Nmrpipe

Manufactured by Bruker

Sourced in United States, Germany

NMRPipe is a software suite developed by Bruker for the processing and analysis of Nuclear Magnetic Resonance (NMR) spectroscopy data. It provides a comprehensive set of tools for handling, manipulating, and visualizing NMR data.

Automatically generated - may contain errors

Lab products found in correlation

Close spelling variants of this product

NMRPipe/NMRDraw (3 citations) NMRPipe software (2 citations)

39 protocols using nmrpipe

NMR Characterization of AtC53 IDR

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

All NMR spectroscopy measurements were performed using Bruker AVIII 600 MHz or Avance 800 MHz spectrometers at 25°C. The data were processed using TopSpin 3.2 (Bruker) and NMRPipe (Delaglio et al, 1995 (link)) and analyzed using CcpNmr Analysis (Skinner et al, 2016 (link)).
Sequence‐specific backbone assignments of AtC53 IDR were achieved using 2D ¹H‐¹⁵N HSQC, 3D HNCA, 3D CBCACONH, 3D HNCACB, 3D HNCO, and 3D HNCACO, including 70 residues of 75 nonproline residues (93%). NMR titrations were performed by adding unlabeled protein (75–300 μM) to 100 μM of ¹⁵N single‐labeled protein in 50 mM sodium phosphate (pH 7.0), 100 mM NaCl and 10% (v/v) D₂O and monitored by two‐dimensional ¹H‐¹⁵N HSQC.

Picchianti L., Sánchez de Medina Hernández V., Zhan N., Irwin N.A., Groh R., Stephani M., Hornegger H., Beveridge R., Sawa‐Makarska J., Lendl T., Grujic N., Naumann C., Martens S., Richards T.A., Clausen T., Ramundo S., Karagöz G.E, & Dagdas Y. (2023). Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and autophagy. The EMBO Journal, 42(10), e112053.

+ Open protocol

+ Expand

NMR Analysis of PEX5 Protein Fragments

Check if the same lab product or an alternative is used in the 5 most similar protocols

NMR experiments for PEX5 (1-113), PEX5 (110-230), PEX5 (228-315) protein fragments were described previously (Gaussmann et al. 2021) . NMR of PEX5 (281-639) was performed at 298 K on a Bruker Avance II 950 MHz spectrometer equipped with cryoprobe. Buffer was exchanged to 20 mM sodium phosphate pH 6.5, 50 mM sodium chloride and 10% D 2 O using size exclusion chromatography. The protein was measured at 750µM in a 5mm Shigemi tube. Sequential assignment of backbone resonances was done by using TROSY versions of standard triple resonance experiments (Sattler M et al. 1999; Weisemann et al. 1993) . NMR spectra were processed using Topspin (Bruker Biospin, Rheinstetten, Germany) or NMRPipe (Delaglio et al. 1995) and analyzed using CcpNMR Analysis 2.4.2 (Vranken et al. 2005) . Secondary chemical shifts, Δδ ( 13 Cα) -Δδ( 13 Cβ) were calculated by subtracting random coil chemical shifts from the observed 13 Cα, 13 Cβ chemical shifts (Kjaergaard and Poulsen 2011; Schwarzinger et al. 2001) .

Gopalswamy M., Zheng C., Gaussmann S., Kooshapur H., Hambruch E., Schliebs W., Erdmann R., Antes I, & Sattler M. (2023). Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14. Biological chemistry, 404(2-3).

