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» Welcome! Welcome, NMR world! Our visitors map. » Log in User Name Remember Me? Not a member yet? Register Now! Password Pitfalls in measurements of R1 relaxation rates of protein backbone 15N nuclei Sep 01, 2024 - 2:47 PM - by nmrlearner Pitfalls in measurements of R1 relaxation rates of protein backbone 15N nuclei Abstract The dynamics of the backbone and side-chains of protein are routinely studied by interpreting experimentally determined 15N spin relaxation rates. R1(15N), the longitudinal relaxation rate, reports on fast motions and encodes, together with the transverse relaxation R2, structural information about the shape of the molecule and the orientation of the amide bond vectors in the internal diffusion frame. Determining error-free 15N longitudinal relaxation rates remains a challenge for small, disordered, and medium-sized proteins. Here, we show that mono-exponential fitting is sufficient, with no statistical preference for bi-exponential fitting up to 800Â*MHz. A detailed comparison of the TROSY and HSQC techniques at medium and high fields showed no statistically significant differences. The least error-prone DD/CSA interference removal technique is the selective inversion of amide signals while avoiding water resonance. The exchange of amide with solvent deuterons appears to affect the rate R1 of solvent-exposed amides in all fields tested and in each DD/CSA interference removal technique in a statistically significant manner. In summary, the most accurate R1(15N) rates in proteins are achieved by selective amide inversion, without the addition of D2O. Importantly, at high magnetic fields stronger than 800Â*MHz, when non-mono-exponential decay is involved, it is advisable to consider elimination of the shortest delays (typically up to 0.32Â*s) or bi-exponential fitting. ... [Read More] 0 Replies | 142 Views NMR Structure Determination for Larger Proteins Using Backbone-Only Data - Science Sep 01, 2024 - 1:51 AM - by nmrlearner NMR Structure Determination for Larger Proteins Using Backbone-Only Data - Science NMR Structure Determination for Larger Proteins Using Backbone-Only Data Science Read here 0 Replies | 135 Views [NMR paper] Solid state NMR spectral editing of histidine, arginine and lysine using Hadamard encoding Aug 31, 2024 - 1:47 PM - by nmrlearner Solid state NMR spectral editing of histidine, arginine and lysine using Hadamard encoding The NMR signals from protein sidechains are rich in information about intra- and inter-molecular interactions, but their detection can be complicated due to spectral overlap as well as conformational and hydrogen exchange. In this work, we demonstrate a protocol for multi-dimensional solid-state NMR spectral editing of signals from basic sidechains based on Hadamard matrix encoding. The Hadamard method acquires multi-dimensional experiments in such a way that both the backbone and under-sampled... More... 0 Replies | 117 Views [NMR paper] NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic Na(2)SO(4) and NaH(2)PO(4) Aug 31, 2024 - 1:47 PM - by nmrlearner NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic Na(2)SO(4) and NaH(2)PO(4) The Hofmeister series categorizes ions based on their effects on protein stability, yet the microscopic mechanism remains a mystery. In this series, NaCl is neutral, Na(2)SO(4) and Na(2)HPO(4) are kosmotropic, while GdmCl and NaSCN are chaotropic. This study employs CD and NMR to investigate the effects of NaCl, Na(2)SO(4), and Na(2)HPO(4) on the conformation, stability, binding, and backbone dynamics (ps-ns and µs-ms time scales) of the WW4 domain with a high stability and accessible side... More... 0 Replies | 80 Views [NMR paper] NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme Aug 31, 2024 - 1:47 PM - by nmrlearner NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme ProXp-ala is a key component of the translational machinery in all three Domains of life. This enzyme helps to maintain the fidelity of proline codon translation through aminoacyl-tRNA^(Pro) proofreading. In the first step of tRNA aminoacylation, the cognate aminoacyl-tRNA synthetase (aaRS) binds and activates an amino acid in the enzyme's synthetic active site. If a non-cognate amino acid passes this first selection step and is charged onto the tRNA, a distinct aaRS editing active site may... More... 0 Replies | 83 Views Crowding Effects on the Structure and Dynamics of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1 - Frontiers Aug 30, 2024 - 11:12 PM - by nmrlearner Crowding Effects on the Structure and Dynamics of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1 - Frontiers Crowding Effects on the Structure and Dynamics of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1 Frontiers Read here 0 Replies | 437 Views Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes - Frontiers Aug 30, 2024 - 10:20 AM - by nmrlearner Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes - Frontiers Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes Frontiers Read here 0 Replies | 172 Views [NMR paper] Development of a new experimental NMR strategy for covalent cysteine protease inhibitors screening: toward enhanced drug discovery Aug 29, 2024 - 12:07 PM - by nmrlearner Development of a new experimental NMR strategy for covalent cysteine protease inhibitors screening: toward enhanced drug discovery In the development of antiviral drugs, proteases and polymerases are among the most important targets. Cysteine proteases, also known as thiol proteases, catalyze the degradation of proteins by cleaving peptide bonds using the nucleophilic thiol group of cysteine. As part of our research, we are examining how cysteine, an essential amino acid found in the active site of the main protease (M^(pro)) enzyme in SARS-CoV-2, interacts with electrophilic groups present in ethacrynic acid (EA) and... More... 0 Replies | 98 Views Page 53 of 100 « First < 3 43 51 52 53 54 55 63 > Last »

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