BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 




Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


» Online Users: 34
0 members and 34 guests
No Members online
Most users ever online was 292, 07-25-2011 at 03:18 PM.
» Welcome!

Welcome, NMR world!


Our visitors map.


» Log in
User Name Not a member yet?
Register Now!
Password
Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR
Jun 18, 2018 - 10:45 AM - by nmrlearner
nmrlearner's Avatar Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR

Abstract

Aquaporins are integral membrane proteins that facilitate water flow across biological membranes. Their involvement in multiple physiological functions and disease states has prompted intense research to discover water channel activity modulators. However, inhibitors found so far are weak and/or lack specificity. For organic compounds, which lack ofÂ*high electron-dense atoms, the identification of binding sites is even more difficult. Nuclear magnetic resonance spectroscopy (NMR) requires large amounts of the protein, and expression and purification of mammalian aquaporins in large quantities is a difficult task. However, since aquaporin Z (AqpZ) can be purified and expressed in good quantities and has a high similarity to human AQP1 (~â??40% identity), it can be used as a model for studying the structure and function of human aquaporins. In the present study, we have used solid-state MAS NMR to investigate the binding of a lead compound [1-(4-methylphenyl)1H-pyrrole-2,5-dione] to AqpZ, through mapping of chemical shift perturbations in the presence of the compound.



Source: Journal of Biomolecular NMR
0 Replies | 1 Views
[NMR paper] Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing
Jun 18, 2018 - 10:45 AM - by nmrlearner
nmrlearner's Avatar Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing

Publication date: August 2018
Source:Journal of Magnetic Resonance, Volume 293

Author(s): Joel Lapin, Alexander A. Nevzorov

An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on 15N-15N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks. This approach is versatile in terms of the parameters that can be specified to achieve the best-fit result. At a minimum the algorithm requires a continuous segment of the main-peak chemical shifts obtained from a uniformly labeled sample and a spin-exchanged experimental spectrum represented as a 2D matrix array. With selective labeling experiments, groups of chemical shifts corresponding to specific locations in the protein backbone can be fixed, thereby decreasing the sampling space. The output from the program consists of a list of top-score main peak assignments, which can be subjected to further scoring... [Read More]
0 Replies | 1 Views
[NMR paper] A generalized approach for NMR studies of lipid-protein interactions based on sparse fluorination of acyl chains.
Jun 16, 2018 - 8:02 PM - by nmrlearner
nmrlearner's Avatar A generalized approach for NMR studies of lipid-protein interactions based on sparse fluorination of acyl chains.

Related Articles A generalized approach for NMR studies of lipid-protein interactions based on sparse fluorination of acyl chains.

Chem Commun (Camb). 2018 Jun 15;:

Authors: De Biasio A, Ibáńez de Opakua A, Bostock MJ, Nietlispach D, Diercks T, Blanco FJ

Abstract
Sparse lipid fluorination enhances the lipids' 1H signal dispersion, enables clean molecular distinction by 19F NMR, and evinces micelle insertion of proteins via fluorine-induced signal shifts. We present a minimal fluorination scheme, and illustrate the concept on di-(4-fluoro)-heptanoylphosphatidylcholine micelles and solubilised seven-helix transmembrane pSRII protein.


PMID: 29905339 [PubMed - as supplied by publisher]



More...
0 Replies | 27 Views
[NMR paper] Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR.
Jun 16, 2018 - 8:02 PM - by nmrlearner
nmrlearner's Avatar Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR.

Related Articles Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR.

Angew Chem Int Ed Engl. 2018 Jun 14;:

Authors: Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L

Abstract
Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid-state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg2+. In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein. Relatively higher flexibility is observed for residues participating in the regulation of chromatin mobility and DNA accessibility. Furthermore, our study reveals that hH4 in the nucleosome array adopts the same structure and show similar internal dynamics as that in the NCP assembly while exhibiting relatively restricted motions in several regions consisting of residues in the N-terminus, Loop 1 and the ?3 helix region.


PMID: 29905032 [PubMed - as supplied by publisher]



... [Read More]
0 Replies | 12 Views
[NMR paper] An NMR study on the intrinsically disordered core transactivation domain of human glucocorticoid receptor.
Jun 16, 2018 - 8:02 PM - by nmrlearner
nmrlearner's Avatar An NMR study on the intrinsically disordered core transactivation domain of human glucocorticoid receptor.

Related Articles An NMR study on the intrinsically disordered core transactivation domain of human glucocorticoid receptor.

