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Biomolecular NMR Assignments

Xiaofang Ma, Yingying Zhang, Bin Liu, Jiahui Yang, Kaifeng Hu
The authors would like to include an additional institution to their affiliation which was initially not included in the original publication of the article.
June 28, 2018: Biomolecular NMR Assignments
Huayong Xie, Yongxiang Zhao, Jing Wang, Zhengfeng Zhang, Jun Yang
Aquaporin Z is the first identified prokaryotic water channel in Escherichia coli with a high water permeability and strict substrate selectivity. Here we report nearly complete (94% of amino acid residues) 13 C and 15 N chemical shift assignments of AqpZ reconstituted in the lipid bilayers using a set of 2D and 3D magic angle spinning solid-state NMR spectra. Secondary structure of AqpZ predicted from chemical shift assignments is generally similar to that of X-ray structure with a number of differences in loop and near-loop regions...
June 25, 2018: Biomolecular NMR Assignments
Carina Immer, Carolin Hacker, Jens Wöhnert
Regulation of gene expression on a post-transcriptional level by small non-coding regulatory RNAs (sRNAs) is very common in bacteria. sRNAs base pair with sequences in their target messenger RNAs (mRNAs) and thereby regulate translation initiation or mRNA stability. Specialized RNA-binding proteins (RBPs) facilitate these regulatory sRNA/mRNA interactions by acting as RNA chaperones. A well-known example for such an RNA chaperone which is widespread in bacteria is the Hfq protein. Recently, the ProQ/FinO protein family was identified as a new class of RNA chaperones involved in sRNA based regulation...
June 22, 2018: Biomolecular NMR Assignments
Michael J Osborne, Luciana Coutinho de Oliveira, Laurent Volpon, Katherine L B Borden
A major component of phase II drug metabolism is the covalent addition of glucuronic acid to metabolites and xenobiotics. This activity is carried out by UDP-glucuronosyltransferases (UGT) which bind the UDP-glucuronic acid donor and catalyze the covalent addition of glucuronic acid sugar moieties onto a wide variety of substrates. UGTs play important roles in drug detoxification and were recently shown to act in an inducible form of multi-drug resistance in cancer patients. Despite their biological importance, structural understanding of these enzymes is limited...
June 22, 2018: Biomolecular NMR Assignments
David P Bowles, Alexandar L Hansen, Calvin A Rhoads, Sidharth Mohan, Chunhua Yuan, Thomas J Magliery
Er-23 is a small, 51 amino acid, disulfide-rich pheromone protein used for cell signaling by Euplotes raikovi. Ten of the 51 amino acids are cysteine, allowing up to five disulfide bonds. Previous NMR work with Er-23 utilized homologously expressed protein, prohibiting isotopic labeling, and consequently the chemical shift assignments were incomplete. We have expressed uniformly 15 N and 13 C-labeled Er-23 in an E. coli expression system. Here we report the full backbone and side chain resonance assignments for recombinant Er-23...
June 6, 2018: Biomolecular NMR Assignments
Antoine Baudin, Anne Guichard, Gavin W Collie, Sabrina Rousseau, Stéphane Chaignepain, Agnès Hocquellet, Mélanie Berbon, Antoine Loquet, Cameron Mackereth, Gilles Guichard, Benoît Odaert
Death receptors (DR) selectively drive cancer cells to apoptosis upon binding to the Tumor necrosis factor-a-Related Apoptosis-Inducing Ligand (TRAIL). Complex formation induces the oligomerization of the death receptors DR4 (TRAIL-R1) and DR5 (TRAIL-R2) and transduces the apoptogenic signal to their respective death domains, leading to Death Inducing Signaling Complex (DISC) formation, caspase activation and ultimately cell death. Several crystal structures of the ExtraCellular Domain from Death Receptor 5 (DR5-ECD) have been reported in complex with the TRAIL ligand or anti-DR5 antibodies, but none for the isolated protein...
June 5, 2018: Biomolecular NMR Assignments
Sofia S Mariasina, Olga A Petrova, Ilya A Osterman, Olga V Sergeeva, Sergey V Efimov, Vladimir V Klochkov, Petr V Sergiev, Olga A Dontsova, Tai-Huang Huang, Chi-Fon Chang, Vladimir I Polshakov
Williams-Beuren syndrome is a genetic disorder characterized by physiological and mental abnormalities, and is caused by hemizygous deletion of several genes in chromosome 7. One of the removed genes encodes the WBSCR27 protein. Bioinformatic analysis of the sequence of WBSCR27 indicates that it belongs to the family of SAM-dependent methyltransferases. However, exact cellular functions of this protein or phenotypic consequences of its deficiency are still unknown. Here we report nearly complete 1 H, 15 N, and 13 C chemical shifts assignments of the 26 kDa WBSCR27 protein from Mus musculus in complex with the cofactor S-adenosyl-L-methionine (SAM)...