+ Open protocol

+ Expand

NMR Characterization of Isotopically Labeled Proteins

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

All NMR experiments were carried out at 298 K on 14.1 T (600 MHz), 18.8 T (800 MHz), or 23.5 T (1000 MHz) Bruker spectrometers equipped with triple resonance single (z) or triple (x,y,z) gradient cryoprobes. The experiments were processed with Topspin 4.1 (Bruker) or NMRPipe^{83 (link)} and analyzed with NMRFAM-SPARKY⁸⁴ and CcpNmrAnalysis^{85 (link)}.
Isotopically labeled proteins for NMR were grown in M9 H₂O or D₂O media supplemented with ¹⁵NH₄Cl (and ¹³C-glucose) as the sole nitrogen (and carbon) source.
DNAJB6 with selective ¹³CH₃-ILVM methyl labeling was grown in M9 D₂O media supplemented with ¹⁵NH₄C and [²H,¹²C]-glucose as the sole carbon source. Then, 60 mg/L of 4-¹³C-α-keto-butyrate (Cambridge isotope laboratories—CDLM-7318), 80 mg/L of α-ketoisovaleric acid, sodium salt precursor (CDLM-7317-PK) and 100 mg/L of L-Methionine (CLM-206-PK) were added 1 h prior to protein induction to achieve selective ¹³CH₃-methyl labeling.

Abayev-Avraham M., Salzberg Y., Gliksberg D., Oren-Suissa M, & Rosenzweig R. (2023). DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones. Nature Communications, 14, 7066.

+ Open protocol

+ Expand

NMR Backbone Assignment of KNL1 and pKNL1

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The sequence-specific backbone assignment of KNL1_1–80, KNL1_23–80 and AURB phosphorylated pKNL1_1–80 was achieved by recording a 2D [¹H,¹⁵N] HSQC and 3D NMR spectra including HNCACB, CBCA(CO)NH, HNCA and HN(CO)CA. For KNL1_1–80 and pKNL1_1–80 the sequential assignments were verified using a (H)CC(CO)NH. All NMR data were collected on a Bruker Avance 500 MHz (¹H Larmor frequency) spectrometer equipped with TCI HCN z-gradient cryoprobe at 298 K (KNL1_23–80) or 283 K (KNL1_1–80 and pKNL1_1–80). All NMR data were processed using Topspin 3.2 (Bruker) or NMRPipe (Delaglio et al., 1995 (link)) and analyzed using CARA (http://www.cara.nmr.ch) or SPARKY (Goddard, T. D. and Kneller, D.G., 2004 ). Chemical shift referencing and secondary structure propensity calculations were performed as previously described (Kumar et al., 2016 (link)).

Bajaj R., Bollen M., Peti W, & Page R. (2018). KNL1 binding to PP1 and microtubules is mutually exclusive. Structure (London, England : 1993), 26(10), 1327-1336.e4.

+ Open protocol

+ Expand

NMR Characterization of Biomolecular Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols

All NMR spectra were recorded on Bruker Avance III 700 and 800 MHz spectrometers equipped with a triple-resonance CryoProbe at 25°C and 15°C. DNA samples (concentration, 0.3–1.0 mM) were dissolved in a buffer containing 10 mM potassium phosphate buffer (pH 6.5). The nuclear overhauser effect spectroscopy in D₂O and H₂O/D₂O (9.5:0.5) were acquired at mixing times of 50, 80, 250, 400 and 500 ms. Total correlation spectroscopy (TOCSY) spectra were recorded with the standard DIPSI-2 spin-lock sequence and a mixing time of 60 and 120 ms. In most of the experiments in H₂O, water suppression was achieved by including a WATERGATE module in the pulse sequence before the acquisition. Spectral assignments were completed by NOESY, TOCSY, double-quantum filtered correlation spectroscopy (DQF-COSY) and (¹³C–¹H)-HSQC using standard methods (40 ). Inter-proton distances were deduced from the NOESY experiments at various mixing times. All spectral analyses were performed using TopSpin (Bruker), NMRPipe (41 (link)) and SPARKY (42 ).

Tsukakoshi K., Yamagishi Y., Kanazashi M., Nakama K., Oshikawa D., Savory N., Matsugami A., Hayashi F., Lee J., Saito T., Sode K., Khunathai K., Kuno H, & Ikebukuro K. (2021). G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Research, 49(11), 6069-6081.

