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[NMR paper] Expression and purification of EPHA2 tyrosine kinase domain for crystallographic and NMR studies.
Sep 30, 2016 - 10:11 AM - by nmrlearner
nmrlearner's Avatar Expression and purification of EPHA2 tyrosine kinase domain for crystallographic and NMR studies.

Expression and purification of EPHA2 tyrosine kinase domain for crystallographic and NMR studies.

Chembiochem. 2016 Sep 29;

Authors: Gande SL, Saxena K, Sreeramulu S, Linhard V, Kudlinzki D, Heinzlmeir S, Reichert AJ, Skerra A, Kuster B, Schwalbe H

Abstract
The receptor tyrosine kinase EPHA2 is overexpressed in several cancer entities (breast, head and neck, non-small cell lung cancer). Small molecule-based inhibition of the activity of the EPHA2 kinase domain (KD) has been seen as an important strategy for achieving therapeutic intervention. However, obtaining structural information by protein crystallography or by NMR spectroscopy aiding drug discovery, has been severely hampered due to the lack of pure and homogeneous protein. Here different fragments of the EPHA2 KD were expressed and purified from both bacterial (Escherichia coli BL21 (DE3) cells) and insect cells (Spodoptera frugiperda, Sf9 cells). [1H,15N]-HSQCs were used to determine the proper folding and homogeneity of all the constructs. E. coli expressed and purified protein constructs though well-folded were unstable and did not crystallize. However, the construct (D596-G900) produced in Sf9 cells yielded in a homogenous, well-folded and crystallized readily, resulting in eleven new EPHA2-ligand co-crystal structures. We have also established a strategy for selective and uniform 15N amino acid labeling of the EPHA2 KD in Sf9 cells for investigating dynamics and EPHA2-drug interactions by NMR.


PMID: 27685543 [PubMed - as supplied by publisher]



... [Read More]
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[NMR paper] NMR Scalar Couplings Across Intermolecular Hydrogen Bonds Between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups.
Sep 30, 2016 - 10:11 AM - by nmrlearner
nmrlearner's Avatar NMR Scalar Couplings Across Intermolecular Hydrogen Bonds Between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups.

NMR Scalar Couplings Across Intermolecular Hydrogen Bonds Between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups.

J Phys Chem B. 2016 Sep 29;

Authors: Chattopadhyay A, Esadze A, Roy S, Iwahara J

Abstract
NMR scalar couplings across hydrogen bonds represent direct evidence of the partial covalent nature of hydrogen bonds and provide structural and dynamic information on hydrogen bonding. In this article, we report heteronuclear (15)N-(31)P and (1)H-(31)P scalar couplings across the intermolecular hydrogen bonds between protein histidine (His) imidazole and DNA phosphate groups. These hydrogen-bond scalar couplings were observed for the Egr-1 zinc-finger-DNA complex. Although His side-chain NH protons are typically undetectable in heteronuclear (1)H-(15)N correlation spectra due to rapid hydrogen exchange, this complex exhibited two His side-chain NH signals around (1)H 14.3 ppm and (15)N 178 ppm at 35 ?C. Through various heteronuclear multi-dimensional NMR experiments, these signals were assigned to two zinc-coordinating His side chains in contact with DNA phosphate groups. The data show that the N?1 atoms of these His side chains are protonated and exhibit the (1)H-(15)N cross peaks. Using heteronuclear (1)H, (15)N, and (31)P NMR experiments, we observed the hydrogen-bond scalar couplings between the His (15)N?1 / (1)H?1 and DNA phosphate (31)P nuclei. These results demonstrate the direct involvement of the zinc-coordinating His side chains in the recognition of DNA by the Cys2His2-class zinc fingers in solution.


PMID:... [Read More]
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[NMR paper] Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction.
Sep 30, 2016 - 10:11 AM - by nmrlearner
nmrlearner's Avatar Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction.

Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction.

J Biomol NMR. 2016 Sep 28;

Authors: Seginer A, Olsen GL, Frydman L

Abstract
Thanks to their special spatiotemporal encoding/decoding scheme, ultrafast (UF) NMR sequences can deliver arbitrary 2D spectra following a single excitation. Regardless of their nature, these sequences have in common their tracing of a path in the [Formula: see text]-[Formula: see text] plane, that will deliver the spectrum being sought after a 1D Fourier transformation versus [Formula: see text]. This need to simultaneously digitize two domains, tends to impose bandwidth limitations along all spectral axes. Along the [Formula: see text]/[Formula: see text] dimension this problem is exacerbated by the fact that odd and even time points are not equispaced, and by additional artifacts such as time shifts between time points sampled while under the action of positive and negative decoding gradients. As a result, odd and even [Formula: see text] points are typically Fourier transformed separately, halving the potential spectral width along this dimension. While this halving of the [Formula: see text] span can be overcome by an interlaced Fourier transform, this post-processing is seldom used because of its sensitivity to hardware inaccuracies requiring even finer corrections of the even/odd [Formula: see text] data points. These corrections have so far been done manually, but are challenging to implement when dealing with low signal-to-noise ratio signals like those associated with biomolecular NMR... [Read More]
0 Replies | 2 Views
[NMR paper] An NMR Study of Biomimetic Fluorapatite - Gelatine Mesocrystals.
Sep 30, 2016 - 10:11 AM - by nmrlearner
nmrlearner's Avatar An NMR Study of Biomimetic Fluorapatite - Gelatine Mesocrystals.

