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 Probing slow timescale dynamics in proteins using methyl 1 H CEST |
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Jun 24, 2017 - 8:20 PM - by nmrlearner
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Probing slow timescale dynamics in proteins using methyl 1 H CEST
Abstract
Although 15N- and 13C-based chemical exchange saturation transfer (CEST) experiments have assumed an important role in studies of biomolecular conformational exchange, 1H CEST experiments are only beginning to emerge. We present a methyl-TROSY 1H CEST experiment that eliminates deleterious 1Hâ??1H NOE dips so that CEST profiles can be analyzed robustly to extract methyl proton chemical shifts of rare protein conformers. The utility of the experiment, along with a version that is optimized for 13CHD2 labeled proteins, is established through studies of exchanging protein systems. A comparison between methyl 1H CEST and methyl 1H CPMG approaches is presented to highlight the complementarity of the two experiments.
Source: Journal of Biomolecular NMR
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0 Replies | 2 Views
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[NMR paper] Bacteriophage Tail Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. |
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Jun 24, 2017 - 8:20 PM - by nmrlearner
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Bacteriophage Tail Tube Assembly Studied by Proton-Detected 4D Solid-State NMR.
Related Articles Bacteriophage Tail Tube Assembly Studied by Proton-Detected 4D Solid-State NMR.
Angew Chem Int Ed Engl. 2017 Jun 23;:
Authors: Zinke M, Fricke P, Samson C, Hwang S, Wall J, Lange S, Zinn-Justin S, Lange A
Abstract
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2%). As a proof-of-principle we acquired 4D (H)COCANH, (H)CACONH and (H)CBCANH spectra of the 20 kDa bacteriophage tail tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.
PMID: 28644511 [PubMed - as supplied by publisher]
... [Read More]
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0 Replies | 2 Views
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[NMR paper] Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology. |
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Jun 24, 2017 - 8:20 PM - by nmrlearner
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Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology.
Related Articles Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology.
J Mol Med (Berl). 2017 Jun 23;:
Authors: Ziarek JJ, Baptista D, Wagner G
Abstract
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors. The goal of this mini-review is to empower the clinical researcher with a general knowledge of the strengths and weaknesses of nuclear magnetic resonance (NMR) spectroscopy in molecular medicine. Although NMR can determine protein structures at atomic resolution, its unrivaled strength lies in sensing subtle changes in a nuclei's chemical environment as a result of intrinsic conformational dynamics, solution conditions, and binding interactions. These can be recorded at atomic resolution, without explicit structure determination, and... [Read More]
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0 Replies | 2 Views
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[NMR paper] Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4. |
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Jun 24, 2017 - 8:20 PM - by nmrlearner
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Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4.
Related Articles Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4.
J Phys Chem B. 2017 Jun 22;:
Authors: Smith LJ, van Gunsteren WF, Hansen N
Abstract
The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather non-trivial task due to (i) the limited number of data compared to degrees of freedom of a protein, (ii) the uncertainty inherent to the function connecting an observable quantity to molecular structure, (iii) the finite quality of biomolecular models and force fields used in structure refinement, and (iv) the conformational freedom of a protein in aqueous solution, which requires extensive conformational sampling and appropriate conformational averaging when calculating or restraining to sets of NMR data. The protein interleukin-4 (IL-4) has been taken as a test case using NOE distances, S2 order-parameters and 3J-couplings as test data and the former two types of data as restraints. It is shown that by combining sets of different, complementary NMR data as restraints in MD simulation inconsistencies in the data or flaws in the model and procedures used to derive protein structure from NMR data can be detected. This leads... [Read More]
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0 Replies | 2 Views
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[NMR paper] Studies of the Binding of Modest Modulators of the Human Enzyme, Sirtuin 6, by STD NMR. |
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Jun 24, 2017 - 8:20 PM - by nmrlearner
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Studies of the Binding of Modest Modulators of the Human Enzyme, Sirtuin 6, by STD NMR.
 Related Articles Studies of the Binding of Modest Modulators of the Human Enzyme, Sirtuin 6, by STD NMR.
Chembiochem. 2017 May 18;18(10):931-940
Authors: Bolívar BE, Welch JT
Abstract
Pyrazinamide (PZA), an essential constituent of short-course tuberculosis chemotherapy, binds weakly but selectively to Sirtuin 6 (SIRT6). Despite the structural similarities between nicotinamide (NAM), PZA, and pyrazinoic acid (POA), these inhibitors modulate SIRT6 by different mechanisms and through different binding sites, as suggested by saturation transfer difference (STD) NMR. Available experimental evidence, such as that derived from crystal structures and kinetic experiments, has been of only limited utility in elucidation of the mechanistic details of sirtuin inhibition by NAM or other inhibitors. For instance, crystallographic structural analysis of sirtuin binding sites does not help us understand important differences in binding affinities among sirtuins or capture... [Read More]
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0 Replies | 2 Views
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[NMR paper] Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study. |
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Jun 24, 2017 - 8:20 PM - by nmrlearner
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Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study.
 Related Articles Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study.
Biophys J. 2016 Dec 20;111(12):2676-2688
Authors: Santos TL, Moraes A, Nakaie CR, Almeida FC, Schreier S, Valente AP
Abstract
A large number of antimicrobial peptides (AMPs) acts with high selectivity and specificity through interactions with membrane lipid components. These peptides undergo complex conformational changes in solution; upon binding to an interface, one major conformation is stabilized. Here we describe a study of the interaction between tritrpticin (TRP3), a cathelicidin AMP, and micelles of different chemical composition. The peptide's structure and dynamics were examined using one-dimensional and two-dimensional NMR. Our data showed that the interaction occurred by conformational selection and the peptide acquired similar structures in all systems studied, despite differences in detergent headgroup... [Read More]
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0 Replies | 2 Views
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[NMR paper] Heterogeneous Microtesla SABRE Enhancement of 15N NMR Signals |
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Jun 24, 2017 - 5:27 AM - by nmrlearner
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Heterogeneous Microtesla SABRE Enhancement of 15N NMR Signals
The hyperpolarization of heteronuclei via Signal Amplification by Reversible Exchange (SABRE) was investigated under conditions of heterogeneous catalysis and microtesla magnetic fields. Immobilization of [IrCl(COD)(IMes)], [IMes = 1,3-bis(2,4,6-trimethylphenyl), imidazole-2-ylidene; COD = cyclooctadiene] catalyst onto silica particles modified with NH2(CH2)3- linkers engenders an effective heterogeneous SABRE (HET-SABRE) catalyst that was used to demonstrate ~102-fold enhancement of 15N NMR signals in pyridine at 9.4 T following parahydrogen bubbling within a magnetic shield. No 15N NMR enhancement was observed from the supernatant liquid following catalyst separation, which along with XRD characterization, supports that the effects result from SABRE under heterogeneous catalytic conditions. The technique can be developed further for producing catalyst-free agents via SABRE with hyperpolarized heteronuclear spins, and thus is promising for biomedical NMR and MRI applications.
More...
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0 Replies | 8 Views
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