+ Open protocol

+ Expand

NMR Spectroscopy of Biomolecules

Check if the same lab product or an alternative is used in the 5 most similar protocols

Nuclear magnetic resonance acquisition was carried out at 25°C on either Bruker Avance III 600 MHz, Bruker Avance II+ 700 MHz or Bruker Avance III HD 800 MHz spectrometers equipped with a cryogenic triple‐resonance TCI probes unless otherwise stated. Topspin (Bruker) and NMRpipe (Delaglio et al, 1995) were used for data processing and Sparky (T. D. Goddard and D. G. Kneller, SPARKY 3, UCSF, https://www.cgl.ucsf.edu/home/sparky/) was used for data analysis. ¹H, ¹⁵N 2D BEST‐TROSY experiments (band‐selective excitation short transients–transverse relaxation‐optimised spectroscopy) were acquired with in‐house optimised Bruker pulse sequences incorporating a recycling delay of 400 ms and 1,024*64 complex points in the ¹H, ¹⁵N dimension, respectively. High‐quality data sets were collected in approximately 9 min.

Gladkova C., Schubert A.F., Wagstaff J.L., Pruneda J.N., Freund S.M, & Komander D. (2017). An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1. The EMBO Journal, 36(24), 3555-3572.

+ Open protocol

+ Expand

NMR Analysis of hHR23A(223–363) Protein

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

NMR data were collected on Bruker 600, 700, 800 and 900 MHz AVANCE spectrometers. All spectrometers were equipped with z-axis gradient, triple resonance cryoprobes. Experiments were performed at 291 K and 298 K. Total sequence-specific assignments were obtained from the following experiments (Bax and Grzesiek 1993 ; Sattler et al. 1995 (link); Clore and Gronenborn 1998 (link)): heteronuclear 2D ¹H-¹⁵N HSQC and ¹H-¹³C HSQC and 3D HNCACB, CBCA(CO)NH, HNCA, HN(CO)CA, HNCO, HN(CA)CO, CC(CO)NH, H(CCCO)NH, HBHA(CO)NH, HCCH-TOCSY (mixing time 10.9 ms) and simultaneously ¹³C/¹⁵N-edited NOESY (mixing time 100 ms) experiments. All data were processed with NMRPipe (Delaglio et al. 1995 (link)) and TopSpin 3.1 (Bruker), and analyzed with CCPN Version 2.3.1 (Vranken et al. 2005 (link)). Proton chemical shifts were referenced directly to internal 2,2-dimethyl-2-silapentane-5-sulfonic acid (DSS) and ¹³C and ¹⁵N chemical shifts were referenced indirectly to DSS using the ¹³C/¹H and ¹⁵N/¹H frequency ratios (0.251449530 and 0.101329118, respectively) at zero-point (Wishart et al. 1995 (link)). Secondary chemical shifts, ΔCα and ΔCβ (and ΔCα-ΔCβ) are calculated by subtracting random coil values (Wishart et al. 1995 (link)) from the Cα and Cβ shifts of each hHR23A(223–363) residue. The ϕ and ψ backbone torsion angles were obtained from TALOS+ Version 3.80F1 (Shen et al. 2009 (link)).

Byeon I.J., Jung J., Byeon C.H., DeLucia M., Ahn J, & Gronenborn A.M. (2019). Complete 1H, 13C, 15N resonance assignments and secondary structure of the Vpr binding region of hHR23A (residues 223-363). Biomolecular NMR assignments, 14(1), 13-17.

+ Open protocol

+ Expand

NMR Backbone Assignment of eIF4G1 Domains

Check if the same lab product or an alternative is used in the 5 most similar protocols

All samples were prepared in NMR buffer (25 mM potassium phosphate pH 6.5, 25 or 150 mM NaCl, 1 mM DTT, and 10% D₂O) and experimental data were acquired at 25°C on a cryoprobe-equipped Bruker AV800 MHz spectrometer. Assignment of the backbone ¹H, ¹⁵N and ¹³C atoms was achieved by following the standard methodology. The 3D HNCA, HNCO, HN(CO)CA, CBCA(CO)NH and CBCANH experiments were used for backbone assignment and 3D (H)CCH-TOCSY were recorded to assign side chain resonances [(Sattler et al., 1999 (link)) and the references therein]. Protein concentrations ranged between 100–200 μM. The chemical shifts were deposited in the Biomagnetic Resonance Database (BMRB) with codes 28,121 (eIF4G1_1-249) and 34,517 (eIF4G1_35-49-Pub1 RRM3). The ¹⁵N backbone amide relaxation T₁ and T₂ parameters were measured with series of ¹H-¹⁵N spectra of standard inversion-recovery and Carr-Purcell-Meiboom-Gill sequences (CPMG). NMR spectra were processed using TOPSPIN v4.1 (Bruker) and NMRPipe, and analyses were done with CcpNmr Analysis.

