Topspin software package

Manufactured by Bruker

Sourced in Germany

TOPSPIN is a software package developed by Bruker for the acquisition, processing, and analysis of NMR spectroscopy data. It provides a comprehensive set of tools for handling NMR experiments and data management.

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15 protocols using topspin software package

NMR Spectral Preprocessing and Analysis

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The NMR spectra were preprocessed using the TOPSPIN software package (Version 3.5, Bruker Biospin, Rheinstetten, Germany). The ¹H CPMG HR-MAS NMR spectra obtained for each tissue sample were subjected to 0.5 Hz exponential line broadening and zero-filled to 64 k points prior to Fourier transformation and then phased and baseline corrected manually.
After this preliminary processing, the spectra were prepared for chemometric analysis using the MNova software package (MestReNova, ver. 11. 0, 4-18998, 2017 Mestrelab Research S. L., Santiago de Compostela, Spain).
The spectral regions δ 4.8–0.5 ppm were normalized with respect to sample weight, then aligned and binned (δ 0.01 ppm). Deconvoluted areas of selected peaks from ¹H CPMG HR-MAS spectra were obtained with an automated/controlled fitting routine based on the Levenberg–Marquardt algorithm applied after manual peak selection, adjusting peak positions, intensities, line widths and Lorentzian/Gaussian ratios, until the residual spectrum was minimized [43 (link)].

Righi V., Reggiani C., Tarentini E., Mucci A., Paganelli A., Cesinaro A.M., Mataca E., Kaleci S., Ferrari B., Meleti M, & Magnoni C. (2021). Metabolomic Analysis of Actinic Keratosis and SCC Suggests a Grade-Independent Model of Squamous Cancerization. Cancers, 13(21), 5560.

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NMR Spectroscopy of Halogenated Benzyl Coenzyme A

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Reaction products of 2- and 3-F-BzCoA with BCR were prepared for NMR spectroscopy as described above. The compounds were dissolved in 0.5 mL deuterated water. ¹H NMR and ¹³C NMR spectra were recorded at 500 and 126 MHz, respectively, with Avance-HD 500 spectrometers operating at 27°C. ¹H-Detected experiments including two-dimensional COSY, NOESY, HSQC, and HMBC were measured with an inverse ¹H/¹³C probe head; direct ¹³C measurements were performed with a QNP ¹³C/³¹P/²⁹Si/¹⁹F/¹H cryoprobe. All experiments were done in full automation using standard parameter sets of the TOPSPIN software package (Bruker). ¹³C NMR spectra were recorded in proton-decoupled mode. Data processing was typically done with the MestreNova software.

Tiedt O., Mergelsberg M., Eisenreich W, & Boll M. (2017). Promiscuous Defluorinating Enoyl-CoA Hydratases/Hydrolases Allow for Complete Anaerobic Degradation of 2-Fluorobenzoate. Frontiers in Microbiology, 8, 2579.

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Kinetic Study of Flufenamic Acid-Cysteine Interaction

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Flufenamic acid or MNS (0.05 mmol) was dissolved in DMSO-d₆ (400 μl) in an NMR tube. N-Acetyl-L-cysteine methyl ester (17.7 mg, 0.10 mmol) solubilized in DMSO-d₆ (100 μl) was added and an NMR spectrum was recorded every 10 min after the addition for 2 h and then every 1 h until 24 h. A Bruker Avance 400 spectrometer was used to record ¹H spectra at 300.1 MHz. Chemical shifts are defined in parts per million and referenced against tetramethylsilane (δ=0). NMR analysis was conducted using Bruker's TopSpin software package.

Daniels M.J., Rivers-Auty J., Schilling T., Spencer N.G., Watremez W., Fasolino V., Booth S.J., White C.S., Baldwin A.G., Freeman S., Wong R., Latta C., Yu S., Jackson J., Fischer N., Koziel V., Pillot T., Bagnall J., Allan S.M., Paszek P., Galea J., Harte M.K., Eder C., Lawrence C.B, & Brough D. (2016). Fenamate NSAIDs inhibit the NLRP3 inflammasome and protect against Alzheimer's disease in rodent models. Nature Communications, 7, 12504.

