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At last, cancer-fighting inhibitors hit deubiquitinase target selectively ... - The Biological SCENE
Oct 22, 2017 - 4:54 PM - by nmrlearner
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The Biological SCENE


At last, cancer-fighting inhibitors hit deubiquitinase target selectively ...
The Biological SCENE
In the body, ubiquitinating enzymes regulate proteins‚??marking them for disposal, for example‚??by adding ubiquitin peptides to them. And deubiquitinases ...

and more »

At last, cancer-fighting inhibitors hit deubiquitinase target selectively ... - The Biological SCENE
... [Read More]
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[NMR paper] A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-dependent Oxidation
Oct 21, 2017 - 4:46 AM - by nmrlearner
nmrlearner's Avatar A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-dependent Oxidation


Metalloproteins utilize O? as an oxidant, and they often achieve a 4-electron reduction without H?O? or oxygen radical release. Several proteins have been designed to catalyze one or two-electron oxidative chemistry, but the de novo design of a protein that catalyzes the net 4-electron reduction of O? has not been reported yet. We report here the construction of a diiron-binding four-helix bundle, made up of two different covalently linked ?2 monomers, through click chemistry. Surprisingly, the prototype protein, DF-C1, showed a large divergence in its reactivity from earlier DFs. DFs release the quinone imine and free H?O? in the oxidation of 4-aminophenol in the presence of O?, whereas FeIII-DF-C1 sequesters the quinone imine into the active site, and catalyzes inside the scaffold an oxidative coupling between oxidized and reduced 4-aminophenol. The asymmetry of the scaffold allowed a fine-engineering of the substrate binding pocket, that ensures selectivity.

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0 Replies | 15 Views
Dynamic nuclear polarization studies of nitroxyl spin probes in agarose gel using Overhauser-enhanced magnetic resonance imaging
Oct 21, 2017 - 4:46 AM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Dynamic nuclear polarization studies of nitroxyl spin probes in agarose gel using Overhauser-enhanced magnetic resonance imaging

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Meenakumari, V., et al., Dynamic nuclear polarization studies of nitroxyl spin probes in agarose gel using Overhauser-enhanced magnetic resonance imaging. Magn Reson Chem, 2017. 55(11): p. 1022-1028.


https://www.ncbi.nlm.nih.gov/pubmed/28599057


Agarose is a tissue-equivalent material and its imaging characteristics similar to those of real tissues. Hence, the dynamic nuclear polarization studies of 3-carboxy-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (carboxy-PROXYL) in agarose gel were carried out. The dynamic nuclear polarization parameters such as spin lattice relaxation time, longitudinal relaxivity, leakage factor, saturation parameter and coupling parameter were estimated for 2 mM carboxy-PROXYL in phosphate-buffered saline solution and water/agarose mixture (99 : 1). From these results, the spin probe concentration was optimized as 2 mM, and the reduction in enhancement was observed for carboxy-PROXYL in water/agarose mixture (99 : 1) compared with phosphate-buffered saline solution. Phantom imaging was also performed with 2 mM concentration of carboxy-PROXYL in various concentrations of agarose gel at various radio frequency power levels. The results from the dynamic nuclear polarization measurements agree well with the phantom imaging results. These... [Read More]
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More government support needed for research - Lethbridge Herald
Oct 20, 2017 - 1:48 PM - by nmrlearner
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Lethbridge Herald


More government support needed for research
Lethbridge Herald
Kay and his U of T colleagues have made advances in the field of biomolecular nuclear magnetic resonance (NMR) spectroscopy. They've developed ways to visualize protein molecules and how they can form abnormal structures that can lead to disease.



More government support needed for research - Lethbridge Herald
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Last unknown structure of HIV-1 solved, another step in efforts to ... - Phys.Org
Oct 20, 2017 - 1:48 PM - by nmrlearner
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Phys.Org


Last unknown structure of HIV-1 solved, another step in efforts to ...
Phys.Org
A University of Alabama at Birmingham team led by Jamil Saad, Ph.D., has solved the last unknown protein structure of HIV-1, the retrovirus that can cause ...

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Last unknown structure of HIV-1 solved, another step in efforts to ... - Phys.Org
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0 Replies | 13 Views
[NMR paper] Comparing pharmacophore models derived from crystallography and NMR ensembles.
Oct 20, 2017 - 1:48 PM - by nmrlearner
nmrlearner's Avatar Comparing pharmacophore models derived from crystallography and NMR ensembles.

Related Articles Comparing pharmacophore models derived from crystallography and NMR ensembles.

J Comput Aided Mol Des. 2017 Oct 19;:

Authors: Ghanakota P, Carlson HA

Abstract
NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-? (PPAR-?). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their... [Read More]
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[NMR paper] NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4.
Oct 20, 2017 - 1:48 PM - by nmrlearner
nmrlearner's Avatar NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4.

Related Articles NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4.

Biochim Biophys Acta. 2017 02;1861(2):37-48

Authors: Padmapriya K, Barthwal R

Abstract
BACKGROUND: Telomere elongation by telomerase gets inhibited by G-quadruplex DNA found in its guanine rich region. Stabilization of G-quadruplex DNA upon ligand binding has evolved as a promising strategy to target cancer cells in which telomerase is over expressed.
METHODS: Interaction of anti-leukemic alkaloid, coralyne, to tetrameric parallel [d(TTGGGGT)]4 (Ttel7), [d(TTAGGGT)]4 (Htel7) and monomeric anti-parallel [dGGGG(TTGGGG)3] (Ttel22) G-quadruplex DNA has been studied using Circular Dichroism (CD) spectroscopy. Titrations of coralyne with Ttel7 and Htel7... [Read More]
0 Replies | 10 Views
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