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Understanding and solving abnormal peak splitting in 3D HCCH-TOCSY and HCC(CO)NH-TOCSY
Apr 02, 2020 - 6:25 PM - by nmrlearner
nmrlearner's Avatar Understanding and solving abnormal peak splitting in 3D HCCH-TOCSY and HCC(CO)NH-TOCSY

Abstract

The 3D HCCH-TOCSY and HCC(CO)NH-TOCSY experiments provide through bond connectivity and are used for side-chain chemical shift assignment by solution-state NMR. Careful design and implementation of the pulse sequence are key to the successful application of the technique particularly when trying to extract the maximum information out of challenging biomolecules. Here we investigate the source of and propose solutions for abnormal peak splitting ranging from 152 to 80¬*Hz and below that were found in three popular TOCSY-based experiment types: H(F1)‚??C(F2)‚??DIPSI‚??H(F3), C(F1)‚??DIPSI‚??C(F2)‚??H(F3), and C(F1)‚??DIPSI‚??N(F2)‚??HN(F3). Peak splitting occurs in the indirect C(F1) or C(F2) dimension before DIPSI and analyses indicate that the artifacts are resulted mainly from the DIPSI transforming a double spin order \(2{C}_{1y}{C}_{2x}\) from 13C‚??13C scalar 1JCC coupling during t1 into observable megnetization. The splitting is recapitulated by numerical simulation and approaches are proposed to remove it. Adding a pure delay of 3.7¬*ms immediately before DIPSI is a simple and effective strategy to achieve 3D HCCH-TOCSY and HCC(CO)NH-TOCSY spectra free of splitting with full crosspeak intensity.



Source: Journal of Biomolecular NMR
0 Replies | 7 Views
[NMR paper] Optimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics.
Apr 02, 2020 - 6:25 PM - by nmrlearner
nmrlearner's Avatar Optimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics.

Related Articles Optimisation of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics.

J Proteome Res. 2020 Mar 31;:

Authors: Anderson JR, Phelan MM, Rubio-Martinez LM, Fitzgerald MM, Jones SW, Clegg PD, Peffers MJ

Abstract
Synovial fluid (SF) is of great interest for the investigation of orthopaedic pathologies as it is in close proximity to various tissues which are primarily altered during these disease processes and can be collected using minimally invasive protocols. Multi 'omic' approaches are commonplace although little consideration is often given for multiple analysis techniques at sample collection. Nuclear magnetic resonance (NMR) metabolomics and liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics are two complementary techniques particularly suited to the study of SF. However, currently there are no agreed standard protocols which are published for SF collection and processing for use with NMR metabolomic analysis. Furthermore, the large protein concentration dynamic range present within SF can mask the detection of lower abundance proteins in proteomics. Whilst combinational ligand libraries (ProteoMinerTM columns) have been developed to reduce this dynamic range, their reproducibility when used in conjunction with SF, or... [Read More]
0 Replies | 4 Views
What do we know about the novel coronavirus's 29 proteins? - Chemical & Engineering News
Apr 02, 2020 - 5:36 AM - by nmrlearner
nmrlearner's Avatar What do we know about the novel coronavirus's 29 proteins? Chemical & Engineering News
What do we know about the novel coronavirus's 29 proteins? - Chemical & Engineering News
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0 Replies | 2 Views
Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly - Science Advances
Apr 02, 2020 - 5:36 AM - by nmrlearner
nmrlearner's Avatar Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly - Science Advances

Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly Science Advances Read here
0 Replies | 2 Views
Low intrinsic efficacy for G protein activation can explain the improved side effect profiles of new opioid agonists - Science
Apr 01, 2020 - 3:54 PM - by nmrlearner
nmrlearner's Avatar Low intrinsic efficacy for G protein activation can explain the improved side effect profiles of new opioid agonists - Science

Low intrinsic efficacy for G protein activation can explain the improved side effect profiles of new opioid agonists Science Read here
0 Replies | 5 Views
[NMR paper] Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser.
Apr 01, 2020 - 3:54 PM - by nmrlearner
nmrlearner's Avatar Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser.

Related Articles Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser.

J Biomol NMR. 2019 Sep;73(8-9):509-518

Authors: Ding J, Swain M, Yu P, Stagno JR, Wang YX

Abstract
Riboswitches are structured*cis-regulators mainly found in the untranslated regions of messenger RNA. The aptamer domain of a riboswitch serves as a sensor for its ligand, the binding of which triggers conformational changes that regulate the behavior of its expression platform. As a model system for understanding riboswitch structures and functions, the*add*adenine riboswitch has been studied extensively. However, there is a need for further investigation of the conformational... [Read More]
0 Replies | 8 Views
[NMR paper] Fabrication of Pascal-triangle Lattice of Proteins by Inducing Ligand Strategy
Apr 01, 2020 - 3:54 PM - by nmrlearner
nmrlearner's Avatar Fabrication of Pascal-triangle Lattice of Proteins by Inducing Ligand Strategy


Angewandte Chemie International Edition, EarlyView.

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0 Replies | 10 Views
The past, present, and future of 1.26 T2
Apr 01, 2020 - 3:54 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

The past, present, and future of 1.26 T2

This article is not directly related to DNP-NMR spectroscopy but offers some very valuable insight how to optimize acquisition parameters.




Rovnyak, David. ďThe Past, Present, and Future of 1.26 T2.Ē Concepts in Magnetic Resonance Part A 47A, no. 2 (March 2018): e21473.


https://doi.org/10.1002/cmr.a.21473.


This mini-*review considers the scientific and historical development of the constant 1.26T2, which represents the acquisition time for which the signal-*to-*noise ratio of a decaying exponential (with time constant T2) is a maximum in the presence of thermal noise. While first reported in 1977, interest in this result greatly increased after about the year 2000, when it began to influence thinking in nonuniform sampling, sensitivity, and pulse sequence design. Overall, 1.26T2 has become a lens through which to view the evolution of NMR data acquisition and processing. An enduring lesson of the 1.26T2 story is the value of describing and analyzing the properties of magnetic resonance signals in the time domain prior to any further spectral analysis and processing, a concept which is at the core of many modern analytic techniques.


Go to The DNP-NMR Blog for more info.
0 Replies | 5 Views
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