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NMR Data Processing and Annotation

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NMR spectra were processed using TOPSPIN software package (version 3.2, Bruker Biospin, Germany). For ¹H NMR spectra, an exponential window function was employed with a line broadening factor of 0.3 Hz and zero-filled to 128 k prior to Fourier transformation. Each spectrum was then manually phase-corrected and baseline-corrected and calibrated with the anomeric proton signal of α-glucose (δ 5.23 ppm). The spectra were segmented into regions with a width of 0.01 ppm (δ 0.5–9.0 ppm) using AMIX software package (V3.9.14, Bruker Biospin). The regions of imperfect water saturation signals (δ 4.50–5.15 ppm) and urea signals (δ 5.50–6.50 ppm) were discarded. The NMR resonances were assigned according to an electronic database (HMDB, http://www.hmdb.ca/) and data from the literature [27 (link), 28 (link)], and were confirmed with 2D NMR results.

Zhang Y., Zhang H., Chang D., Guo F., Pan H, & Yang Y. (2018). Metabolomics approach by 1H NMR spectroscopy of serum reveals progression axes for asymptomatic hyperuricemia and gout. Arthritis Research & Therapy, 20, 111.

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NMR Structural Characterization of St14f-StFDL1 Complex

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The ¹H-¹⁵N-HSQC spectrum of the St14f free (red) and StFDL1 peptide complex (blue) at 298 K using a Bruker AVANCE III 950 MHz spectrometer equipped with a ¹H/¹³C/¹⁵N TCI CryoProbe (Bruker BioSpin).
¹⁵N Lys-labeled St14f was prepared at 250 µM in a buffer containing 10 mM Tris, pH 7.5, 1 mM DTT, and 10% D₂O. The complex sample was prepared with a final concentration of 1 mM StFDL1 peptide and 250 µM ¹⁵N Lys-labeled St14f. The spectrum was processed using the TopSpin software package (Bruker BioSpin). Assignments were carried out using single point mutations of St14f (Fig. S2).

Harada K.I., Furuita K., Yamashita E., Taoka K.I., Tsuji H., Fujiwara T., Nakagawa A, & Kojima C. (2022). Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition. Scientific Reports, 12, 11596.

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NMR Characterization of CO-Bound Proteins

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Prior to NMR experiments, samples were exchanged into 50mM KP_i pH 7.4, 100mM KCl, 1mM camphor, 90% H₂O/10% D₂O. The protein was transferred to a septum-sealed reaction vial and flushed with carbon monoxide. Approximately 4μL of freshly prepared 250mM Na₂S₂O₄ in 1M KP_i pH 8 was added in 1μL aliquots to reduce the protein in a sealed vial purged with carbon monoxide. Reduction was monitored by eye, with the fully reduced protein a bright cherry red. The reduced and CO-bound protein was transferred anaerobically to a susceptibility-matched NMR tube (Shigemi). NMR data were acquired on a Bruker Avance NEO spectrometer operating at 800.13 MHz (¹H) and 81.08 MHz (¹⁵N) at 25°C. Data acquisition, processing and analysis were performed using the Topspin software package (Bruker Biospin, Inc.). ¹H, ¹⁵N TROSY-HSQC spectra were acquired as 2048 (¹H) x 128 (¹⁵N) complex points datasets with 16 scans.

Alvarez G., Le T., Wong N., Echave J., Pochapsky T.C, & Asciutto E.K. (2022). Hydroxylation regiochemistry is robust to active site mutations in cytochrome P450cam (CYP101A1). Biochemistry, 61(17), 1790-1800.

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Solid-State NMR Spectroscopy Protocol

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¹⁹F, ³¹P and ³⁵Cl MAS-NMR spectra were collected using a 600 MHz, 14.1 T, Avance NEO spectrometer (Bruker, Germany) using the parameters listed in Table 1. The ³⁵Cl MAS-NMR spectra were referenced to 0 ppm of the signal in solid NaCl purchased commercially (29 (link), 30 (link)). The spectra were processed and analyzed using the TopSpin software package (Bruker, version 4.0.8).

