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Avance 800 mhz

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The Avance 800 MHz is a high-resolution nuclear magnetic resonance (NMR) spectrometer designed for advanced research applications. It provides a magnetic field strength of 800 MHz, enabling the acquisition of high-quality NMR data for the structural elucidation and characterization of complex molecules.

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Q tof mass spectrometer, by Thermo Fisher Scientific (2 mentions) Chirascan spectrometer, by Applied Photophysics (2 mentions) Evolution 300 uv visible spectrophotometer, by Bruker (2 mentions) Ltq fleet instrument spectrometer, by Thermo Fisher Scientific (2 mentions) Avance 3 500, by Bruker (2 mentions) Tensor 27 ftir spectrometer, by Bruker (2 mentions) Silica gel, by Qingdao Marine Chemical (2 mentions) Amicon ultra filter, by Merck Group (1 mentions) Sigmaplot 11, by Grafiti LLC (1 mentions) Topspin software, by Bruker (1 mentions) Topspin, by Bruker (1 mentions) Autopol 3 automatic polarimeter, by Rudolph Research Analytical (1 mentions) 6130 quadrupole mass spectrometer, by Agilent Technologies (1 mentions) 1200 series high performance liquid chromatography, by Agilent Technologies (1 mentions) Chirascan plus cd spectrometer, by Applied Photophysics (1 mentions) P 2000 polarimeter, by Jasco (1 mentions) Avance drx 500, by Bruker (1 mentions) Xwinnmr, by Bruker (1 mentions) Drx 500 mhz, by Bruker (1 mentions) Avance 600 mhz, by Bruker (1 mentions)

24 protocols using avance 800 mhz

1

NMR Analysis of Ca2+/CaM-IQ Complex

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Samples of Ca2+2/CaMEF12-IQ complex for NMR analysis were prepared by exchanging the protein complex into a buffer containing 20 mM Tris-d11 (pH 7.5) with 1 mM CaCl2, and 92% H2O/8% D2O. All NMR experiments were performed at 303K on a Bruker Avance 800 MHz spectrometer equipped with a four channel interface and triple resonance cryogenic (TCI) probe. The 15N-1H HSQC spectrum (Fig. 1) was recorded with 256 × 2048 complex points for 15N(F1) and 1H(F2), respectively. Assignment of backbone resonances was obtained by analyzing the following spectra: HNCA, HNCACB, CBCA(CO)NH, HNCO (Ikura et al, 1990 (link)). Side chain resonances were assigned by analyzing HCCH-TOCSY (Ikura et al, 1991 (link)). The NMR data were processed using NMRPipe (Delaglio et al, 1995 (link)) and analyzed using Sparky NMRFAM (Lee et al, 2015 (link)).
Salveson I., Anderson D.E., Hell J.W, & Ames J.B. (2019). Chemical Shift Assignments of a Calmodulin Intermediate with Two Ca2+ Bound in Complex with the IQ-motif of Voltage-gated Ca2+ Channels (CaV1.2). Biomolecular NMR assignments, 13(1), 233-237.
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2

NMR Spectroscopy of Spin-labeled Actin-Tβ4 Complex

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Spin-labeled actin samples were dialyzed against NMR buffer (5 mM Tris-HCl, pH 6.9, 0.1 mM CaCl2, 1 mM ATP) overnight and the15N labeled Tβ4 stock solutions were added to the actin solution, and then concentrated with an Amicon Ultra filter (Millipore). The final concentrations of Tβ4 and G-actin were 100 μM and 170 μM, respectively. D2O and NaN3 were added to the NMR sample (final concentrations, 10% and 0.01%, respectively) and 0.3 ml of the sample solution was transferred to a 5 mm Shigemi tube for NMR measurements.
The 1H-15N HSQC spectra were acquired at 25 °C with a Bruker Avance 800 MHz spectrometer equipped with a cryogenic probe. To collect the spectrum of the diamagnetic state, 2 mM of ascorbic acid was added to the sample and incubated for 0.5 hour at 4 °C before NMR measurements.
Huang S., Umemoto R., Tamura Y., Kofuku Y., Uyeda T.Q., Nishida N, & Shimada I. (2016). Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin. Scientific Reports, 6, 33690.
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3

