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Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins
Sep 08, 2017 - 12:52 PM - by nmrlearner
nmrlearner's Avatar Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins

Abstract

Using fine-tuned hydrogen bonding criteria, a library of coiled peptide fragments has been generated from a large set of high-resolution protein X-ray structures. This library is shown to be an improved representation of ?/? torsion angles seen in intrinsically disordered proteins (IDPs). The ?/? torsion angle distribution of the library, on average, provides good agreement with experimentally observed chemical shifts and 3JHN-H? coupling constants for a set of five disordered proteins. Inspection of the coil library confirms that nearest-neighbor effects significantly impact the ?/? distribution of residues in the coil state. Importantly, 3JHN-H? coupling constants derived from the nearest-neighbor modulated backbone ? distribution in the coil library show improved agreement to experimental values, thereby providing a better way to predict 3JHN-H? coupling constants for IDPs, and for identifying locations that deviate from fully random behavior. This article is protected by copyright. All rights reserved.




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[NMR paper] Fast simulations of multidimensional NMR spectra of proteins and peptides.
Sep 08, 2017 - 12:52 PM - by nmrlearner
nmrlearner's Avatar Fast simulations of multidimensional NMR spectra of proteins and peptides.

Related Articles Fast simulations of multidimensional NMR spectra of proteins and peptides.

Magn Reson Chem. 2017 Sep 06;:

Authors: Vosegaard T

Abstract
To simulate full multidimensional NMR spectra of peptides and proteins in a reasonable time frame, a strategy for separating the time-consuming full-density matrix calculations from the chemical shift prediction and calculation of coupling patterns is presented. The simulation setup uses SIMPSON to calculate TOCSY transfer amplitudes and average distances as a source for NOESY transfer amplitudes. Simulated (1) H 1D, 2D TOCSY, and 2D NOESY NMR spectra of peptides with sequence PAGYN and NFGAIL and of ubiquitin are presented. In all cases, the simulations lasted from a few seconds to tens of seconds on a normal laptop computer.


PMID: 28879664 [PubMed - as supplied by publisher]



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[NMR paper] A neuronal MCT2 knockdown in the rat somatosensory cortex reduces both the NMR lactate signal and the BOLD response during whisker stimulation.
Sep 08, 2017 - 12:52 PM - by nmrlearner
nmrlearner's Avatar A neuronal MCT2 knockdown in the rat somatosensory cortex reduces both the NMR lactate signal and the BOLD response during whisker stimulation.

Related Articles A neuronal MCT2 knockdown in the rat somatosensory cortex reduces both the NMR lactate signal and the BOLD response during whisker stimulation.

PLoS One. 2017;12(4):e0174990

Authors: Mazuel L, Blanc J, Repond C, Bouchaud V, Raffard G, Déglon N, Bonvento G, Pellerin L, Bouzier-Sore AK

Abstract
Although several in vitro and ex vivo evidence support the existence of lactate exchange between astrocytes and neurons, a direct demonstration in vivo is still lacking. In the present study, a lentiviral vector carrying a short hairpin RNA (shRNA) was used to downregulate the expression of the monocarboxylate transporter type 2 (MCT2) in neurons of the rat somatosensory cortex (called... [Read More]
0 Replies | 36 Views
[NMR paper] Conformational NMR Study of Bistriazolyl Anion Receptors.
Sep 08, 2017 - 12:52 PM - by nmrlearner
nmrlearner's Avatar Conformational NMR Study of Bistriazolyl Anion Receptors.

Related Articles Conformational NMR Study of Bistriazolyl Anion Receptors.

Acta Chim Slov. 2016;63(3):484-8

Authors: Makuc D, Merckx T, Dehaen W, Plavec J

Abstract
Conformational features of pyridine- and pyrimidine-based bistriazolyl anion receptors dissolved in acetonitrile-d3 were assessed by multidimensional, heteronuclear NMR spectroscopy. NOESY correlation signals suggested preorganization of both host molecules in solution in the absence of anions. In addition, only a single set of signals was observed in the 1H NMR spectra, which suggested a symmetrical conformation of anion receptors or their conformational exchange that is fast on the NMR time-scale. Furthermore, the predominant conformations of the pyridine- and pyrimidine-based anion receptors are preserved upon addition of chloride, bromide, and acetate anions. Chemical shift changes observed upon addition of anions showed that the NH (thio)urea and triazole protons are involved in anion-receptor interactions through hydrogen bonding.


PMID: 27640375 [PubMed - indexed for MEDLINE]



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[NMR paper] An NMR Method to Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins.
Sep 07, 2017 - 10:42 PM - by nmrlearner
nmrlearner's Avatar An NMR Method to Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins.

Related Articles An NMR Method to Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins.

Angew Chem Int Ed Engl. 2017 Sep 06;:

Authors: Hogeweg A, Sowislok A, Schrader T, Beuck C

Abstract
Targeting protein surfaces involved in protein-protein interactions using supramolecular chemistry is a rapidly growing field. NMR spectroscopy is the method of choice to map ligand binding sites with single residue resolution by amide chemical shift perturbation and line broadening. However, large aromatic ligands affect NMR signals over a greater distance, and the binding site cannot be determined unambiguously by relying on backbone signals only. We employed Lys- and Arg-specific H2(C)N NMR experiments to directly observe the side chain atoms in close contact with the ligand, for which the most drastic changes in the NMR signals are expected. Binding of lysine- and arginine-specific supramolecular tweezers to the small hPin1 WW domain was studied as a model... [Read More]
0 Replies | 57 Views
[NMR paper] NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).
Sep 07, 2017 - 10:42 PM - by nmrlearner
nmrlearner's Avatar NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).

Related Articles NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).

Biomol NMR Assign. 2017 Sep 05;:

Authors: Lykouras MV, Tsika AC, Lichière J, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA

Abstract
Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130-190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids. In this study we describe the high yield expression of the macro domain... [Read More]
0 Replies | 32 Views
PhD/Postdoc positions, available on DNP/MAS NMR and multi-frequency EPR
Sep 07, 2017 - 10:42 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

PhD/Postdoc positions, available on DNP/MAS NMR and multi-frequency EPR

The original posting can be found here:


DNP EPR Postdoc Position




The University of Konstanz with its "Institutional Strategy to promote Top-Level Research" has been receiving continuous funding since 2007 within the framework of the Excellence Initiative by the German Federal and State Governments.


PhD/Postdoc positions available on DNP/MAS NMR and multi-frequency EPR (67 % EG 13 TV-L)


The positions are to be filled as soon as possible and initially limited for two years.


We are a newly established research group in the Chemistry Department. Our research encompasses the development of magnetic resonance spectroscopy, particularly dynamic nuclear polarization (DNP) / magic-angle spinning (MAS) NMR and multi-frequency electron-paramagnetic resonance (EPR) and their application in structural biology, enzymology, and catalysis.


Possible research projects are:


To investigate if and how the high polarization generated in the photo-excited triplet states of certain chro-mophores can be used for DNP/MAS NMR.


The development of "DNP pulse sequences". This project has an experimental component, as well as a theoretical component.


The application and... [Read More]
0 Replies | 36 Views
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