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Biomolecular NMR Assignments

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https://www.readbyqxmd.com/read/28284018/chemical-shift-assignments-of-the-first-and-second-rrms-of-nrd1-a-fission-yeast-mapk-target-rna-binding-protein
#1
Ayaho Kobayashi, Teppei Kanaba, Ryosuke Satoh, Yutaka Ito, Reiko Sugiura, Masaki Mishima
Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1...
March 11, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28284017/backbone-assignments-for-the-spout-methyltransferase-mtt-tm-a-knotted-protein-from-thermotoga-maritima
#2
David J Burban, Patricia A Jennings
The SPOUT family of methyltransferase proteins is noted for containing a deep trefoil knot in their defining backbone fold. This unique fold is of high interest for furthering the understanding of knots in proteins. Here, we report the (1)H, (13)C, (15)N assignments for MTT Tm , a canonical member of the SPOUT family. This protein is unique, as it is one of the smallest members of the family, making it an ideal system for probing the unique properties of the knot. Our present work represents the foundation for further studies into the topology of MTT Tm , and understanding how its structure affects both its folding and function...
March 10, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28275980/-1-h-15-n-13-c-resonance-assignment-of-plant-dehydrin-early-response-to-dehydration-10-erd10
#3
Cesyen Cedeño, Szymon Żerko, Peter Tompa, Wiktor Koźmiński
Early response to dehydration 10 protein (ERD10) is an intrinsically disordered protein from Arabidopsis thaliana. The protein is upregulated during stress however its mechanism of action at atomic level is not well understood. In the present work multidimensional NMR methodologies are used in order to facilitate the process of chemical shift assignment. The information provided here supports further NMR spectroscopy experiments aimed at elucidation of ERD10 behaviour during molecular recognition events with other proteins...
March 8, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28271277/sequence-specific-backbone-resonance-assignments-and-microsecond-timescale-molecular-dynamics-simulation-of-human-eosinophil-derived-neurotoxin
#4
Donald Gagné, Chitra Narayanan, Khushboo Bafna, Laurie-Anne Charest, Pratul K Agarwal, Nicolas Doucet
Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response...
March 7, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28265855/nmr-resonance-assignments-for-the-n-terminal-domain-of-the-%C3%AE-subunit-of-the-e-coli-%C3%AE-clamp-loader-complex
#5
Esmael M Alyami, Alessandro A Rizzo, Penny J Beuning, Dmitry M Korzhnev
The β-clamp protein and the γ clamp loader complex are essential components of bacterial DNA replication machinery. The β-clamp is a ring-shaped homodimer that encircles DNA and increases the efficiency of replication by providing a binding platform for DNA polymerases and other replication-related proteins. The β-clamp is loaded onto DNA by the five-subunit γ clamp loader complex in a multi-step ATP-dependent process. The initial steps of this process involve the cooperative binding of the β-clamp by the five subunits of ATP-bound clamp loader, which induces or traps an open conformation of the clamp...
March 6, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28260216/near-complete-backbone-resonance-assignments-of-acid-denatured-human-cytochrome-c-in-dimethylsulfoxide-a-prelude-to-studying-interactions-with-phospholipids
#6
Andreas Ioannis Karsisiotis, Oliver M Deacon, Colin Macdonald, Tharin M A Blumenschein, Geoffrey R Moore, Jonathan A R Worrall
Human cytochrome c plays a central role in the mitochondrial electron transfer chain and in the intrinsic apoptosis pathway. Through the interaction with the phospholipid cardiolipin, cytochrome c triggers release of pro-apoptotic factors, including itself, from the mitochondrion into the cytosol of cells undergoing apoptosis. The cytochrome c/cardiolipin complex has been extensively studied through various spectroscopies, most recently with high-field solution and solid-state NMR spectroscopies, but there is no agreement between the various studies on key structural features of cytochrome c in its complex with cardiolipin...
March 4, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28258550/chemical-shift-assignments-of-ribosomal-protein-s1-from-mycobacterium-tuberculosis
#7
Jinglin Fu, Biling Huang, Donghai Lin, Xinli Liao
RpsA, also known as ribosomal protein S1, is an essential protein required for translation initiation of mRNAs when their Shine-Dalgarno sequence is degenerated (Sorensen et al. 1998). In addition, RpsA of Mycobacterium tuberculosis (M. tb) is involved in trans-translation, which is an effective system mediated by tmRNA-SmpB to release stalled ribosomes from mRNA in the presence of rare codons (Keiler 2008). Shi et al. found that POA binds to RpsA of Mtb and disrupts the formation of RpsA-tmRNA complex (Shi et al...
March 4, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28258549/backbone-and-side-chain-resonance-assignments-for-the-tmrna-binding-protein-smpb-from-mycobacterium-tuberculosis
#8
Juanjuan Yang, Yindi Liu, Zhao Liu, Chun Meng, Donghai Lin
Small protein B (SmpB) is an essential molecule in trans-translation which is a universal biological pathway for protein synthesis in bacteria. Trans-translation can release stalled ribosomes from defective mRNAs and target tag-protein fragments for degradation, and then restart protein synthesis. The SmpB-tmRNA complex coordinating with other components of the trans-translation system, plays vital roles in Mycobacterium tuberculosis under both stress conditions and non-replicating conditions. Thus, elucidation of molecular details and dynamic properties of the SmpB-tmRNA interaction is a crucial step towards effectively blocking trans-translation process to shorten the duration of tuberculosis treatment...
