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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
Srinivasan Sundararaj, Dmitry Shishmarev, Yiechang Lin, Shouvik Aditya, Marco G Casarotto
Ahnak is a ~ 700 kDa polypeptide that was originally identified as a tumour-related nuclear phosphoprotein, but later recognized to play a variety of diverse physiological roles related to cell architecture and migration. A critical function of Ahnak is modulation of Ca2+ signaling in cardiomyocytes by interacting with the β subunit of the L-type Ca2+ channel (CaV 1.2). Previous studies have identified the C-terminal region of Ahnak, designated as P3 and P4 domains, as a key mediator of its functional activity...
March 28, 2018: Biomolecular NMR Assignments
Sosuke Yoshinaga, Norihito Ishida, Tatsuichiro Tsuji, Akihiro Sonoda, Kaori Yunoki, Mitsuhiro Takeda, Etsuko Toda, Yuya Terashima, Kouji Matsushima, Hiroaki Terasawa
FROUNT is a cytoplasmic protein that interacts with the membrane-proximal C-terminal regions (Pro-Cs) of the CCR2 and CCR5 chemokine receptors. The interactions between FROUNT and the chemokine receptors play an important role in the migration of inflammatory immune cells. Therefore, FROUNT is a potential drug target for inflammatory diseases. However, the structural basis of the interactions between FROUNT and the chemokine receptors remains to be elucidated. We previously identified the C-terminal region (residues 532-656) of FROUNT as the structural domain responsible for the Pro-C binding, referred to as the chemokine receptor-binding domain (CRBD), and then constructed its mutant, bearing L538E/P612S mutations, with improved NMR spectral quality, referred to as CRBD_LEPS...
March 28, 2018: Biomolecular NMR Assignments
Elena Rostkova, Selena G Burgess, Richard Bayliss, Mark Pfuhl
The microtubule regulatory protein colonic and hepatic tumor overexpressed gene (chTOG), also known as cytoskeleleton associated protein 5 (CKAP5) plays an important role in organizing the cytoskeleton and in particular in the assembly of k-fibres in mitosis. Recently, we dissected the hitherto poorly understood C-terminus of this protein by discovering two new domains-a cryptic TOG domain (TOG6) and a smaller, helical domain at the very C-terminus. It was shown that the C-terminal domain is important for the interaction with the TACC domain in TACC3 during the assembly of k-fibres in a ternary complex that also includes clathrin...
March 26, 2018: Biomolecular NMR Assignments
Florian Celli, Ambre Petitalot, Camille Samson, François-Xavier Theillet, Sophie Zinn-Justin
Lamins are the main components of the nucleoskeleton. They form a protein meshwork that underlies the inner nuclear membrane. Mutations in the LMNA gene coding for A-type lamins (lamins A and C) cause a large panel of human diseases, referred to as laminopathies. These diseases include muscular dystrophies, lipodystrophies and premature aging diseases. Lamin A exhibits a C-terminal region that is different from lamin C and is post-translationally modified. It is produced as prelamin A and it is then farnesylated, cleaved, carboxymethylated and cleaved again in order to become mature lamin A...
March 26, 2018: Biomolecular NMR Assignments
Domenico Sanfelice, Hans Koss, Tom D Bunney, Gary S Thompson, Brendan Farrell, Matilda Katan, Alexander L Breeze
Fibroblast growth factors receptors (FGFR) are transmembrane protein tyrosine kinases involved in many cellular process, including growth, differentiation and angiogenesis. Dysregulation of FGFR enzymatic activity is associated with developmental disorders and cancers; therefore FGFRs have become attractive targets for drug discovery, with a number of agents in late-stage clinical trials. Here, we present the backbone resonance assignments of FGFR3 tyrosine kinase domain in the ligand-free form and in complex with the canonical FGFR kinase inhibitor PD173074...
March 26, 2018: Biomolecular NMR Assignments
David Bolton, Leonid S Brown, Vladimir Ladizhansky
Anabaena Sensory Rhodopsin (ASR) is a unique photochromic membrane-embedded photosensor which interacts with soluble transducer and is likely involved in a light-dependent gene regulation in the cyanobacterium Anabaena sp. PCC 7120. We report partial spectroscopic1 H,13 C and15 N assignments of perdeuterated and back-exchanged ASR reconstituted in lipids. The reported assignments are in general agreement with previously determined assignments of carbon and nitrogen resonances in fully protonated samples. Because the back-exchange was performed on ASR in a detergent-solubilized state, the location of detected residues reports on the solvent accessibility of ASR in detergent...
March 23, 2018: Biomolecular NMR Assignments
Tao Li, Shuangli Li, Chunjie Liang, Jiang Zhu, Maili Liu, Yunhuang Yang
The nuclear transport factor 2 (NTF2) like superfamily includes members of the NTF2 family, delta-5-3-ketosteroid isomerases, and the beta subunit of ring hydroxygenases. This family plays important roles in both eukaryotic and prokaryotic cells, and is taken as a classic example of divergent evolution because proteins in this family exhibit diverse biological functions, although share common structural features. We cloned the gene RHE_RS02845 encoding a predicted NTF2-like domain-containing protein in Rhizobium etli, and prepared U-13 C/15 N-labeled protein samples for its three-dimensional NMR structural determination...
March 23, 2018: Biomolecular NMR Assignments
Benoit Bragantini, Clément Rouillon, Bruno Charpentier, Xavier Manival, Marc Quinternet
We report the nearly complete1 H,15 N and13 C resonance assignment and the solution structure of the external DII domain of the yeast Rvb2 protein, a member of the AAA+ATPase superfamily.
March 22, 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
Alvaro I Herrera, Nicoleta T Ploscariu, Brian V Geisbrecht, Om Prakash
Staphylococcus aureus is a widespread and persistent pathogen of humans and livestock. The bacterium expresses a wide variety of virulence proteins, many of which serve to disrupt the host's innate immune system from recognizing and clearing bacteria with optimal efficiency. The extracellular adherence protein (Eap) is a multidomain protein that participates in various protein-protein interactions that inhibit the innate immune response, including both the complement system (Woehl et al in J Immunol 193:6161-6171, 2014) and Neutrophil Serine Proteases (NSPs) (Stapels et al in Proc Natl Acad Sci USA 111:13187-13192, 2014)...
April 2018: Biomolecular NMR Assignments
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