Related Articles An NMR Study of Biomimetic Fluorapatite - Gelatine Mesocrystals.

Sci Rep. 2015;5:15797

Authors: Vyalikh A, Simon P, Rosseeva E, Buder J, Scheler U, Kniep R

Abstract
The mesocrystal system fluoroapatite-gelatine grown by double-diffusion is characterized by hierarchical composite structure on a mesoscale. In the present work we apply solid state NMR to characterize its structure on the molecular level and provide a link between the structural organisation on the mesoscale and atomistic computer simulations. Thus, we find that the individual nanocrystals are composed of crystalline fluorapatite domains covered by a thin boundary apatite-like layer. The latter is in contact with an amorphous layer, which fills the interparticle space. The amorphous layer is comprised of the organic matrix... [Read More]
0 Replies | 3 Views
Structural biology Faster spinning for better structure resolution - Nature.com
Sep 29, 2016 - 7:20 PM - by nmrlearner
nmrlearner's Avatar

Structural biology Faster spinning for better structure resolution
Nature.com
Magic angle spinning (MAS) solid-state nuclear magnetic resonance (ssNMR) spectroscopy is a useful technique for structure determination, especially of membrane proteins. This method typically requires that protons in proteins be largely replaced with ...



Structural biology Faster spinning for better structure resolution - Nature.com
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Two Research Fellow positions and one PhD studentship at University of Southampton #DNPNMR
Sep 29, 2016 - 7:20 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Two Research Fellow positions and one PhD studentship at University of Southampton #DNPNMR

From the Ampere Magnetic Resonance List






Dear Colleagues,


I have two open Reserach Fellow Positions and a fully funded PhD studentship in my group (http://www.southampton.ac.uk/chemist...ff/pileio.page) at the University of Southampton.


* Post-Doctoral Research Fellowship in nuclear magnetic resonance in the research group of Dr Giuseppe Pileio, in collaboration with Prof Malcolm H Levitt. The project, funded by EPSRC(UK), concerns the development of NMR hardware and methodology that combines supercritical fluids with long-lived states NMR and dissolution-DNP to prolong the storage of hyperpolarised spin order and allow it to be transported remotely from the production site. The position is tenable from 1 December 2016 or as soon as possible thereafter with initial appointment for 2 years but with the possibility of a further extension of 1 more years, subject to project requirements. For further details and how to apply please follow this link: https://jobs.soton.ac.uk/Vacancy.aspx?id=14426&forced=1


* A 3 years PhD studentship is also available on the same project with application deadline 31... [Read More]
0 Replies | 6 Views
Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction
Sep 29, 2016 - 6:58 AM - by nmrlearner
nmrlearner's Avatar Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction

Abstract

Thanks to their special spatiotemporal encoding/decoding scheme, ultrafast (UF) NMR sequences can deliver arbitrary 2D spectra following a single excitation. Regardless of their nature, these sequences have in common their tracing of a path in the \({\hbox {F}_{1}}\) ?? \(t_{2}\) plane, that will deliver the spectrum being sought after a 1D Fourier transformation versus \(t_{2}\) . This need to simultaneously digitize two domains, tends to impose bandwidth limitations along all spectral axes. Along the \(t_{2}\) / \({\hbox {F}_{2}}\) dimension this problem is exacerbated by the fact that odd and even time points are not equispaced, and by additional artifacts such as time shifts between time points sampled while under the action of positive and negative decoding gradients. As a result, odd and even \(t_{2}\) points are typically Fourier transformed separately, halving the potential spectral width along this dimension. While this halving of the \({\hbox {F}_{2}}\) span can be overcome by an interlaced Fourier transform, this post-processing is... [Read More]
0 Replies | 34 Views
Research Scientist (PhD) - Chemistry | Vitae Pharmaceuticals
Sep 29, 2016 - 6:58 AM - by nmrlearner
nmrlearner's Avatar Research Scientist (PhD) - Chemistry | Vitae Pharmaceuticals

US - Philadelphia Suburbs, Knowledge, Skills, and Abilities:Ph.D in synthetic organic chemistry.Solid understanding of modern structure determination methods (2D NMR, MS, etc.) and separation techniques.Fundamental unde

More...
0 Replies | 54 Views
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