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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...
February 23, 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...
February 16, 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 (K d 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...
February 16, 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...
February 16, 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...
February 15, 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...
February 14, 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...
January 25, 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)...
January 25, 2018: Biomolecular NMR Assignments
Lucila Andrea Acevedo, Linda K Nicholson
Cyclophilins are enzymes that catalyze the isomerization of a prolyl-peptide bond and are found in both prokaryotes and eukaryotes. LRT2 (also known as OsCYP2) is a cyclophilin in rice (Oryza sativa), that has importance in lateral root development and stress tolerance. LRT2 is 172 amino acids long and has a molecular weight of 18.3 kDa. Here, we report the backbone and sidechain resonance assignments of 1H, 13C, 15N in the LRT2 protein using several 2D and 3D heteronuclear NMR experiments at pH 6.7 and 298 K...
January 20, 2018: Biomolecular NMR Assignments
Munirah S Abd Rahim, Lisa A M Sommer, Anja Wacker, Martin Schaad, Sonja A Dames
FAT C-terminal (FATC) is a circa 33 residue-long domain. It controls the kinase functionality in phosphatidylinositol-3 kinase-related kinases (PIKKs). Recent NMR- and CD-monitored interaction studies indicated that the FATC domains of all PIKKs can interact with membrane mimetics albeit with different preferences for membrane properties such as surface charge and curvature. Thus they may generally act as membrane anchoring unit. Here, we present the 1H, 15N, and 13C chemical shift assignments of the DPC micelle immersed FATC domains of the human PIKKs ataxia-telangiectasia mutated (ATM, residues 3024-3056) and DNA protein kinase catalytic subunit (DNA-PKcs, residues 4096-4128), both fused to the 56 residue long B1 domain of Streptococcal protein G (GB1)...
January 18, 2018: Biomolecular NMR Assignments
Usha Yadav, Monica Sundd
Glycine cleavage complex H protein (GcvH) is one of the four components that form the glycine cleavage complex (GCS), essential for the synthesis of C1 (one-carbon units) for cell metabolism, by the oxidative cleavage of glycine. The activity of this complex is induced in the presence of exogenous glycine, and is repressed by purines. GCS, in cooperation with GCA (serine hydroxymethyltransferase) regulates the endogenous levels of glycine and C1 units in the cell. GcvH, the lipoamide containing component of the complex, plays an indispensable role in this reaction, as its prosthetic group shuttles between the active site of the three other components of the GCS complex sequentially...
January 15, 2018: Biomolecular NMR Assignments
Valéry Larue, Marjorie Catala, Anissa Belfetmi, Loussiné Zargarian, Olivier Mauffret, Carine Tisné
During HIV-1 assembly, the Pr55Gag polyprotein precursor (Gag) interacts with the genomic RNA, with lipids of the plasma membrane, with host proteins (ALIX, TSG101) through the ESCRT complex, with the viral protein Vpr and are involved in intermolecular interactions with other Pr55Gag proteins. This network of interactions is responsible for the formation of the viral particle, the selection of genomic RNA and the packaging of Vpr. The C-terminal domain of Gag encompassed in NCp15 is involved in the majority of these interactions, either by its nucleocapsid or its p6 domains...
January 13, 2018: Biomolecular NMR Assignments
Rui Wang, Jiahai Zhang, Shanhui Liao, Xiaoming Tu
Neural precursor cell-expressed, developmently downregulated 8 (NEDD8) is a small ubiquitin-like modifier, which plays important roles in many cellular processes. Although it has been well studied in many eukaryotes, NEDD8 is still uncharacterized in some unicellular parasites, such as Trypanosoma brucei (T. brucei). Here we report the resonance assignments of NEDD8 from T. brucei.