Kaur M., Shahid S., Karpukhina N., Anderson P, & Wong F.S. (2024). Characterization of chemical reactions of silver diammine fluoride and hydroxyapatite under remineralization conditions. Frontiers in Oral Health, 5, 1332298.

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NMR Sample Preparation and Analysis

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The duplexes were prepared in 10 mM NaH₂PO₄, 100 mM NaCl, and 50 μM Na₂EDTA (pH 7), in volumes of 180 μL or 500 μL, utilized in either 3 mm or 5 mm NMR tubes, respectively. For experiments to examine non-labile protons samples were prepared in 99.996% D₂O. Examination of labile protons was performed in 9:1 H₂O:D₂O. Water suppression was accomplished using the Watergate pulse program.^{47 (link)} All spectra were processed using the TOPSPIN software package (Bruker Biospin Inc., Billerica, MA) and further analyzed using TOPSPIN and SPARKY⁴⁸ software. Spectra were referenced to the chemical shift of the water resonance at the corresponding temperature, with respect to trimethylsilyl propanoic acid (TSP).

Politica D.A., Malik C.K., Basu A.K, & Stone M.P. (2015). Base-Displaced Intercalated Structure of the N-(2′-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct. Chemical research in toxicology, 28(12), 2253-2266.

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NMR Characterization of Glycolipid Interactions

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Two sets of experiments were performed using DMSO-d₆ or D₂O/deuterated SDS micelles as solvent. NMR experiments were recorded at 298 K on a Bruker AV500 spectrometer (Bruker, Billerica, MA, USA). Spectra were obtained with standard sequences from the TOPSPIN software package (Bruker). For the DMSO experiments, a ∼ 2 mM concentration for the βGlcN(1↔1)αGlcN-LAMs was employed. For experiments in the presence of deuterated SDS micelles, 23.80 μl of a stock solution of DA257 (4.2 mM in DMSO-d₆) was mixed with 45.5 μl of SDS and further diluted with D₂O to give a final concentration of 0.5 ml of the ligand in the presence of SDS (20 mM). The components were mixed up by vortexing. The Bruker pulse sequence noesygpph19 was used for the NOESY experiments. Mixing times of 250 and 350 ms were used. The two-dimensional spectra were acquired with 1 K–2 K data points in the F2 dimension and 256 data points in the F1 dimension. The residual water signal was suppressed by presaturation. Prior to Fourier transformation, all spectra were multiplied with a sine-squared function.

Garate J.A., Stöckl J., del Carmen Fernández-Alonso M., Artner D., Haegman M., Oostenbrink C., Jiménez-Barbero J., Beyaert R., Heine H., Kosma P, & Zamyatina A. (2015). Anti-endotoxic activity and structural basis for human MD-2·TLR4 antagonism of tetraacylated lipid A mimetics based on βGlcN(1↔1)αGlcN scaffold. Innate Immunity, 21(5), 490-503.

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NMR Characterization of Polysaccharide Solutions

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The NMR spectra were obtained with a Bruker 600 MHz Avance III spectrometer, using a 5-mm QCI ¹H/¹³C/¹⁵N/³¹P probe equipped with a z-gradient (Bruker). The NMR spectra were obtained for each ²H₂O PS solution at 25°C, using acetone (δ_H 2.225, δ_C 31.05 ppm) as an internal reference. The PS (10 mg) was repeatedly exchanged with ²H₂O (99.9%) via intermediate lyophilization. The data were acquired and processed using the Topspin software package (version 3.1; Bruker) and the SPARKY program (Goddard and Kneller 2001 ). The signals were assigned using 1D and 2D experiments, COSY, TOCSY, NOESY, HSQC with and without carbon decoupling, and HMBC. The TOCSY experiments were carried out with mixing times of 30, 60 and 100 ms, while NOESY was performed with mixing times of 100 and 300 ms. The ¹H,¹³C HMBC spectrum was recorded with a 60-ms delay for the evolution of long-range spin couplings.

Górska S., Hermanova P., Ciekot J., Schwarzer M., Srutkova D., Brzozowska E., Kozakova H, & Gamian A. (2016). Chemical characterization and immunomodulatory properties of polysaccharides isolated from probiotic Lactobacillus casei LOCK 0919. Glycobiology, 26(9), 1014-1024.

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