Chaves-Arquero B., Martínez-Lumbreras S., Sibille N., Camero S., Bernadó P., Jiménez M.Á., Zorrilla S, & Pérez-Cañadillas J.M. (2022). eIF4G1 N-terminal intrinsically disordered domain is a multi-docking station for RNA, Pab1, Pub1, and self-assembly. Frontiers in Molecular Biosciences, 9, 986121.

+ Open protocol

+ Expand

NMR Spectroscopy of Labeled PAC3 Homodimer

Check if the same lab product or an alternative is used in the 5 most similar protocols

¹³C- and ¹⁵N-labeled non-tagged PAC3 homodimer (0.3 mM) and ¹⁵N-labeled non-tagged PAC3 homodimer (0.1 mM), dissolved in PBS (pH 6.8) containing 10% D₂O (v/v), 1 mM EDTA, and 0.01% NaN₃, were used for spectral assignment and relaxation experiments. All NMR data were acquired at 303 K using DMX-500, AVANCE-500, and AVANCE-800 spectrometers equipped with a 5-mm triple-resonance cryogenic probe (Bruker, Billerica, MA, USA). The NMR data were processed using TOPSPIN (Bruker) and NMRPipe [32 (link)]. Conventional 3D NMR experiments [33 (link)] were carried out for chemical shift assignments of the heteronuclear single-quantum correlation (HSQC) peaks originating from the PAC3 homodimer. Spectral assignments were carried out using SPARKY [34 ] and CCPNMR [35 (link)] software. ¹⁵N relaxation parameters, T₁, T₂, and ¹⁵N-¹H heteronuclear nuclear Overhauser effect (NOE) were obtained at 303 K using an AVANCE-800 spectrometer and analyzed using the Protein Dynamics software in the Dynamics Center (Bruker).

Satoh T., Yagi-Utsumi M., Okamoto K., Kurimoto E., Tanaka K, & Kato K. (2019). Molecular and Structural Basis of the Proteasome α Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer. International Journal of Molecular Sciences, 20(9), 2231.

+ Open protocol

+ Expand

NMR Characterization of Shr-Heme Interactions

Check if the same lab product or an alternative is used in the 5 most similar protocols

Shr proteins were dialyzed against 50 mM NaH₂PO₄/Na₂HPO₄ pH 6.8, 100 mM NaCl. Buffer-matched Hb in the carbonmonoxy form was titrated into the samples to make Hb(heme basis):Shr^H2 at the following ratios: 0:1, 0.2:1, 0.4:1, 0.6:1, 1:1, and 2:1. For the apo-Hb:HID experiments, heme-free Hb (apo-Hb) was prepared as previously described and added to Shr^H1 or Shr^H2 at a 4:1 ratio (70 (link)–72 (link, no link found)). For the holo-Mb experiments with Shr^H1 and Shr^H2, the holo form of myoglobin (holo-Mb) was purchased from Sigma-Aldrich and further purified by gel-filtration chromatography with a Superdex S75 size-exclusion column prior to addition to Shr^H1 or Shr^H2. An ¹H-¹⁵N HSQC spectrum was recorded at each titration point. NMR experiments were performed at 298K on Bruker DRX 500 and 600 MHz spectrometers equipped with triple resonance cryogenic probes. NMR spectra were processed using NMRPipe and TopSpin 3.5 (Bruker BioSpin) and analyzed using NMRFAM-SPARKY (73 (link), 74 (link)). Resonances arising from disordered regions of the protein were excluded from quantification.

Macdonald R., Mahoney B.J., Soule J., Goring A.K., Ford J., Loo J.A., Cascio D, & Clubb R.T. (2023). The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme–iron from human hemoglobin. Proceedings of the National Academy of Sciences of the United States of America, 120(5), e2211939120.

+ 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?

Revolutionizing how scientists
search and build protocols!