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[NMR paper] Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain.
Dec 14, 2017 - 12:56 PM - by nmrlearner
nmrlearner's Avatar Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain.

Related Articles Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain.

J Biomol NMR. 2017 Dec 12;:

Authors: Sharaf NG, Brereton AE, Byeon IL, Karplus PA, Gronenborn AM

Abstract
In the original publication of the article, the given name and family name of the author P. Andrew Karplus was published incorrectly. The name should read as "P. Andrew" - Given name and "Karplus" - Family name.


PMID: 29234947 [PubMed - as supplied by publisher]



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0 Replies | 10 Views
[NMR paper] Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.
Dec 13, 2017 - 6:15 PM - by nmrlearner
nmrlearner's Avatar Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.

Related Articles Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.

PLoS One. 2017;12(12):e0189700

Authors: Feng Y

Abstract
The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.


PMID: 29232406 [PubMed - in process]



... [Read More]
0 Replies | 13 Views
[NMR paper] Erratum to: Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.
Dec 13, 2017 - 6:15 PM - by nmrlearner
nmrlearner's Avatar Erratum to: Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.

Related Articles Erratum to: Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR.

J Biomol NMR. 2017 Dec 11;:

Authors: Takeuchi K, Arthanari H, Shimada I, Wagner G

Abstract
The authors regret a mistake appeared in the supplement of this paper.


PMID: 29230599 [PubMed - as supplied by publisher]



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0 Replies | 16 Views
[NMR paper] c-MYC G-quadruplex binding by the RNA polymerase I inhibitor BMH-21 and analogues revealed by a combined NMR and biochemical Approach.
Dec 13, 2017 - 6:15 PM - by nmrlearner
nmrlearner's Avatar c-MYC G-quadruplex binding by the RNA polymerase I inhibitor BMH-21 and analogues revealed by a combined NMR and biochemical Approach.

Related Articles c-MYC G-quadruplex binding by the RNA polymerase I inhibitor BMH-21 and analogues revealed by a combined NMR and biochemical Approach.

Biochim Biophys Acta. 2017 Dec 08;:

Authors: Musso L, Mazzini S, Rossini A, Castagnoli L, Scaglioni L, Artali R, Di Nicola M, Zunino F, Dallavalle S

Abstract
BACKGROUND: Pyridoquinazolinecarboxamides have been reported as RNA polymerase I inhibitors and represent a novel class of potential antitumor agents. BMH-21, was reported to intercalate with GC-rich rDNA, resulting in nucleolar stress as a primary mechanism of cytotoxicity.
METHODS: The interaction of BMH-21 and analogues with DNA G-quadruplex structures was studied by NMR and molecular modelling. The cellular response was investigated in a panel of human tumor cell lines and protein expression was examined by Western Blot analysis.
RESULTS AND CONCLUSIONS: We explored the ability of BMH-21 and its analogue 2 to bind to G-quadruplex present in the c-MYC promoter, by NMR and molecular modelling studies. We provide evidence that both compounds are not typical DNA intercalators but are effective binders of the tested G-quadruplex. The interaction with c-MYC G-quadruplex was reflected in down-regulation of c-Myc expression in human tumor cells. The inhibitory effect was almost complete in lymphoma cells... [Read More]
0 Replies | 15 Views
[NMR paper] Comparative NMR and NIRS analysis of oxygen-dependent metabolism in exercising finger flexor muscles.
Dec 13, 2017 - 6:15 PM - by nmrlearner
nmrlearner's Avatar Comparative NMR and NIRS analysis of oxygen-dependent metabolism in exercising finger flexor muscles.

Related Articles Comparative NMR and NIRS analysis of oxygen-dependent metabolism in exercising finger flexor muscles.

Am J Physiol Regul Integr Comp Physiol. 2017 Dec 01;313(6):R740-R753

Authors: Bendahan D, Chatel B, Jue T

Abstract
Muscle contraction requires the physiology to adapt rapidly to meet the surge in energy demand. To investigate the shift in metabolic control, especially between oxygen and metabolism, researchers often depend on near-infrared spectroscopy (NIRS) to measure noninvasively the tissue O2 Because NIRS detects the overlapping myoglobin (Mb) and hemoglobin (Hb) signals in muscle, interpreting the data as an index of cellular or vascular O2 requires deconvoluting the relative contribution. Currently, many in the NIRS field ascribe the signal to Hb. In contrast, 1H NMR has only detected the Mb signal in contracting muscle, and comparative NIRS and NMR experiments indicate a predominant Mb contribution. The present study has examined the question of the NIRS signal origin by measuring simultaneously the 1H... [Read More]
0 Replies | 16 Views
Perspectives on paramagnetic NMR from a life sciences infrastructure
Dec 13, 2017 - 6:15 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Perspectives on paramagnetic NMR from a life sciences infrastructure

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Ravera, E., G. Parigi, and C. Luchinat, Perspectives on paramagnetic NMR from a life sciences infrastructure. J Magn Reson, 2017. 282(Supplement C): p. 154-169.


https://www.ncbi.nlm.nih.gov/pubmed/28844254


The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as "paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the... [Read More]
0 Replies | 14 Views
Finding a Silver Bullet in a Stack of Proteins
Dec 13, 2017 - 2:15 AM - by nmrlearner
nmrlearner's Avatar Finding a Silver Bullet in a Stack of Proteins



Biochemistry
DOI: 10.1021/acs.biochem.7b01177



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0 Replies | 18 Views
Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain
Dec 12, 2017 - 2:13 PM - by nmrlearner
nmrlearner's Avatar Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain

Abstract

In the original publication of the article, the given name and family name of the author P. Andrew Karplus was published incorrectly. The name should read as "P. Andrew" ?? Given name and "Karplus" ?? Family name.



Source: Journal of Biomolecular NMR
0 Replies | 19 Views
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