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[NMR paper] High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release.
May 24, 2018 - 1:05 PM - by nmrlearner
nmrlearner's Avatar High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release.

Related Articles High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release.

Glycobiology. 2017 Oct 01;27(10):966-977

Authors: Gagnon SML, Legg MSG, Sindhuwinata N, Letts JA, Johal AR, Schuman B, Borisova SN, Palcic MM, Peters T, Evans SV

Abstract
The human ABO(H) blood group A- and B-synthesizing glycosyltransferases GTA and GTB have been structurally characterized to high resolution in complex with their respective trisaccharide antigen products. These findings are particularly timely and relevant given the dearth of glycosyltransferase structures collected in complex with their saccharide reaction products. GTA and GTB utilize the same acceptor substrates, oligosaccharides terminating with... [Read More]
0 Replies | 6 Views
Multiple frequency saturation pulses reduce CEST acquisition time for quantifying conformational exchange in biomolecules
May 24, 2018 - 12:57 AM - by nmrlearner
nmrlearner's Avatar Multiple frequency saturation pulses reduce CEST acquisition time for quantifying conformational exchange in biomolecules

Abstract

Exchange between conformational states is required for biomolecular catalysis, allostery, and folding. A variety of NMR experiments have been developed to quantify motional regimes ranging from nanoseconds to seconds. In this work, we describe an approach to speed up the acquisition of chemical exchange saturation transfer (CEST) experiments that are commonly used to probe millisecond to second conformational exchange in proteins and nucleic acids. The standard approach is to obtain CEST datasets through the acquisition of a series of 2D correlation spectra where each experiment utilizes a single saturation frequency to 1H, 15N or 13C. These pseudo 3D datasets are time consuming to collect and are further lengthened by reduced signal to noise stemming from the long saturation pulse. In this article, we show how usage of a multiple frequency saturation pulse (i.e., MF-CEST) changes the nature of data collection from series to parallel, and thus decreases the total acquisition time by an integer factor corresponding to the number of frequencies in the pulse. We demonstrate the applicability of MF-CEST on a Src homology 2 (SH2) domain from phospholipase C╬│ and the secondary active transport protein EmrE as model systems by collecting 13C methyl and 15N backbone datasets. MF-CEST can also be extended to additional sites within proteins and nucleic acids. The only notable drawback of MF-CEST as applied to backbone 15N experiments occurs when a large chemical shift difference between the major and minor populations is present (typically greater than ~Ô??8┬*ppm). In these cases, ambiguity may arise between the... [Read More]
0 Replies | 18 Views
[NMR paper] Backbone NMR assignments of HypF-N under conditions generating toxic and non-toxic oligomers.
May 24, 2018 - 12:57 AM - by nmrlearner
nmrlearner's Avatar Backbone NMR assignments of HypF-N under conditions generating toxic and non-toxic oligomers.

Related Articles Backbone NMR assignments of HypF-N under conditions generating toxic and non-toxic oligomers.

Biomol NMR Assign. 2018 May 21;:

Authors: Patel JR, Xu Y, Capitini C, Chiti F, De Simone A

Abstract
The HypF protein is involved in the maturation and regulation of hydrogenases. The N-terminal domain of HypF (HypF-N) has served as a key model system to study the pathways of protein amyloid formation and the nature of the toxicity of pre-fibrilar protein oligomers. This domain can aggregate into two forms of oligomers having significantly different toxic effects when added to neuronal cultures. Here, NMR assignments of HypF-N backbone resonances are presented in its native state and under the conditions favouring the formation of toxic and non-toxic oligomers. The analyses of chemical shifts provide insights into the protein conformational state and the possible pathways leading to the formation of different types of oligomers.


PMID: 29786756 [PubMed - as supplied by publisher]



More...
0 Replies | 17 Views
[NMR paper] Rapid measurement of long-range distances in proteins by multidimensional 13C-19F REDOR NMR under fast magic-angle spinning.
May 24, 2018 - 12:57 AM - by nmrlearner
nmrlearner's Avatar Rapid measurement of long-range distances in proteins by multidimensional 13C-19F REDOR NMR under fast magic-angle spinning.

Related Articles Rapid measurement of long-range distances in proteins by multidimensional 13C-19F REDOR NMR under fast magic-angle spinning.

