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Biomolecular NMR Assignments

Naoto Iwakawa, Yutaka Mahana, Arina Ono, Izuru Ohki, Erik Walinda, Daichi Morimoto, Kenji Sugase, Masahiro Shirakawa
Epigenetic regulation is essential to various biological phenomena such as cell differentiation and cancer. DNA methylation is one of the most important epigenetic signals, as it is directly involved in gene silencing of transposable elements, genomic imprinting, and chromosome X inactivation. To mediate these processes, methyl-CpG-binding domain (MBD) proteins recognize specific signals encoded in the form of DNA methylation patterns. AtMBD6, one of the 12 MBD proteins in Arabidopsis thaliana, shares a high sequential homology in the MBD domain with mammalian MBD proteins, but a detailed characterization of its structural and functional properties remains elusive...
September 21, 2018: Biomolecular NMR Assignments
Luciana Coutinho de Oliveira, Laurent Volpon, Michael J Osborne, Katherine L B Borden
The dysregulation of translation contributes to many pathogenic conditions in humans. Discovering new translational mechanisms is important to understanding the diversity of this process and its potential mechanisms. Such mechanisms can be initially observed in viruses. With this in mind, we studied the viral protein genome-linked VPg factor from the largest genus of plant viruses. Studies in plants show that VPg binds to the eukaryotic translation initiation factor eIF4E for translation of viral RNAs. VPg contains no known eIF4E binding motifs and no sequence homology to any known proteins...
September 21, 2018: Biomolecular NMR Assignments
Jingyu Zhan, Md Alamgir Hossain, Ashish Sethi, Toyoyuki Ose, Gregory W Moseley, Paul R Gooley
The C-terminal domain of the P protein of rabies virus is a multifunctional domain that interacts with both viral and host cell proteins. Here we report the 1 H, 13 C and 15 N chemical shift assignments of this domain from P protein of the Nishigahara strain of rabies virus, a pathogenic laboratory strain well established for studies of virulence functions of rabies virus proteins, including P protein. The data and secondary structure analysis are in good agreement with the reported predominantly helical structure of the same domain from the CVS strain of rabies solved by crystallography...
September 20, 2018: Biomolecular NMR Assignments
Ashish Kabra, Catherine A Benson, Ying Li
Ubiquitination is one of the most prevalent forms of post-translational modifications that are important for regulating many cellular processes in eukaryotes. Deubiquitinases are proteases that hydrolyze the isopeptide or peptide bonds formed between ubiquitin and the target proteins or within a polyubiquitin chain. Deubiquitinase A (DUBA) is a deubiquitinase known to be a negative regulator of innate immune responses in humans by suppressing production of type I interferons (INF-I). Excess INF-I production has been associated with autoimmune diseases...
September 19, 2018: Biomolecular NMR Assignments
Khandekar Jishan Bari, Shrikant Sharma, Kandala V R Chary
The high solubility and stability of crystallins present in the human eye lens maintains its transparency and refractive index with negligible protein turnover. Monomeric γ-crystallins and oligomeric β-crystallins are made up of highly homologous double Greek key domains. These domains are symmetric and possess higher stability as a result of the complex topology of individual Greek key motifs. γS-crystallin is one of the most abundant structural βγ-crystallins present in the human eye lens. In order to understand the structural stability of individual domains of human γS-crystallin in isolation vis-à-vis full length protein, we set out to structurally characterize its C-terminal domain (abbreviated hereafter as γS-CTD) by solution NMR...
September 19, 2018: Biomolecular NMR Assignments
Janeka Gartia, Ravi Pratap Barnwal, Raveendra Anangi, Ashok R Giri, Glenn King, Kandala V R Chary
Helicoverpa species are polyphagous pests, with the larval stages causing major damage to economically valuable crops such as cotton, tomato, corn, sorghum, peas, sunflower, wheat and other pulses. Over the years, Helicoverpa armigera has developed resistance to most classes of chemical insecticides, and consequently it is now largely controlled on cotton plants via the use of Bt transgenic crops that express insecticidal Cry toxins which in-turn expedited resistance development in a number of pest species including H...