June 4, 2018: Biomolecular NMR Assignments
Jeffrey A Purslow, Vincenzo Venditti
N6 -methyladenosine (m6 A) is the most abundant and reversible post-transcriptional modification in eukaryotic mRNA and long non-coding RNA (lncRNA). The central role of m6 A in various physiological processes has generated considerable biological and pharmacological interest. Alkbh5 (AlkB homologue 5) belongs to the AlkB family and is a non-heme Fe(II)/α-ketoglutarate-dependent dioxygenase that selectively catalyzes the oxidative demethylation of m6 A. Herein, we report the backbone 1 H, 15 N, 13 C chemical shift assignment of a fully active, 26 kDa construct of human Alkbh5...
June 1, 2018: Biomolecular NMR Assignments
Jayneil R Patel, Yingqi Xu, Claudia Capitini, Fabrizio Chiti, Alfonso De Simone
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...
May 21, 2018: Biomolecular NMR Assignments
Holly M Isbell, Adina M Kilpatrick, Zesen Lin, Ryan Mahling, Madeline A Shea
Human voltage-gated sodium (NaV ) channels are critical for initiating and propagating action potentials in excitable cells. Nine isoforms have different roles but similar topologies, with a pore-forming α-subunit and auxiliary transmembrane β-subunits. NaV pathologies lead to debilitating conditions including epilepsy, chronic pain, cardiac arrhythmias, and skeletal muscle paralysis. The ubiquitous calcium sensor calmodulin (CaM) binds to an IQ motif in the C-terminal tail of the α-subunit of all NaV isoforms, and contributes to calcium-dependent pore-gating in some channels...
May 4, 2018: Biomolecular NMR Assignments
Alok K Sharma, Seung-Joo Lee, Alan C Rigby, Sharon A Townson
K-Ras is a key driver of oncogenesis, accounting for approximately 80% of Ras-driven human cancers. The small GTPase cycles between an inactive, GDP-bound and an active, GTP-bound state, regulated by guanine nucleotide exchange factors and GTPase activating proteins, respectively. Activated K-Ras regulates cell proliferation, differentiation and survival by signaling through several effector pathways, including Raf-MAPK. Oncogenic mutations that impair the GTPase activity of K-Ras result in a hyperactivated state, leading to uncontrolled cellular proliferation and tumorogenesis...
May 2, 2018: Biomolecular NMR Assignments
Glaucia M S Pinheiro, Gisele C Amorim, Anwar Iqbal, C H I Ramos, Fabio C L Almeida
Protein folding in the cell is usually aided by molecular chaperones, from which the Hsp70 (Hsp = heat shock protein) family has many important roles, such as aiding nascent folding and participating in translocation. Hsp70 has ATPase activity which is stimulated by binding to the J-domain present in co-chaperones from the Hsp40 family. Hsp40s have many functions, as for instance the binding to partially folded proteins to be delivered to Hsp70. However, the presence of the J-domain characterizes Hsp40s or, by this reason, as J-proteins...
April 30, 2018: Biomolecular NMR Assignments
Christian Köhler, Göran Carlström, Stefan Tångefjord, Tineke Papavoine, Matti Lepistö, Karl Edman, Mikael Akke
The glucocorticoid receptor (GR) is a nuclear hormone receptor that regulates key genes controlling development, metabolism, and the immune response. GR agonists are efficacious for treatment of inflammatory, allergic, and immunological disorders. Steroid hormone binding to the ligand-binding domain (LBD) of GR is known to change the structural and dynamical properties of the receptor, which in turn control its interactions with DNA and various co-regulators and drive the pharmacological response. Previous biophysical studies of the GR LBD have required the use of mutant forms to overcome issues with limited protein stability and high aggregation propensity...
April 17, 2018: Biomolecular NMR Assignments
Alexander M Barclay, Dhruva D Dhavale, Joseph M Courtney, Paul T Kotzbauer, Chad M Rienstra
Fibrils of the protein α-synuclein (α-syn) are implicated in the pathogenesis of Parkinson's disease and related neurodegenerative disorders. We have reported a high-resolution structure (PDB 2N0A) of an α-syn fibril form prepared by in vitro incubation of monomeric protein in 50 mM sodium phosphate buffer pH 7.4 with 0.1 mM EDTA and 0.01% sodium azide. In parallel with this structure determination, ongoing studies of small molecule ligands binding to α-syn fibrils, prepared in 2-amino-2-(hydroxymethyl)-1,3-propanediol (Tris) buffer, have been in progress, and it is therefore of interest to determine the structural similarity of these forms...