Structural Analysis of MBD Mutant MeCP2

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Purified uniformly-13C/15N wild-type (KVS) and its double (TVN) and triple (TAN) mutants were prepared in a mixed solvent of 90% H2O and 10% 2H2O (50 mM sodium phosphate, 50 mM NaCl, pH 6). All NMR experiments were carried out with protein concentrations of ∼0.5 mM on a Bruker Avance 800 MHz NMR spectrometer using a triple-resonance cryo probe. The near-complete 1H, 13C and 15N resonance assignments of MBD mutant MeCP2 protein TAN and its complex with hmC/mC DNA were deposited to the BMRB under the accession numbers 51020 and 34745, respectively. The chemical-shift perturbations were measured as [(ΔH)2 + (ΔN/10)2]1/2, where ΔH and ΔN signify the changes in 1HN and 15N chemical shifts, respectively. A suite of 3D double- and triple-resonance NMR experiments were performed for sequence-specific 1H, 13C, and 15N backbone resonance assignments largely as discussed earlier (19 (link),20 ). In addition, we recorded 3D HCCH-TOCSY, [15N,1H]-NOESY-HSQC, as well as aliphatic and aromatic [13C,1H]-NOESY-HSQCs for almost complete assignment of 1H, 13C and 15N side-chain resonances, dihedral-angle restraints, and NOE-derived distance restrains for 3D structure calculation of the protein. NMR spectra were processed using TopSpin4.0.8 and analyzed using CARA (21 (link)) and CCPN (22 (link)).
Singh H., Das C.K., Buchmuller B.C., Schäfer L.V., Summerer D, & Linser R. (2023). Epigenetic CpG duplex marks probed by an evolved DNA reader via a well-tempered conformational plasticity. Nucleic Acids Research, 51(12), 6495-6506.
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4

NMR Spectroscopy of Niduclavin and Niduporthin

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All spectra were recorded on a Bruker Avance 800 MHz spectrometer located at the Danish Instrument Centre for NMR Spectroscopy of Biological Macromolecules at Carlsberg Laboratory. Spectra were acquired using standard pulse sequences. The deuterated solvent was DMSO-d6 and signals were referenced by solvent signals for DMSO-d6 at δH = 2.50 ppm and δC = 39.5 ppm. The NMR data was processed in MestReNova V.10.0.2–15465. Chemical shifts are reported in ppm (δ) and scalar couplings are reported in hertz (Hz). The sizes of the J coupling constants in the tables are the experimentally measured values from the 1D 1H and DQF-COSY spectra. There are minor variations in the measurements, which may be explained by the uncertainty of J and the spectral digital resolution. Descriptions of NMR structural elucidations of niduclavin and niduporthin are provided in S2 Text and NMR data are provided in S1 Dataset.
Nielsen M.L., Isbrandt T., Petersen L.M., Mortensen U.H., Andersen M.R., Hoof J.B, & Larsen T.O. (2016). Linker Flexibility Facilitates Module Exchange in Fungal Hybrid PKS-NRPS Engineering. PLoS ONE, 11(8), e0161199.
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5