September 18, 2018: Biomolecular NMR Assignments
Steven A Beasley, Roela Bardhi, Donald E Spratt
ITCH (aka Atrophin-1-interacting protein 4) is a prominent member of the NEDD4 HECT (Homologous to E6AP C-Terminus) E3 ubiquitin ligase family that regulates numerous cellular functions including inflammatory responses through T-cell activation, cell differentiation, and apoptosis. Known intracellular targets of ITCH-dependent ubiquitylation include receptor proteins, signaling molecules, and transcription factors. The HECT C-terminal lobe of ITCH contains the conserved catalytic cysteine required for the covalent attachment of ubiquitin onto a substrate and polyubiquitin chain assembly...
September 18, 2018: Biomolecular NMR Assignments
Juan M Lopez, Ricardo Antiparra, Guy Lippens, Mirko Zimic, Patricia Sheen, Helena Maruenda
Chagas disease is a trypanosomiasis disease inflicted by Trypanosoma cruzi parasite. In Latin America, at least 10 million people are infected and annually, 10,000 casualties are deplored. Macrophage infectivity potentiator protein is one of the major virulence factors secreted by T. cruzi (TcMIP) in order to infect its host but little is known about its mechanism of action. Studies confer TcMIP an important role in the extracellular matrix transmigration and basal lamina penetration. Here, we report the backbone 1 H, 13 C, and 15 N resonance assignment of TcMIP and the comparison of the secondary structure obtained against reported X-ray crystallography data...
September 18, 2018: Biomolecular NMR Assignments
Wenbo Zhang, Cong Zhao, Yunfei Hu, Changwen Jin
The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated proteins in eukaryotic cells. It consists of a 20S barrel-shaped core particle capped by two 19S regulatory particle at both ends. The Rpn5 subunit is a non-ATPase subunit located in the lid subcomplex of the 19S regulatory particle and is identified to inhibit the Rpn11 deubiquitinase activity in the isolated lid. The protein contains a C-terminal proteasome-CSN-eIF3 (PCI) domain and an N-terminal α-solenoid domain, the latter has been shown to be highly flexible in the isolated lid and may participate in interactions with different subunits of the proteasome...
September 18, 2018: Biomolecular NMR Assignments
Dmitriy S Blokhin, Aydar G Bikmullin, Liliya I Nurullina, Natalia S Garaeva, Shamil Z Validov, Vladimir V Klochkov, Albert V Aganov, Iskander Sh Khusainov, Marat M Yusupov, Konstantin S Usachev
Ribosome binding factor A (RbfA) is a 14.9 kDa adaptive protein of cold shock, which is important for bacterial growth at low temperatures. RbfA can bind to the free 30S ribosomal subunit and interacts with the 5'-terminal helix (helix I) of 16S rRNA. RbfA is important for the efficient processing of 16S rRNA and for the maturation (assembly) of 30S ribosomal subunits. Here we report backbone and side chains 1 H, 13 C and 15 N chemical shift assignments of RbfA from Staphylococcus aureus. Analysis of the backbone chemical shifts by TALOS+ suggests that RbfA contains four α-helixes and three β-strands with α1-β1-β2-α2-α3-β3-α4 topology...
September 17, 2018: Biomolecular NMR Assignments
David P Bowles, Chunhua Yuan, Kimberly R Stephany, Jason J Lavinder, Alexandar L Hansen, Thomas J Magliery
Repressor of primer (Rop, or ROM, RNA I modulator) is a 63 amino acid four-helix bundle protein that exists in solution as an anti-parallel homodimer. This protein has been extensively studied, including by X-ray crystallography, NMR, rational design, and combinatorial mutagenesis. Previous NMR experiments with wild-type Rop were carried out at pH 2.3 and pH 6.3. In this paper, we report complete N-H backbone assignments for three variants of Rop under the same pH 6.3 conditions: wild-type Rop; a cysteine-free pseudo-wild type variant (C38A C52V); and a core-repacked variant of the Cys-free variant (T19V L41V C38A C52V)...
