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[NMR paper] Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and*their interactions with human lectins using NMR spectroscopy.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and*their interactions with human lectins using NMR spectroscopy.

Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and*their interactions with human lectins using NMR spectroscopy.

Angew Chem Int Ed Engl. 2020 Sep 11;:

Authors: Lenza MP, Oyenarte I, Diercks T, Quintana JI, Gimeno A, Bosch A, Coelho H, Diniz A, Peccati F, Delgado S, Valle M, Millet O, Abrescia NGA, Palazón A, Marcelo F, Jimenez-Oses G, Jimenez-Barbero J, Arda A, Ereño-Orbea J

Abstract
The glycan structures of the receptor binding domain of the SARS-CoV2 spike glycoprotein expressed in human*HEK293F cells*have been studied by using NMR. The different possible interacting epitopes have been deeply analysed and characterized, providing evidence of the presence of glycan structures*not found*in previous MS-based analyses. The interaction of the RBD*13C-labelled glycans with different*human lectins, which are expressed in different organs and tissues that may be affected during the infection process, has also been evaluated by NMR. In particular,*15N-labelled galectins (galectins-3, -7 and -8 N-terminal), Siglecs (siglec-8, siglec-10), and C-type lectins (DC-SIGN, MGL) have been employed. Complementary experiments*from*the glycoprotein perspective or from the lectin's point of view have permitted to disentangle the specific interacting epitopes in each case. Based on these findings, 3D models of the interacting complexes have been proposed.


PMID: 32915505 [PubMed - as supplied by publisher]


... [Read More]
0 Replies | 31 Views
[NMR paper] Structural Biology of Human GPCR Drugs and Endogenous Ligands - Insights from NMR Spectroscopy.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar Structural Biology of Human GPCR Drugs and Endogenous Ligands - Insights from NMR Spectroscopy.

Structural Biology of Human GPCR Drugs and Endogenous Ligands - Insights from NMR Spectroscopy.

Methods. 2020 Sep 07;:

Authors: Ferré G, Eddy M

Abstract
G protein-coupled receptors (GPCRs) represent the largest class of "druggable" proteins in the human genome. For more than a decade, crystal structures and, more recently, cryoEM structures of GPCR complexes have provided unprecedented insight into GPCR drug binding and cell signaling. Nevertheless, structure determination of receptors in complexes with weakly binding molecules or complex polypeptides remains especially challenging, including for hormones, many of which have so far eluded researchers. Nuclear magnetic resonance (NMR) spectroscopy has emerged as a promising approach to determine structures of ligands bound to their receptors and to provide insights into the dynamics and pharmacokinetics of GPCR-bound drugs. The capability to investigate compounds with weak binding affinities has also been leveraged in NMR applications to identify novel lead compounds in drug screening campaigns. We review recent structural biology studies of GPCR ligands by NMR, highlighting new methodologies enabling studies of GPCRs with native sequences and in native-like membrane environments that provide insights into important drugs and endogenous ligands.


PMID: 32911074 [PubMed - as supplied by publisher]



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0 Replies | 20 Views
[NMR paper] Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle-Assisted NMR Spin Relaxation.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle-Assisted NMR Spin Relaxation.

Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle-Assisted NMR Spin Relaxation.

Angew Chem Int Ed Engl. 2020 Sep 09;:

Authors: Wardenfelt S, Xiang X, Xie M, Yu L, Bruschweiler-Li L, Bruschweiler R

Abstract
The quantitative and comprehensive description of the internal dynamics of proteins is critical for understanding their function. Nanoparticle-assisted 15 N NMR spin relaxation is a new method that uses a simple read-out allowing the observation of ps - ?s dynamics of proteins when transiently interacting with the surface of nanoparticles. The method is applied here to the widely studied protein human ubiquitin in the presence of anionic and cationic silica nanoparticles (SNP) of different size. The resulting backbone dynamics profiles are highly reproducible and strikingly similar to each other, indicating that, with the exception of the disordered tail, specific protein-SNP interactions are unimportant. The dynamics profiles closely match the sub-ns dynamics S 2 values observed by model-free analysis of standard 15 N relaxation of ubiquitin in free solution. These results indicate that the bulk of ubiquitin backbone dynamics in solution is confined to sub-ns timescales and, hence, it is dynamically considerably more restrained than some previous NMR studies have suggested.


