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TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates
Sep 04, 2021 - 10:34 AM - by nmrlearner
nmrlearner's Avatar TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates

Abstract

Accurate rotational correlation times ( \({\tau }_{\text{c}}\) ) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of \({\tau }_{c}\) using transverse and longitudinal relaxation rates becomes increasingly unsuitable due to the non-trivial contribution of remote dipoleâ??dipole interactions to longitudinal relaxation. Derivations using cross-correlated relaxation experiments, such as TRACT, overcome these limitations but are erroneously calculated in 65% of the citing literature. Herein, we developed an algebraic solutions to the Goldman relationship that facilitate rapid, point-by-point calculations for straightforward identification of appropriate spectral regions where global tumbling is likely to be dominant. The rigid-body approximation of the Goldman relationship has been previously shown to underestimate TRACT-based rotational correlation time estimates. This motivated us to develop a second algebraic solution that employs a simplified model-free spectral density function including an order parameter term that could, in principle, be set to an average backbone S2 â?? 0.9 to further improve the accuracy of \({\tau }_{\text{c}}\) estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the Hâ??N internuclear... [Read More]
0 Replies | 92 Views
Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs - pnas.org
Sep 04, 2021 - 10:34 AM - by nmrlearner
nmrlearner's Avatar Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs - pnas.org

Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs pnas.org Read here
0 Replies | 105 Views
Protein Crystallization And Crystallography Market Size, Trends, and Key Players – Bruker Corporation, Rigaku Corporation, Hampton Research, Agilent Technologies, Corning Incorporated, Tecan Group, SARomics Biostructures, Spectris plc, Charles River
Sep 04, 2021 - 10:34 AM - by nmrlearner
nmrlearner's Avatar Protein Crystallization And Crystallography Market Size, Trends, and Key Players – Bruker Corporation, Rigaku Corporation, Hampton Research, Agilent Technologies, Corning Incorporated, Tecan Group, SARomics Biostructures, Spectris plc, Charles River L - The Manomet Current

Protein Crystallization And Crystallography Market Size, Trends, and Key Players – Bruker Corporation, Rigaku Corporation, Hampton Research, Agilent Technologies, Corning Incorporated, Tecan Group, SARomics Biostructures, Spectris plc, Charles River L The Manomet Current Read here
0 Replies | 138 Views
[NMR paper] An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling
Sep 04, 2021 - 10:34 AM - by nmrlearner
nmrlearner's Avatar An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling

Paramagnetic nuclear magnetic resonance (NMR) methods have emerged as powerful tools for structure determination of large, sparsely protonated proteins. However traditional applications face several challenges, including a need for large datasets to offset the sparsity of restraints, the difficulty in accounting for the conformational heterogeneity of the spin-label, and noisy experimental data. Here we propose an integrative approach to structure determination combining sparse paramagnetic NMR...

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0 Replies | 88 Views
[NMR paper] Examining the Transient Dark State in Protein-Quantum Dot Interaction by Relaxation-Based Solution NMR
Sep 03, 2021 - 2:54 AM - by nmrlearner
nmrlearner's Avatar Examining the Transient Dark State in Protein-Quantum Dot Interaction by Relaxation-Based Solution NMR

We probed the "dark" state involved in the protein-quantum dot (QD) interaction using a relaxation-based solution nuclear magnetic resonance (NMR) approach. We examined the dynamics and exchange kinetics of the ubiquitin-CdTe model system, which undergoes a fast exchange in the transverse relaxation time scale. We applied the recently developed dark-state exchange saturation transfer (DEST), lifetime line broadening (?R(2)), and exchange-induced chemical shift (?(ex)) solution NMR techniques to...

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0 Replies | 80 Views
[NMR paper] NMR hawk-eyed view of AlphaFold2 structures
Sep 03, 2021 - 2:54 AM - by nmrlearner
nmrlearner's Avatar NMR hawk-eyed view of AlphaFold2 structures

The prediction of the three-dimensional structure of proteins from the amino acid sequence made a stunning breakthrough reaching atomic accuracy. Using the neural network-based method AlphaFold2 three-dimensional structures of almost the entire human proteome have been predicted and made available (https://www.alphafold.ebi.ac.uk). To gain insight into how well AlphaFold2 structures represent the conformation of proteins in solution, I here compare the AlphaFold2 structures of selected small...

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0 Replies | 86 Views
[NMR paper] Acetonitrile allows indirect replacement of non-deuterated lipid detergents by deuterated lipid detergents for the NMR study of detergent-soluble proteins
Sep 03, 2021 - 2:54 AM - by nmrlearner
nmrlearner's Avatar Acetonitrile allows indirect replacement of non-deuterated lipid detergents by deuterated lipid detergents for the NMR study of detergent-soluble proteins

Detergent-soluble proteins (DSPs) are commonly dissolved in lipid buffers for NMR experiments, but the huge lipid proton signal prevents recording of high-quality spectra. The use of costly deuterated lipids is thus required to replace non-deuterated ones. With conventional methods, detergents like dodecylphosphocholine (DPC) cannot be fully exchanged due to their high binding affinity to hydrophobic proteins. We propose an original and simple protocol which combines the use of acetonitrile,...

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0 Replies | 94 Views
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