January 11, 2018: Biomolecular NMR Assignments
Sunghyuk Lim, Diana Cudia, Qinhong Yu, Igor Peshenko, Alexander M Dizhoor, James B Ames
Retinal degeneration 3 protein (RD3) binds to retinal membrane guanylyl cyclase (RetGC) and suppresses the basal activity of RetGC in photoreceptor cells that opposes the allosteric activation of the cyclase by GCAP proteins. Mutations in RD3 that disrupt its inhibition of RetGC are implicated in human retinal degenerative disorders. Here we report both backbone and sidechain NMR assignments for the RD3 protein (BMRB accession no. 27305).
January 11, 2018: Biomolecular NMR Assignments
Chunjie Liang, Ting He, Tao Li, Yunhuang Yang, Jiang Zhu, Maili Liu
AHSA1 protein family is one of the four largest families in the Bet v1-like protein superfamily. The functions and structures of proteins in AHSA1 family are still largely unknown. CHU_1110 with 167 amino acids and a molecular weight of 19.2 kDa is a member of the AHSA1 family from Cytophaga hutchinsonii, a soil bacterium known for its ability to digest crystalline cellulose. Here we report the complete 1H, 13C and 15N chemical shift assignments of CHU_1110. The secondary structural elements of CGL2373 are consistent with the canonical AHSA1 structure...
January 9, 2018: Biomolecular NMR Assignments
Xiaofang Ma, Yingying Zhang, Bin Liu, Jiahui Yang, Kaifeng Hu
Receptor tyrosine kinase-like orphan receptor 1 (ROR1) expresses at high level in many cancers and has been suggested as a potential therapeutic target. It was reported that the Kringle (KNG) domain of ROR1 extracellular region is involved in ROR1/ROR2 heterooligomerization. Monoantibodies that target KNG domain of ROR1 could induce apoptosis of chronic lymphocytic leukemia cells. Here we present the backbone and side chain assignments of KNG domain of ROR1, which lays a foundation for its further structural and function research...
January 8, 2018: Biomolecular NMR Assignments
Xinhui Kou, Xinghong Liu, Yixiang Liu, Conggang Li, Maili Liu, Ling Jiang
PhoB is a response regulator of the PhoR/PhoB two-component signal transduction system that is involved in the regulation of the phosphate (Pho) regulon of Escherichia coli. PhoB has two domains, receiver domain and effector domain. The receiver domain can be phosphorylated by its cognate histidine kinase PhoR and the phosphorylation induces conformational changes of the full length protein of PhoB that promote the DNA binding and transcription. Three-dimensional crystal structures of PhoB receiver domain (PhoBN) have been solved under apo or BeF3- (a phosphoryl analog) binding forms and it has been found that PhoBN is dimerized in both situations...
January 3, 2018: Biomolecular NMR Assignments
Denis Martinez, Valérie Prouzet-Mauléon, Michel Hugues, François Doignon, Benoît Odaert
The protein Rgd1 is involved in the regulation of cytoskeleton formation and in signalling pathways that control cell polarity and growth in Saccharomyces cerevisiae. Rgd1p is composed of a F-BAR domain required for membrane binding and a RhoGAP domain responsible for activating Rho3p and Rho4p, two GTPases respectively involved in bud growth and cytokinesis. Rgd1p is recruited to the membrane through interactions with phosphoinositide lipids, which bind the two isolated domains and stimulate the RhoGAP activity on Rho4p...
December 26, 2017: Biomolecular NMR Assignments
Fabien Kieken, Karine Loth, Nico van Nuland, Peter Tompa, Tom Lenaerts
Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the1 H,15 N and13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains...
December 9, 2017: Biomolecular NMR Assignments
Julien Marquevielle, M V Vasantha Kumar, Jean-Louis Mergny, Gilmar F Salgado
Single stranded guanine rich DNA (or RNA) sequences adopt noncanonical secondary structures called G-quadruplexes (G4). Functionally, quadruplexes control gene transcription and regulate activities such as replication, gene recombination or alternative splicing. Hence they are potential targets for cancer, neuronal, and viral related diseases. KRAS is one of the most mutated oncogenes in the genome of cancer cells and contains a nuclease hypersensitive element (NHE) sequence capable of forming G-quadruplexes via its six runs of guanines...
November 30, 2017: Biomolecular NMR Assignments
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