mM TrisHCl, pH 7.4, 300 mM NaCl, and supplemented with 10 mM 3-bromo-1,1,1-trifluoroacetone (BTFA) and 5 mM dithiothreitol (DTT). Protein was incubated overnight at 4 °C without agitation, after which the unreacted BTFA and DTT were removed by gel filtration on a 120 ml bed volume column. 125 nmol of BTFA labeled protein was exchanged into NMR buffer (50 mM potassium phosphate, pH 7.4, 50 mM NaCl, and 10% D2O) using a 10-kDa molecular mass cut-off filter and adjusted to a final concentration of 250 µM. 19F-NMR spectra were acquired at 25 °C on an Agilent 400 MHz spectrometer using a 30° pulse angle, a 1 s delay, and − 84 ppm transmitter offset frequency for 10,000 scans. Raw data were processed and analyzed using Bruker, TopSpin version 4.0.6 (https://www.bruker.com/).
+ 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!