October 2018: Biomolecular NMR Assignments
Yoshihito Kitaoku, Gaston Courtade, Dejan M Petrović, Tamo Fukamizo, Vincent G H Eijsink, Finn L Aachmann
The apo-form of the 24.4 kDa AA9 family lytic polysaccharide monooxygenase TaLPMO9A from Thermoascus aurantiacus has been isotopically labeled and recombinantly expressed in Pichia pastoris. In this paper, we report the 1 H, 13 C, and 15 N chemical shift assignments, as well as an analysis of the secondary structure of the protein based on the secondary chemical shifts.
October 2018: Biomolecular NMR Assignments
Rebecca L Newcomer, Helen B Belato, Carolyn M Teschke, Andrei T Alexandrescu
Phage L encodes a trimeric 43 kDa decoration protein (Dec) that noncovalently binds and stabilizes the capsids of the homologous phages L and P22 in vitro. At physiological pH Dec was unsuitable for NMR. We were able to obtain samples amenable for NMR spectroscopy by unfolding Dec to pH 2 and refolding it to pH 4. Our unfolding/refolding protocol converted trimeric Dec to a folded 14.4 kDa monomer. We verified that the acid-unfolding protocol did not perturb the secondary structure, or the capsid-binding function of refolded Dec...
October 2018: Biomolecular NMR Assignments
Konstantin S Usachev, Alexander A Golubev, Shamil Z Validov, Vladimir V Klochkov, Albert V Aganov, Iskander Sh Khusainov, Marat M Yusupov
Elongation Factor P (EF-P) is a 20.5 kDa protein that provides specialized translation of special stalling amino acid motifs. Proteins with stalling motifs are often involved in various processes, including stress resistance and virulence. Thus it has been shown that the virulent properties of microorganisms can be significantly reduced if the work of EF-P is disrupted. In order to elucidate the structure, dynamics and function of EF-P from Staphylococcus aureus (S. aureus), here we report backbone and side chains 1 H, 13 C and 15 N chemical shift assignments of EF-P...
October 2018: Biomolecular NMR Assignments
Donald Gagné, Chitra Narayanan, Khushboo Bafna, Laurie-Anne Charest, Pratul K Agarwal, Nicolas Doucet
After publication of this article, the authors noticed that a 15 N-13 C dimension error was unwillingly coded in the 3D NMR spectrum "" processing script used to perform backbone assignments for this enzyme. The authors noticed that some OBS, CAR and LAB values in the "" had been switched in the y and z dimensions, probably resulting from a wrong NMRPipe selection when reading the Varian NMR experimental parameters. They have carefully re-processed, re-analyzed, re-assigned, in addition to checking all scripts to evaluate the extent of this processing error on the published assignments...
October 2018: Biomolecular NMR Assignments
Bin Liu, Shiqi Fang, Xiaofang Ma, Zhiqiang Bai, Kaifeng Hu
MarH is an essential epimerase that catalyzes the isomerization of 3R-β-methyl-indolepyruvate (β-MeInPy) to 3S-β-MeInPy, which is the important precursor for biosynthesis of Maremycins. Biophysical study of the structure of MarH would be informative for better understanding of its catalytic mechanism and feasible application of the enzyme in isomerization reaction. Here, we report the backbone and side-chain NMR chemical shift assignments of MarH, which lays a foundation for further structural and mechanical study of the enzyme...
October 2018: Biomolecular NMR Assignments
A Katharina Weickhmann, Heiko Keller, Elke Duchardt-Ferner, Elisabeth Strebitzer, Michael A Juen, Johannes Kremser, Jan Philip Wurm, Christoph Kreutz, Jens Wöhnert
Riboswitches are structured RNA elements in the 5'-untranslated regions of bacterial mRNAs that are able to control the transcription or translation of these mRNAs in response to the specific binding of small molecules such as certain metabolites. Riboswitches that bind with high specificity to either S-adenosylmethionine (SAM) or S-adenosylhomocysteine (SAH) are widespread in bacteria. Based on differences in secondary structure and sequence these riboswitches can be grouped into a number of distinct classes...
October 2018: 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.
October 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...
October 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...
October 2018: Biomolecular NMR Assignments
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