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Biomolecular NMR Assignments

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https://www.readbyqxmd.com/read/28091961/-1-h-13-c-and-15-n-backbone-and-side-chain-resonance-assignments-of-the-znf-ubp-domain-of-usp20-vdu2
#1
Yuanyuan Yang, Yi Wen, Naixia Zhang
Deubiquitinase USP20/VDU2 has been identified as a regulator of multiple proteins including hypoxia-inducible factor (HIF)-1α, β2-adrenergic receptor, and tumor necrosis factor receptor associated factor 6 etc. It contains four structural domains, including an N-terminal zinc-finger ubiquitin binding domain (ZnF-UBP) that potentially helps USP20 to recruit its ubiquitin substrates. Here we report the (1)H, (13)C and (15)N backbone and side-chain resonance assignments of the ZnF-UBP domain of USP20/VDU2. The BMRB accession number is 26901...
January 13, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28032262/nmr-assignments-and-ligand-binding-studies-on-a-two-domain-family-gh19-chitinase-allergen-from-japanese-cedar-cryptomeria-japonica-pollen
#2
Tomoya Takashima, Takayuki Ohnuma, Tamo Fukamizo
A two-domain family GH19 chitinase from Japanese cedar (Cryptomeria japonica) pollen, CJP-4, which consists of an N-terminal CBM18 domain and a GH19 catalytic domain, is known to be an important allergen, that causes pollinosis. We report here the resonance assignments of the NMR spectrum of CJP-4. The backbone resonances were almost completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of a chitin dimer to the enzyme solution perturbed the chemical shifts of the resonances of amino acid residues forming a long extended binding site spanning from the CBM18 domain to the GH19 catalytic domain...
December 28, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28025808/backbone-resonance-assignments-of-monomeric-sod1-in-dilute-and-crowded-environments
#3
Naoto Iwakawa, Daichi Morimoto, Erik Walinda, Kenji Sugase, Masahiro Shirakawa
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that leads to movement disorders. In motor neurons of ALS patients, intracellular aggregates of superoxide dismutase 1 (SOD1) have often been observed. To elucidate the aggregation mechanism, it is important to analyze the folding equilibrium of SOD1 between folded and aggregation-prone unfolded states. However, in most cases, this folding equilibrium has been studied in dilute solution even though the aggregate formation occurs in a highly crowded intracellular environment...
December 26, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28004358/-13-c-and-15-n-chemical-shift-assignments-of-mammalian-y145stop-prion-protein-amyloid-fibrils
#4
Theint Theint, Philippe S Nadaud, Krystyna Surewicz, Witold K Surewicz, Christopher P Jaroniec
The Y145Stop prion protein (PrP23-144), which has been linked to the development of a heritable prionopathy in humans, is a valuable in vitro model for elucidating the structural and molecular basis of amyloid seeding specificities. Here we report the sequential backbone and side-chain (13)C and (15)N assignments of mouse and Syrian hamster PrP23-144 amyloid fibrils determined by using 2D and 3D magic-angle spinning solid-state NMR. The assigned chemical shifts were used to predict the secondary structures for the core regions of the mouse and Syrian hamster PrP23-144 amyloids, and the results compared to those for human PrP23-144 amyloid, which has previously been analyzed by solid-state NMR techniques...
December 21, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27990612/-1-h-13-c-and-15-n-nmr-assignments-of-an-unusual-ca-2-binding-protein-from-entamoeba-histolytica-in-its-apo-form
#5
Deepshikha Verma, Mutyala Sakuntala, Aruna Murmu, Alok Bhattacharya, Kandala V R Chary
We report almost complete sequence specific (1)H, (13)C and (15)N NMR assignments of an unusual Ca(2+)-binding protein from Entamoeba histolytica (EhCaBP6) in its apo form as a prelude to its structural and functional characterization.
December 19, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27981425/-1-h-15-n-13-c-backbone-resonance-assignments-of-human-soluble-catechol-o-methyltransferase-in-complex-with-s-adenosyl-l-methionine-and-3-5-dinitrocatechol
#6
Sylwia Czarnota, Nicola J Baxter, Matthew J Cliff, Jonathan P Waltho, Nigel S Scrutton, Sam Hay
Catechol O-methyltransferase (COMT) is an enzyme that plays a major role in catechol neurotransmitter deactivation. Inhibition of COMT can increase neurotransmitter levels, which provides a means of treatment for Parkinson's disease, schizophrenia and depression. COMT exists as two isozymes: a soluble cytoplasmic form (S-COMT), expressed in the liver and kidneys and a membrane-bound form (MB-COMT), found mostly in the brain. Here we report the backbone (1)H, (15)N and (13)C chemical shift assignments of S-COMT in complex with S-adenosyl-L-methionine, 3,5-dinitrocatechol and Mg(2+)...