J Biomol NMR. 2018 May 21;:

Authors: Shcherbakov AA, Hong M

Abstract
The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are 13C-15N distances, which are usually measured using the rotational-echo double-resonance (REDOR) technique. However, these measurements are restricted to distances of up to ~ 5*┼ due to the low gyromagnetic ratios of 15N and 13C. Here we present a robust 2D 13C-19F REDOR experiment to measure multiple distances to ~ 10*┼. The technique targets proteins that contain a small number of recombinantly or synthetically incorporated fluorines. The 13C-19F REDOR sequence is combined with 2D 13C-13C correlation to resolve multiple distances in highly 13C-labeled proteins. We show that, at the high magnetic fields which are important for obtaining well resolved 13C spectra, the deleterious effect of the large 19F chemical shift anisotropy for REDOR is ameliorated by fast magic-angle spinning and is further taken into account in numerical simulations. We demonstrate this 2D 13C-13C resolved 13C-19F REDOR technique on 13C,... [Read More]
0 Replies | 13 Views
[NMR paper] Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.
May 24, 2018 - 12:57 AM - by nmrlearner
nmrlearner's Avatar Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

Related Articles Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

J Proteome Res. 2017 Oct 06;16(10):3774-3786

Authors: Wang C, He L, Li DW, Bruschweiler-Li L, Marshall AG, BrŘschweiler R

Abstract
Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of... [Read More]
0 Replies | 14 Views
(13)C Dynamic Nuclear Polarization Using a Trimeric Gd(3+) Complex as an Additive #DNPNMR
May 24, 2018 - 12:57 AM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

(13)C Dynamic Nuclear Polarization Using a Trimeric Gd(3+) Complex as an Additive #DNPNMR

Niedbalski, P., et al., (13)C Dynamic Nuclear Polarization Using a Trimeric Gd(3+) Complex as an Additive. J. Phys. Chem. A, 2017. 121(27): p. 5127-5135.


https://www.ncbi.nlm.nih.gov/pubmed/28631929


Dissolution dynamic nuclear polarization (DNP) is one of the most successful techniques that resolves the insensitivity problem in liquid-state nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) by amplifying the signal by several thousand-fold. One way to further improve the DNP signal is the inclusion of trace amounts of lanthanides in DNP samples doped with trityl OX063 free radical as the polarizing agent. In practice, stable monomeric gadolinium complexes such as Gd-DOTA or Gd-HP-DO3A are used as beneficial additives in DNP samples, further boosting the DNP-enhanced solid-state (13)C polarization by a factor of 2 or 3. Herein, we report on the use of a trimeric gadolinium complex as a dopant in (13)C DNP samples to improve the (13)C DNP signals in the solid-state at 3.35 T and 1.2 K and consequently, in the liquid-state at 9.4 T and 298 K after dissolution. Our results have shown that doping the (13)C DNP sample with a complex which holds three Gd(3+) ions led to an improvement of DNP-enhanced (13)C polarization by a factor of 3.4 in the solid-state, on par with those achieved using monomeric Gd(3+) complexes but only requires about one-fifth of the concentration. Upon dissolution, liquid-state (13)C NMR signal enhancements close to 20000-fold,... [Read More]
0 Replies | 9 Views
[NMR paper] Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.
May 22, 2018 - 8:59 PM - by nmrlearner
nmrlearner's Avatar Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.

Related Articles Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.

Structure. 2018 May 01;:

Authors: An SY, Kim EH, Suh JY

Abstract
Proteins assemble to form functional complexes via the progressive evolution of nonspecific complexes formed by transient encounters. This target search process generally involves multiple routes that lead the initial encounters to the final complex. In this study, we have employed NMR paramagnetic relaxation enhancement to visualize the encounter complexes between histidine-containing phosphocarrier protein and the N-terminal domain of enzyme I and*demonstrate that protein association can be significantly enhanced by engineering on-pathways. Specifically, mutations in surface charges away from*the binding interface can elicit new on-pathway encounter complexes, increasing their binding affinity by an order of magnitude. The... [Read More]
0 Replies | 16 Views
[NMR paper] A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.
May 22, 2018 - 8:59 PM - by nmrlearner
nmrlearner's Avatar A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.

Related Articles A solution NMR toolset to probe the molecular mechanisms of amyloid inhibitors.

Chem Commun (Camb). 2018 May 03;54(37):4644-4652

Authors: Ahmed R, Melacini G

Abstract
The self-association of the amyloid beta (A?) peptide into toxic oligomers is implicated in the early events leading to Alzheimer's disease (AD). Blocking the formation of A? oligomers and their interactions with the extracellular and cellular environment through small molecules and biopharmaceuticals is therefore a promising preventive strategy for AD. However, given the heterogeneity and transient nature of the A? oligomeric species, detailed structural and kinetic characterizations of such oligomers and oligomer:inhibitor complexes have proven to be challenging. Here, we discuss recent advancements in solution NMR that have been instrumental in overcoming these limitations and we provide two representative examples of A? inhibitors from our work to demonstrate the applications of such experiments, i.e.... [Read More]
0 Replies | 14 Views
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