March 4, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28258548/backbone-resonance-assignments-of-the-escherichia-coli-62%C3%A2-kda-protein-hsp31
#9
Jihong Kim, Dongwook Choi, Chankyu Park, Kyoung-Seok Ryu
Dimeric Hsp31 protein was first characterized as a holding chaperone of Escherichia coli (E. coli), and has been suggested as having protease activity due to the presence of a potential catalytic triad, Cys185, His186, and Asp214. However, it has recently been reported that Hsp31 displays a relatively strong glyoxalase III activity that can decompose reactive carbonyl species (methylglyoxal and glyoxal) in the absence of additional cofactor. Hsp31 is a representative member of the DJ-1/ThiJ/PfpI protein superfamily, and the importance of DJ-1 protein in Parkinson's disease has been well known...
March 3, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28258547/-1-h-15-n-and-13-c-resonance-assignments-and-secondary-structure-of-pulg-the-major-pseudopilin-from-klebsiella-oxytoca-type-2-secretion-system
#10
Aracelys López-Castilla, Bruno Vitorge, Léa Khoury, Nelly Morellet, Olivera Francetic, Nadia Izadi-Pruneyre
Bacteria use complex transporters to secrete functionally relevant proteins to the extracellular medium. The type 2 secretion system (T2SS) translocates folded proteins involved in bacterial nutrient acquisition, virulence and adaptation. The T2SS pseudopilus is a periplasmic filament, assembled by the polymerization of PulG subunits, the major pseudopilin. Pseudopilin proteins have a conserved N-terminal hydrophobic segment followed by a more variable C-terminal periplasmic and globular domain. To better understand the mechanism of assembly and function of the T2SS, we have been studying the structure and dynamics of PulG by NMR, as well as its interaction with other components of the secretion machinery...
March 3, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28251507/chemical-shift-assignments-of-the-connexin37-carboxyl-terminal-domain
#11
Hanjun Li, Gaelle Spagnol, Tasha K Pontifex, Janis M Burt, Paul L Sorgen
Connexin37 (Cx37) is a gap junction protein involved in cell-to-cell communication in the vasculature and other tissues. Cx37 suppresses proliferation of vascular cells involved in tissue development and repair in vivo, as well as tumor cells. Global deletion of Cx37 in mice leads to enhanced vasculogenesis in development, as well as collateralgenesis and angiogenesis in response to injury, which together support improved tissue remodeling and recovery following ischemic injury. Here we report the (1)H, (15)N, and (13)C resonance assignments for an important regulatory domain of Cx37, the carboxyl terminus (CT; C233-V333)...
March 1, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28247282/backbone-1-h-13-c-and-15-n-nmr-resonance-assignments-of-the-kr%C3%A3-ppel-like-factor-4-activation-domain
#12
Brigid S Conroy, Emma R Weiss, Steven P Smith, David N Langelaan
Krüppel-like factor 4 (KLF4) is a transcription factor involved in diverse biological processes, including development, cellular differentiation and proliferation, and maintenance of tissue homeostasis. KLF4 has also been associated with disease states, such as cardiovascular disease and several cancers. KLF4 contains an activation domain, repression domain, and a structurally characterized C-terminal zinc finger domain that mediates its binding to DNA. The structurally uncharacterized KLF4 activation domain is critical for transactivation by KLF4 and mediates its binding to the transcriptional coactivator CBP/p300...
February 28, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28239762/-1-h-13-c-and-15-n-backbone-chemical-shift-assignments-of-camelid-single-domain-antibodies-against-active-state-%C3%A2%C2%B5-opioid-receptor
#13
Remy Sounier, Yinshan Yang, Joanna Hagelberger, Sébastien Granier, Hélène Déméné
Nanobodies are single chain antibodies that have become a highly valuable and versatile tool for biomolecular and therapeutic research. One application field is the stabilization of active states of flexible proteins, among which G-protein coupled receptors represent a very important class of membrane proteins. Here we present the backbone and side-chain assignment of the (1)H, (13)C and (15)N resonances of Nb33 and Nb39, two nanobodies that recognize and stabilize the µ-opioid receptor to opioids in its active agonist-bound conformation...
April 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28236226/nmr-resonance-assignments-of-the-fkbp-domain-of-human-aryl-hydrocarbon-receptor-interacting-protein-like-1-aipl1-in-complex-with-a-farnesyl-ligand
#14
Liping Yu, Ravi P Yadav, Nikolai O Artemyev
Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a specialized chaperone of phosphodiesterase 6, a key effector enzyme in the phototransduction cascade. The FKBP domain of AIPL1 is known to bind the farnesyl moiety of PDE6. Mutations in AIPL1, including many missense mutations in the FKBP domain, have been associated with Leber congenital amaurosis, a severe blinding disease. Here, we report the backbone and sidechain assignments of the N-terminal FKBP(Δloop) (with a loop deletion) of AIPL1 in complex with a farnesyl ligand...
April 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28004358/-13-c-and-15-n-chemical-shift-assignments-of-mammalian-y145stop-prion-protein-amyloid-fibrils
#15
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...
April 2017: 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
#16
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+)...
April 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27798771/nmr-assignments-for-the-insertion-domain-of-bacteriophage-sf6-coat-protein
#17
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...
April 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/27771830/solid-state-nmr-chemical-shift-assignments-for-al-09-vl-immunoglobulin-light-chain-fibrils
#18
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...
April 2017: 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
#19
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...
April 2017: 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
#20
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...
April 2017: Biomolecular NMR Assignments
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