December 15, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27981424/backbone-chemical-shift-assignments-and-secondary-structure-analysis-of-the-u1-protein-from-the-bas-congo-virus
#7
Garry W Buchko, Matthew C Clifton, Ellen G Wallace, Kateri A Atkins, Peter J Myler
The Bas-Congo virus (BASV) is the first rhabdovirus associated with a human outbreak of acute hemorrhagic fever. The single-stranded, negative-sense RNA genome of BASV contains the five core genes present in all rhabdoviral genomes plus an additional three genes, annotated U1, U2, and U3, with weak (<21%) sequence similarity only to a handful of genes observed in a few other rhabdoviral genomes. The function of the rhabdoviral U proteins is unknown, but, they are hypothesized to play a role in viral infection or replication...
December 15, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27943001/-1-h-13-c-and-15-n-resonance-assignments-of-the-new-lysostaphin-family-endopeptidase-catalytic-domain-from-staphylococcus-aureus
#8
Vytas Raulinaitis, Helena Tossavainen, Olli Aitio, Raili Seppala, Perttu Permi
Lysostaphin family endopeptidases, produced by Staphylococcus genus, are zinc-dependent enzymes that cleave pentaglycine bridges of cell wall peptidoglycan. They act as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Consequently, these enzymes are compelling targets for new drugs as well as are potential antimicrobial agents themselves against Staphylococcus pathogens, which depend on cell wall to retain their immunity against antibiotics. The rapid spread of methicillin and vancomycin-resistant Staphylococcus aureus strains draws demand for new therapeutic approaches...
December 9, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27804064/backbone-resonance-assignments-of-the-f-actin-binding-domain-of-mouse-%C3%AE-n-catenin
#9
Tadateru Nishikawa, Noboru Ishiyama, Feng Wang, Mitsuhiko Ikura
α-Catenin is a filamentous actin (F-actin) binding protein that links the classical cadherin-catenin complex to the actin cytoskeleton at adherens junctions (AJs). Its C-terminal F-actin binding domain is required for regulating the dynamic interaction between AJs and the actin cytoskeleton during tissue development. Thus, obtaining the molecular details of this interaction is a crucial step towards understanding how α-catenin plays critical roles in biological processes, such as morphogenesis, cell polarity, wound healing and tissue maintenance...
November 1, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27798771/nmr-assignments-for-the-insertion-domain-of-bacteriophage-sf6-coat-protein
#10
Therese N Tripler, Carolyn M Teschke, Andrei T Alexandrescu
The P22 bacteriophage group is a subgroup of the λ phage supercluster, comprised of the three major sequence types Sf6, P22, and CUS-3, based on their capsid proteins. Our goal is to investigate the extent to which structure-function relationships are conserved for the viral coat proteins and I-domains in this subgroup. Sf6 is a phage that infects the human pathogen Shigella flexneri. The coat protein of Sf6 assembles into a procapsid, which further undergoes maturation during DNA packaging into an infectious virion...
October 31, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27771830/solid-state-nmr-chemical-shift-assignments-for-al-09-vl-immunoglobulin-light-chain-fibrils
#11
Dennis W Piehl, Luis M Blancas-Mejía, Marina Ramirez-Alvarado, Chad M Rienstra
Light chain (AL) amyloidosis is a systemic disease characterized by the formation of immunoglobulin light-chain fibrils in critical organs of the body. The light-chain protein AL-09 presents one severe case of cardiac AL amyloidosis, which contains seven mutations in the variable domain (VL) relative to its germline counterpart, κI O18/O8 VL. Three of these mutations are non-conservative-Y87H, N34I, and K42Q-and previous work has shown that they are responsible for significantly reducing the protein's thermodynamic stability, allowing fibril formation to occur with fast kinetics and across a wide-range of pH conditions...
October 22, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27738883/backbone-assignment-of-the-binary-complex-of-the-full-length-sulfolobus-solfataricus-dna-polymerase-iv-and-dna
#12
Eunjeong Lee, Jason D Fowler, Zucai Suo, Zhengrong Wu
Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several β-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes...
October 13, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27730489/nmr-resonance-assignments-for-the-tetramethylrhodamine-binding-rna-aptamer-3-in-complex-with-the-ligand-5-carboxy-tetramethylrhodamine
#13
Elke Duchardt-Ferner, Michael Juen, Christoph Kreutz, Jens Wöhnert
RNA aptamers are used in a wide range of biotechnological or biomedical applications. In many cases the high resolution structures of these aptamers in their ligand-complexes have revealed fundamental aspects of RNA folding and RNA small molecule interactions. Fluorescent RNA-ligand complexes in particular find applications as optical sensors or as endogenous fluorescent tags for RNA tracking in vivo. Structures of RNA aptamers and aptamer ligand complexes constitute the starting point for rational function directed optimization approaches...
October 11, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27714507/nmr-assignments-of-the-gacs-histidine-kinase-periplasmic-detection-domain-from-pseudomonas-aeruginosa-pao1
#14
Ahmad Ali-Ahmad, Olivier Bornet, Firas Fadel, Yves Bourne, Florence Vincent, Christophe Bordi, Françoise Guerlesquin, Corinne Sebban-Kreuzer
Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen. It can infect vulnerable patients such as those with cystic fibrosis or hospitalized in intensive care units where it is responsible for both acute and chronic infection. The switch between these infections is controlled by a complex regulatory system involving the central GacS/GacA two-component system that activates the production of two small non-coding RNAs. GacS is a histidine kinase harboring one periplasmic detection domain, two inner-membrane helices and three H1/D1/H2 cytoplasmic domains...