Structural Insights into SpDcp2 Regulatory Domain

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The regulatory (1–94) and catalytic (95–243) domains of SpDcp2 were purified as described previously (Floor et al. 2010 (link)). NMR experiments were carried out in 150 mM NaCl, 2 mM MgCl2, 5 mM DTT, and 50 mM HEPES (pH 7.0) at 25°C. Titrations on the regulatory domain were performed at 250 μM protein in a volume of 500 μL by addition of increasing amounts of nucleotide analogs and the simultaneous addition of two equivalents of magnesium chloride. Titrations on the catalytic domain were identical except that 360 μM protein was used. All titration experiments were conducted on a Bruker Avance 800 MHz spectrometer outfitted with a cryogenic probe. The NMR data were processed using NMRPipe software package and visualized using Sparky (version 3.114). Composite chemical shift perturbations were calculated according to the equation:
δobs=(δHapo−δHbound)2+(δNapo−δNbound5)2.
Chemical shift perturbations were fit to a quadratic two-state binding model to extract Kdusing SigmaPlot 11.0 software (Systat Software Inc.):
δobs=δmax(KD+[L]0+[P]0)−(KD+[L]0+[P]0)2−(4[P]0[L]0)2[P]0
where [L]0 is a ligand concentration, [P]0 is a protein concentration, and δmax is the maximal perturbation of the chemical shift.
Ziemniak M., Mugridge J.S., Kowalska J., Rhoads R.E., Gross J.D, & Jemielity J. (2016). Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex. RNA, 22(4), 518-529.
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6

σ54 AID Structural Investigation

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Samples were prepared by mixing 15N-labeled, and later deuterated with 1H-13C labeled Leu δ and Val γ, σ54 AID constructs with either unlabeled or 2H NtrC1C and premixed ADP-BeF3−, ADP alone, or with the ATP-hydrolysis deficient mutant NtrC1C(E239A) and ATP. ADP-BeF3− was used over NtrC1C(E239A) and ATP for long NMR experiments to avoid spectral changes due to low background levels of ATP hydrolysis during the acquisition. NMR data were collected at 298 K on Bruker Avance 800 MHz or 600MHz spectrometers. Chemical shifts were referenced to that of water in order to properly align them across different experiments. Chemical shift changes of all σ54 AID amides were observed using 1H-15N HSQC experiments and chemical shift changes of Leu and Val side chains using 1H-13C methyl-TROSY experiments [43 (link)]. Amide assignments were carried out using 3D 15N-NOESY-HSQC experiments to both identify the amino acid type of amides by their side chain shifts and connect amides to their neighbor Hα resonances with the sequential assignment approach [56 ]. Data were processed with NMRPipe [59 (link)] and assignment analysis used the programs CARA [60 ] or MestReNova [61 ].
Siegel A.R, & Wemmer D.E. (2016). Role of the σ54 Activator Interacting Domain in Bacterial Transcription Initiation. Journal of molecular biology, 428(23), 4669-4685.
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7

Preparing Protein Samples for NMR Analysis

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Samples of D13DBD-DNA for NMR analysis were prepared as described above, and exchanged into a buffer containing 20 mM sodium phosphate (pH 7.0) and 95% H2O/5% D2O, and finally concentrated to 0.3 ml giving a final protein concentration of 0.5 mM. All NMR experiments were performed at 310K on a Bruker Avance 800 MHz spectrometer equipped with a four channel interface and triple resonance cryogenic (TCI) probe. The 15N-1H HSQC spectrum (Fig. 1) was recorded with 256 × 2048 complex points for 15N(F1) and 1H(F2). Assignment of backbone resonances was obtained by analyzing the following spectra: HNCA, HNCACB, CBCA(CO)NH, HNCO. Side-chain assignments were obtained by analyzing constant-time 13C-1H HSQC, 13C-edited NOESY-HSQC (mixing time of 120 ms) and HCCH-TOCSY experiments as described previously (Muhandiram et al., 1993 ). The NMR data were processed using NMRPipe and analyzed using Sparky.
Turner M., Zhang Y., Carlson H.L., Stadler H.S, & Ames J.B. (2014). Chemical Shift Assignments of Mouse HOXD13 DNA Binding Domain Bound to Duplex DNA. Biomolecular NMR assignments, 9(2), 267-270.
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8