PMID: 32909358 [PubMed - as supplied by publisher]



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0 Replies | 19 Views
[NMR paper] NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2.

NMR Structure and Dynamics Studies of Yeast Respiratory Supercomplex Factor 2.

Structure. 2020 Sep 03;:

Authors: Zhou S, Pettersson P, Huang J, Brzezinski P, Pomès R, Mäler L, Ädelroth P

Abstract
The Saccharomyces cerevisiae respiratory supercomplex factor 2 (Rcf2) is a 224-residue protein located in the mitochondrial inner membrane where it is involved in the formation of supercomplexes composed of cytochrome bc1 and cytochrome c oxidase. We previously demonstrated that Rcf2 forms a dimer in dodecylphosphocholine micelles, and here we report the solution NMR structure of this Rcf2 dimer. Each Rcf2 monomer has two soluble ? helices and five putative transmembrane (TM) ? helices, including an unexpectedly charged TM helix at the C terminus, which mediates dimer formation. The NOE contacts indicate the presence of inter-monomer salt bridges and hydrogen bonds at the dimer interface, which stabilize the Rcf2 dimer structure. Moreover, NMR chemical shift change mapping upon lipid titrations as well as molecular dynamics analysis reveal possible structural changes upon embedding Rcf2 into a native lipid environment. Our results contribute to the understanding of respiratory supercomplex formation and regulation.


PMID: 32905793 [PubMed - as supplied by... [Read More]
0 Replies | 15 Views
[NMR paper] Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii.

Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii.

FEBS J. 2020 Sep 09;:

Authors: Zahn S, Kubatova N, Pyper DJ, Cassidy L, Saxena K, Tholey A, Schwalbe H, Soppa J

Abstract
The genome of the halophilic archaeon Haloferax volcanii encodes more than 40 one-domain zinc finger µ-proteins. Only one of these, HVO_2753, contains four C(P)XCG motifs, suggesting the presence of two zinc binding pockets (ZBPs). Homologues of HVO_2753 are widespread in many euryarchaeota. An in frame deletion mutant HVO_2753 grew indistinguishably from the wildtype in several media, but had a severe defect in swarming and in biofilm formation. For further analyses the protein was produced homologously as well as heterologously in E. coli. HVO_2753 was stable and folded in low salt, in contrast to many other haloarchaeal proteins. Only haloarchaeal HVO_2753 homologs carry a very hydrophilic N-terminus, and NMR analysis showed that this region is very flexible and not part of the core structure. Surprisingly, both NMR analysis as well as a fluorimetric assay revealed that HVO_2753 binds only one zinc ion, despite the presence of two ZBPs. Notably, the... [Read More]
0 Replies | 21 Views
[NMR paper] A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

Related Articles A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

Glycobiology. 2020 Sep 08;:

Authors: Nestor G, Ruda A, Anderson T, Oscarson S, Widmalm G, Gronenborn AM

Abstract
Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Man?(1->2)Man?OMe and Man?(1->2) Man?(1->6)Man?OMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Man?(1->2)Man?(1->6)Man?OMe... [Read More]
0 Replies | 16 Views
[NMR paper] Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose.
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose.

Related Articles Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose.

Glycobiology. 2020 Sep 08;:

Authors: Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH

Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to... [Read More]
0 Replies | 22 Views
[NMR paper] NMR in target driven drug discovery: why not?
Sep 13, 2020 - 9:18 AM - by nmrlearner
nmrlearner's Avatar NMR in target driven drug discovery: why not?

Related Articles NMR in target driven drug discovery: why not?

J Biomol NMR. 2020 Sep 08;:

Authors: Keiffer S, Carneiro MG, Hollander J, Kobayashi M, Pogoryelev D, Ab E, Theisgen S, Müller G, Siegal G

Abstract
No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.


PMID: 32901320 [PubMed - as supplied by... [Read More]
0 Replies | 18 Views
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