October 6, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27709416/-1-h-15-n-and-13-c-resonance-assignments-for-free-and-ieevd-peptide-bound-forms-of-the-tetratricopeptide-repeat-domain-from-the-human-e3-ubiquitin-ligase-chip
#15
Huaqun Zhang, Cameron McGlone, Matthew M Mannion, Richard C Page
The ubiquitin ligase CHIP catalyzes covalent attachment of ubiquitin to unfolded proteins chaperoned by the heat shock proteins Hsp70/Hsc70 and Hsp90. CHIP interacts with Hsp70/Hsc70 and Hsp90 by binding of a C-terminal IEEVD motif found in Hsp70/Hsc70 and Hsp90 to the tetratricopeptide repeat (TPR) domain of CHIP. Although recruitment of heat shock proteins to CHIP via interaction with the CHIP-TPR domain is well established, alterations in structure and dynamics of CHIP upon binding are not well understood...
October 5, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27704363/backbone-1-h-15-n-and-13-c-resonance-assignments-of-the-tom1-vhs-domain
#16
Jeffrey F Ellena, Wen Xiong, Xiaolin Zhao, Narasimhamurthy Shanaiah, Daniel G S Capelluto
Efficient trafficking of ubiquitinated receptors (cargo) to endosomes requires the recruitment of adaptor proteins that exhibit ubiquitin-binding domains for recognition and transport. Tom1 is an adaptor protein that not only associates with ubiquitinated cargo but also represents a phosphoinositide effector during specific bacterial infections. This phosphoinositide-binding property is associated with its N-terminal Vps27, Hrs, STAM (VHS) domain. Despite its biological relevance, there are no resonance assignments of Tom1 VHS available that can fully characterize its molecular interactions...
October 4, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27699617/backbone-and-side-chain-resonance-assignments-of-plasmodium-falciparum-sumo
#17
Jai Shankar Singh, Vaibhav Kumar Shukla, Mansi Gujrati, Ram Kumar Mishra, Ashutosh Kumar
One of the most debilitating diseases Malaria, in its different forms, is caused by protozoan of Plasmodium species. Deadliest among these forms is the "cerebral malaria" which is afflicted upon by Plasmodium falciparum. Plasmodium adopts numerous strategies including various post-translational modifications (PTMs) to infect and survive in the human host. These PTMs have proven their critical requirement in the Plasmodium biology. Recently, sumoylation has been characterized as one of the important PTMs and many of its putative substrates have been identified in Plasmodium...
October 3, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27699616/backbone-and-methyl-resonance-assignments-of-the-42%C3%A2-kda-human-hsc70-nucleotide-binding-domain-in-the-adp-state
#18
Erik R P Zuiderweg, Jason E Gestwicki
Hsc70 is the constitutively expressed mammalian heat shock 70 kDa (Hsp70) cytosolic chaperone. It plays a central role in cellular proteostasis and protein trafficking. Here, we present the backbone and methyl group assignments for the 386-residue nucleotide binding domain of the human protein. This domain controls the chaperone's allostery, binds multiple co-chaperones and is the target of several classes of known chemical Hsp70 inhibitors. The NMR assignments are based on common triple resonance experiments with triple labeled protein, and on several (15)N and (13)C-resolved 3D NOE experiments with methyl-reprotonated samples...
October 3, 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27638737/-1-h-13-c-and-15-n-resonance-assignments-and-secondary-structure-information-for-methylobacterium-extorquens-pqqd-and-the-complex-of-pqqd-with-pqqa
#19
Robert L Evans, John A Latham, Judith P Klinman, Carrie M Wilmot, Youlin Xia
The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. RiPPs represent a rapidly expanding and diverse class of natural products-many of which have therapeutic potential-and the biosynthetic pathways for these are gaining attention. Five gene products from the pqq operon (PqqA, PqqB, PqqC, PqqD, and PqqE) are essential for PQQ biosynthesis. The substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD...
October 2016: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27632081/chemical-shift-assignment-of-the-intrinsically-disordered-n-terminus-and-the-rubredoxin-domain-in-the-folded-metal-bound-and-unfolded-oxidized-state-of-mycobacterial-protein-kinase-g
#20
Matthias Wittwer, Sonja A Dames
Mycobacterium tuberculosis protein kinase G (PknG) is a 82 kDa multidomain eukaryotic-like serine/threonine kinase mediating the survival of pathogenic mycobacteria within host macrophages. The N-terminal sequence preceding the catalytic kinase domain contains an approximately 75 residues long tail, which was predicted to show no regulatory secondary structure (1-75 = NORS) but harbors the major in vivo phosphorylation site (T63), and a rubredoxin-like metal binding motif (74-147 = RD). In the reduced rubredoxin motif, four conserved cysteine residues that are present as two C-X-X-C-G motifs coordinate a metal ion...
October 2016: Biomolecular NMR Assignments
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