April 2018: Biomolecular NMR Assignments
Rina Yogo, Saeko Yanaka, Koichi Kato
Fcγ receptor (FcγR) promotes various immune responses through interactions with the Fc portion of immunoglobulin G (IgG). FcγRIIIb is a glycosylphosphatidylinositol-linked protein expressed on neutrophils and triggers degranulation and opsonic phagocytosis. The extracellular region of FcγR is composed of two Ig-fold domains and can be cleaved as a soluble form (sFcγRIIIb), which is also reactive with complement receptor type 3. Although structure and Fc interaction of sFcγRIIIb have been characterized by X-ray crystallography, little has been known about its structure in solution...
April 2018: Biomolecular NMR Assignments
Olena Dobrovolska, Maxim Bril'kov, Øyvind Ødegård-Fougner, Rein Aasland, Øyvind Halskau
The ASHH2 CW domain is responsible for recognizing the methylation state at lysine 4 of histone 3 N-terminal tails and implicated in the recruitment of the ASHH2 methyltransferase enzyme correctly to the histones. The ASHH2 CW domain binds H3 lysine motifs that can be either mono-, di-, or tri-methylated [ARTK(meX)QTAR, where X denotes the number of methylations], but binds strongest to monomethylated instances (Kd values reported in the range of 1 µm to 500 nM). Hoppmann et al. published the uncomplexed NMR structure of an ASHH2 CW domain in 2011...
April 2018: Biomolecular NMR Assignments
Lauriane Lecoq, Shishan Wang, Thomas Wiegand, Stéphane Bressanelli, Michael Nassal, Beat H Meier, Anja Böckmann
Each year, nearly 900,000 deaths are due to serious liver diseases caused by chronic hepatitis B virus infection. The viral particle is composed of an outer envelope and an inner icosahedral nucleocapsid formed by multiple dimers of a ~ 20 kDa self-assembling core protein (Cp). Here we report the solid-state 13 C and 15 N resonance assignments of the assembly domain, Cp149, of the core protein in its capsid form. A secondary chemical shift analysis of the 140 visible residues suggests an overall alpha-helical three-dimensional fold matching that derived for Cp149 from the X-ray crystallography of the capsid, and from solution-state NMR of the Cp149 dimer...
April 2018: Biomolecular NMR Assignments
Danyun Zeng, Benjamin P Brown, Markus W Voehler, Sheng Cai, Nicholas J Reiter
Ribonuclase P (RNase P) is an essential metallo-endonuclease that catalyzes 5' precursor-tRNA (ptRNA) processing and exists as an RNA-based enzyme in bacteria, archaea, and eukaryotes. In bacteria, a large catalytic RNA and a small protein component assemble to recognize and accurately cleave ptRNA and tRNA-like molecular scaffolds. Substrate recognition of ptRNA by bacterial RNase P requires RNA-RNA shape complementarity, intermolecular base pairing, and a dynamic protein-ptRNA binding interface. To gain insight into the binding specificity and dynamics of the bacterial protein-ptRNA interface, we report the backbone and side chain 1 H, 13 C, and 15 N resonance assignments of the hyperthermophilic Thermatoga maritima RNase P protein in solution at 318 K...
April 2018: Biomolecular NMR Assignments
Harshad Paithankar, Pankaj V Jadhav, Amit S Naglekar, Shilpy Sharma, Jeetender Chugh
TAR RNA binding protein (TRBP) is a double-stranded RNA binding protein involved in various biological processes like cell growth, development, death, etc. The protein exists as two isoforms TRBP2 and TRBP1. TRBP2 contains additional 21 amino acids at its N-terminus, which are proposed to be involved in its membrane localization, when compared to TRBP1. The resonance assignment (19-228) of the double-stranded RNA binding domains (dsRBD 1 and 2) of TRBP2 has been reported earlier. Here, we report 1 H, 13 C and 15 N resonance assignment for dsRBD1 of TRBP2 (1-105) containing the additional N-terminal residues...
April 2018: Biomolecular NMR Assignments
Michael Feichtinger, Tomáš Sára, Gerald Platzer, Borja Mateos, Fedir Bokhovchuk, Patrick Chène, Robert Konrat
Yes associated protein (YAP) is an intrinsically disordered protein that plays a major role in the Hippo pathway, regulating organ size, cell proliferation, apoptosis, and is associated with cancer development. Therefore, the binding between YAP and TEAD is an interesting target for cancer therapy. The TEAD binding domain of YAP was mapped to protein residues 50-171. To obtain further structural insights into this 12 kDa segment of YAP, we report a backbone and a partial sidechain assignment of recombinant YAP 50-171...
April 2018: Biomolecular NMR Assignments
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