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Biomolecular NMR Assignments

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https://www.readbyqxmd.com/read/28593560/-1-h-13-c-and-15-n-nmr-chemical-shift-assignments-of-a-thaliana-rcd1-rst
#1
Helena Tossavainen, Maarit Hellman, Julia P Vainonen, Jaakko Kangasjärvi, Perttu Permi
The A. thaliana RCD1 (radical-induced cell death1) protein is a cellular signaling hub protein which interacts with numerous plant transcription factors from different families. It consists of three conserved domains and intervening unstructured regions, the C-terminal RST domain being responsible for the interactions with the transcription factors. It has been shown that many partner proteins interact with RCD1 RST via their intrinsically disordered regions, and that the domain is able to house partners with divergent folds...
June 7, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28593559/-1-h-13-c-and-15-n-nmr-assignments-of-a-bacterial-immunoglobulin-like-domain-group-2-of-a-protein-of-a-bacterium-paenarthrobacter-aurescens-tc1
#2
Asmita D Pawar, Deepshikha Verma, Rajeev Raman, Yogendra Sharma, Kandala V R Chary
The bacterial immunoglobulin-like (Big) domain is one of the prevalent domain types, which facilitates cell-cell adhesion by assembling into multi-domain architectures. We selected a four Big_2 domain protein (named 'Arig') from a Gram positive, Paenarthrobacter aurescens TC1 (known earlier as Arthrobacter aurescens TC1). In an attempt to characterize structural and ligand-binding features of individual Big_2 domains, we have cloned, overexpressed, isolated and purified the second Big_2 domain of Arig along with a few of its adjacent Big_2 domain residues (residue 143 to 269) referred to as 'Arig2'...
June 7, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28589219/-1-h-13-c-and-15-n-backbone-chemical-shift-assignments-of-4e-bp144-87-and-4e-bp144-87-bound-to-eif4e
#3
Naotaka Sekiyama, Andras Boeszoermenyi, Haribabu Arthanari, Gerhard Wagner, Mélissa Léger-Abraham
The eukaryotic translational initiation factor 4G (eIF4G) interacts with the cap-binding protein eIF4E through a consensus binding motif, Y(X)4LΦ (where X is any amino acid and Φ is a hydrophobic residue). 4E binding proteins (4E-BPs), which also contain a Y(X)4LΦ motif, regulate the eIF4E/eIF4G interaction. The non- or minimally-phosphorylated form of 4E-BP1 binds eIF4E, preventing eIF4E from interacting with eIF4G, thus inhibiting translation initiation. 4EGI-1, a small molecule inhibitor of the eIF4E/eIF4G interaction that is under investigation as a novel anti-cancer drug, has a dual activity; it disrupts the eIF4E/eIF4G interaction and stabilizes the binding of 4E-BP1 to eIF4E...
June 6, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28589218/h-n-n-c-%C3%AE-and-c-%C3%AE-assignments-of-the-two-periplasmic-domains-of-neisseria-meningitidis-dsbd
#4
Roxanne P Smith, Biswaranjan Mohanty, Martin L Williams, Martin J Scanlon, Begoña Heras
DsbD is a disulfide bond reductase present in the inner membrane of many Gamma-Proteobacteria. In the human pathogen Neisseria meningitidis, DsbD is required for viability and represents a potential target for the development of antibiotics. Here we report the chemical shift assignments (H(N), N, C(α) and C(β)) for the reduced and oxidized forms of the two periplasmic domains of N. meningitidis DsbD, n-NmDsbD and c-NmDsbD. The backbone amide resonances in all four forms were completely assigned, and the secondary structures for the core regions of the proteins were calculated using (13)C(αβ) shifts...
June 6, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28573456/backbone-nmr-assignments-of-tryparedoxin-the-central-protein-in-the-hydroperoxide-detoxification-cascade-of-african-trypanosomes-in-the-oxidized-and-reduced-form
#5
Annika Wagner, Erika Diehl, R Luise Krauth-Siegel, Ute A Hellmich
Tryparedoxin (Tpx) is a pivotal protein in the redox-metabolism of trypanosomatid parasites. Tpx has previously been identified as a potential target for drug development in the fight against human African sleeping sickness caused by Trypanosoma brucei. Tpx belongs to the thioredoxin superfamily and acts as an oxidoreductase in the parasite's cytoplasm. It contains a WCPPC active site motif, which enables the protein to undergo thiol-disulfide exchange. To promote future protein-drug interaction analyses, we report the (1)H, (13)C and (15)N backbone chemical shift assignments for both the oxidized and reduced states of Tpx...
June 1, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28560616/-1-h-13-c-and-15-n-backbone-and-sidechain-resonance-assignments-of-a-monomeric-variant-of-e-coli-deoxyribose-5-phosphate-aldolase
#6
Marianne Schulte, Matthias Stoldt, Philipp Neudecker, Jӧrg Pietruszka, Dieter Willbold, Vineet Panwalkar
Deoxyribose-5-phosphate aldolase (DERA) catalyses the reversible conversion of 2-deoxyribose-5-phosphate (dR5P) into glyceraldehyde-3-phosphate (G3P) and acetaldehyde. For industrial applications, this enzyme is used in organic synthesis for aldol reactions between acetaldehyde as a donor and a wide range of aldehydes as acceptors. Here, we present a near complete set of sequence-specific (1)H, (13)C and (15)N resonance assignments of a 28 kDa monomeric variant of the Escherichia coli DERA. These assignments provide the basis for ongoing structural and dynamic analysis of DERA substrate specificity...
May 30, 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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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