NMR Characterization of HuR-RNA Interactions

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Proteins for NMR were dissolved in NMR buffer (100 mM NaCl, 10 mM NaPO4 pH 6.8, 10% D2O). 15N NMR data were acquired using Bruker Avance 800 MHz spectrometer with a TCI cryoprobe. ILV 13C NMR data were acquired using on a Bruker Avance III 600 MHz spectrometer. NMR data were acquired at 25°C, processed using NMRPipe [29 (link)] and analyzed using NMRView [30 (link)]. For 15N and ILV chemical shift mapping, 80 μM 15N/ILV-labeled HuR RRM1/2 was titrated with unlabeled AREc-fos RNA at increasing molar ratios of 1:0, 1:0.5, 1:1, and 1:1.7. AZA-9 was titrated at 1:1 and 1:2 molar ratios into 50 μM 15N/ ILV-labeled HuR RRM1/2 in NMR buffer with 10% d6-DMSO. Higher protein concentrations or higher molar ratios of AZA-9 resulted in sample precipitation. The 15N titrations were monitored by acquiring 2D 1H-15N TROSY spectra, and the ILV titrations were monitored by acquiring 2D 1H-13C HSQC spectra. The published backbone amide assignments of HuR RRM1/2 (BMRB entry 26628) [20 (link)] and the ILV assignments made herein were used in the NMR analysis.
Kaur K., Wu X., Fields J.K., Johnson D.K., Lan L., Pratt M., Somoza A.D., Wang C.C., Karanicolas J., Oakley B.R., Xu L, & De Guzman R.N. (2017). The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro. PLoS ONE, 12(4), e0175471.
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9

Structural Characterization of LcrG Protein

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NMR data were acquired at 25 °C using a Bruker Avance 800 MHz spectrometer equipped with a cryogenic triple resonance probe, processed with NMRPipe [48 (link)], and analyzed by NMRView [49 (link)]. Two-dimensional 1H-15N HSQC spectra [50 ] were acquired using 0.5–0.8 mM of protein samples. For backbone assignments of LcrG, 15N/13C LcrG* (0.9 mM) was used to acquire 2D 1H-15N HSQC, 3D HNCA, 3D HNCACB, and 3D CBCA(CO)NHA[50 –52 ] datasets. Secondary structures were identified from the Cα, and Cβ chemical shifts [28 (link)]. To assign the backbone resonances of LcrG in the complex, 15N/13C LcrG* (0.6 mM) was complexed with unlabeled LcrV at a molar ratio of 1:1.2 and 2D 1H-15N HSQC [50 ], 3D HNCA and 3D HNCACB [52 ] were acquired.
Chaudhury S., de Azevedo Souza C., Plano G.V, & De Guzman R.N. (2015). The LcrG tip chaperone protein of the Yersinia pestis type III secretion system is partially folded. Journal of molecular biology, 427(19), 3096-3109.
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10

NMR Characterization of 14-3-3ζ-Cby Interaction

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All NMR experiments were performed using 15N, 13C, 2H-labeled protein samples in 50 mM sodium phosphate, 100 mM NaCl at pH 6.8. Samples contained 10% D2O and 1 mM 2,2-dimethyl-2-sila-pentane-5-sulfonic acid (DSS) as 1H chemical shift reference. NMR experiments for the backbone resonance assignment of 14-3-3ζΔC12 were conducted at 25°C on a Bruker Avance 800 MHz (Singapore) spectrometer equipped with cryogenic probe. Sequential assignments were obtained from 1H-15N TROSY HSQC, HNCACB, HN(CO)CACB and 15N-NOESY-HSQC spectra. Data were processed using NMRPipe [53 (link)] and analyzed using CARA [54 ].
For the NMR titrations, either phosphorylated Cby 7-mer or 18-mer peptides were titrated into 600 μL of ~ 200 μM 15N, 13C, 2H labeled 14-3-3ζΔC12 until a 3:1 (peptide: 14-3-3ζΔC12) molar ratio was reached. A 1H-15N HSQC spectrum was collected for each titration point for a total of 12 points for the pCby WT 7-mer and 18-mer and 6 points for the pCby S22P 18-mer. All spectra were analyzed using NMRView [55 (link)].
Killoran R.C., Fan J., Yang D., Shilton B.H, & Choy W.Y. (2015). Structural Analysis of the 14-3-3ζ/Chibby Interaction Involved in Wnt/β-Catenin Signaling. PLoS ONE, 10(4), e0123934.
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