NMR data were collected at 298K on a 700 MHz Bruker NMR instrument equipped with a conventional TXI triple resonance probe and on a 800 MHz Varian NMR instrument equipped with a cryogenically cooled triple resonance probe. Ligands that were added to proteins were dissolved in DMSO-d6. NMR experiments were performed using pulse sequences and standard experimental parameters provided with Bruker Topspin 3.0. RXRα LBD chemical shift assignments37 (link) were validated and/or transferred to various complexed states using standard 2D and 3D NMR TROSY-based methods, including HSQC, HNCO, HNCA, HN(CO)CA and HN(CA)CB and 15 (link)N-NOESY-HSQC experiments. Data were processed using Bruker Topspin 3.0 or NMRPipe58 (link) and analyzed with NMRViewJ59 (link). NMR chemical shift perturbations (ΔδCSP) for PPARγ LBD in the monomer form and heterodimerized to RXRα LBD were calculated from published values51 (link) as follows: ΔδCSP = |ΔδHN| + (0.154 * |ΔδN|) + (0.341 * |ΔδC’|); with ΔδHN , ΔδN and ΔδC’ as the backbone 1 (link)HN, 15 (link)N and 13 (link)C’ (carbonyl) NMR chemical shift differences between monomer and heterodimer, respectively, and mapped onto the PPARγ LBD crystal structure (PDB 2PRG).
Nmrviewj59
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NMRViewJ59 is a nuclear magnetic resonance (NMR) software package developed by Bruker. It is a tool used for the analysis and processing of NMR data. The core function of NMRViewJ59 is to provide users with a comprehensive set of tools for visualizing, manipulating, and interpreting NMR spectra.
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2 protocols using nmrviewj59
1
NMR Characterization of PPARγ-RXRα Heterodimer
2
NMR Characterization of PPARγ-RXRα Heterodimer
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NMR data were collected at 298 K on a 700 MHz Bruker NMR instrument equipped with a conventional TXI triple resonance probe and on a 800-MHz Varian NMR instrument equipped with a cryogenically cooled triple resonance probe. Ligands that were added to proteins were dissolved in DMSO-d6. NMR experiments were performed using pulse sequences and standard experimental parameters provided with Bruker Topspin 3.0. RXRα LBD chemical shift assignments37 (link) were validated and/or transferred to various complexed states using standard 2D and 3D NMR TROSY-based methods, including HSQC, HNCO, HNCA, HN(CO)CA and HN(CA)CB and 15N-NOESY-HSQC experiments. Data were processed using Bruker Topspin 3.0 or NMRPipe58 (link) and analysed with NMRViewJ59 (link). NMR chemical shift perturbations (ΔδCSP) for PPARγ LBD in the monomer form and heterodimerized to RXRα LBD were calculated from published values51 (link) as follows: ΔδCSP=|ΔδHN|+(0.154 × |ΔδN|)+(0.341 × |ΔδC′|); with ΔδHN, ΔδN and ΔδC′ as the backbone 1HN, 15N and 13C′ (carbonyl) NMR chemical shift differences between monomer and heterodimer, respectively, and mapped onto the PPARγ LBD crystal structure (PDB 2PRG).
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