BMB Rep. 2017 Oct;50(10):522-527

Authors: Kim DH, Wright A, Han KH

Abstract
A large number of transcriptional activation domains (TADs) are intrinsically unstructured, meaning they are devoid of a three-dimensional structure. The fact that these TADs are transcriptionally active without forming a 3-D structure raises the question of what features in these domains enable them to function. One of two TADs in human glucocorticoid receptor (hGR) is located at its N-terminus and is responsible for ~70% of the transcriptional activity of hGR. This 58-residue intrinsically-disordered TAD, named tau1c in an earlier study, was shown to form three helices under trifluoroethanol, which might be important for its activity. We carried out heteronuclear multi-dimensional NMR experiments on hGR tau1c in a more... [Read More]
0 Replies | 13 Views
Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins
Jun 16, 2018 - 7:20 AM - by nmrlearner
nmrlearner's Avatar Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins

Publication date: Available online 15 June 2018
Source:Biophysical Journal

Author(s): Jasmina Radoicic, Sang Ho Park, Stanley J. Opella

Macrodiscs, which are magnetically alignable lipid bilayer discs with diameters of >30*nm, were obtained by solubilizing protein-containing liposomes with styrene-maleic acid copolymers. Macrodiscs provide a detergent-free phospholipid bilayer environment for biophysical and functional studies of membrane proteins under physiological conditions. The narrow resonance linewidths observed from membrane proteins in styrene-maleic acid macrodiscs advance structure determination by oriented sample solid-state NMR spectroscopy.







More...
0 Replies | 17 Views
[NMR paper] Setting the magic angle for fast magic-angle spinning probes
Jun 15, 2018 - 7:18 PM - by nmrlearner
nmrlearner's Avatar Setting the magic angle for fast magic-angle spinning probes

Publication date: Available online 15 June 2018
Source:Journal of Magnetic Resonance

Author(s): Susanne Penzel, Albert A. Smith, Matthias Ernst, Beat H. Meier

Fast magic-angle spinning, coupled with 1H detection is a powerful method to improve spectral resolution and signal to noise in solid-state NMR spectra. Commercial probes now provide spinning frequencies in excess of 100 kHz. Then, one has sufficient resolution in the 1H dimension to directly detect protons, which have a gyromagnetic ratio approximately four times larger than 13C spins. However, the gains in sensitivity can quickly be lost if the rotation angle is not set precisely. The most common method of magic-angle calibration is to optimize the number of rotary echoes, or sideband intensity, observed on a sample of KBr. However, this typically uses relatively low spinning frequencies, where the spinning of fast-MAS probes is often unstable, and detection on the 13C channel, for which fast-MAS probes are typically not optimized. Therefore, we compare the KBr-based optimization of the magic angle with two alternative approaches: optimization of the splitting observed in 13C-labeled glycine-ethylester on the carbonyl due to the C?–C’ J-coupling, or optimization of the H–N J-coupling spin echo in the protein sample itself. The latter method has the particular advantage that no separate... [Read More]
0 Replies | 21 Views
13C dynamic nuclear polarization using isotopically enriched 4-oxo-TEMPO free radicals #DNPNMR
Jun 15, 2018 - 7:18 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

13C dynamic nuclear polarization using isotopically enriched 4-oxo-TEMPO free radicals #DNPNMR

Niedbalski, Peter, Christopher Parish, Andhika Kiswandhi, and Lloyd Lumata. “13C Dynamic Nuclear Polarization Using Isotopically Enriched 4-Oxo-TEMPO Free Radicals.” Magnetic Resonance in Chemistry 54, no. 12 (2016): 962–67.


https://doi.org/10.1002/mrc.4480


The nitroxide-based free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) is a widely used polarizing agent in NMR signal amplification via dissolution dynamic nuclear polarization (DNP). In this study, we have thoroughly investigated the effects of 15N and/or 2H isotopic labeling of 4-oxo-TEMPO free radical on 13C DNP of 3 M [1-13C] sodium acetate samples in 1 : 1 v/v glycerol : water at 3.35 T and 1.2 K. Four variants of this free radical were used for 13C DNP: 4-oxo-TEMPO, 4-oxo-TEMPO-15N, 4-oxo-TEMPO-d16 and 4-oxo-TEMPO-15N,d16. Our results indicate that, despite the striking differences seen in the electron spin resonance (ESR) spectral features, the 13C DNP efficiency of these 15N and/or 2H-enriched 4-oxo-TEMPO free radicals are relatively the same compared with 13C DNP performance of the regular 4-oxo-TEMPO. Furthermore, when fully deuterated glassing solvents were used, the 13C DNP signals of these samples all doubled in the same manner, and the 13C polarization buildup was faster by a factor of 2 for all samples. The data here suggest that the hyperfine coupling contributions of these isotopically enriched 4-oxo-TEMPO free radicals... [Read More]
0 Replies | 22 Views
» Stats
Members: 3,202
Threads: 21,345
Posts: 21,731
Top Poster: nmrlearner (18,789)
Welcome to our newest member, bpadmanabhan
Powered by vBadvanced CMPS v3.2.2

All times are GMT. The time now is 01:00 PM.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2018, Jelsoft Enterprises Ltd.
vBCredits II Deluxe v1.2.0 Copyright © 2010 DragonByte Technologies
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

Map