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Biomolecular NMR Assignments

Chao Chen, Hongwu Yang, Jinsong Xuan, Qiu Cui, Yingang Feng
Cellulosomes are highly efficient multienzyme complexes for lignocellulose degradation secreted by some lignocellulolytic bacteria. Cellulosomes are assembled through protein modules named cohesin and dockerin, and multiple cohesin modules in the scaffold protein generally determine the complexity of the cellulosomes. Some cellulosomal proteins contain multiple dockerin modules, which may generate more complex cellulosomal architectures. Genome mining revealed that cellulosomal proteins containing double dockerin modules and a protease module exist in many cellulosome-producing bacteria, and these proteins together with cellulosomal protease inhibitors were proposed to have regulatory roles...
October 30, 2018: Biomolecular NMR Assignments
João Filipe Neves, Isabelle Landrieu, Hamida Merzougui, Emmanuelle Boll, Xavier Hanoulle, François-Xavier Cantrelle
14-3-3 proteins are a group of seven dimeric adapter proteins that exert their biological function by interacting with hundreds of phosphorylated proteins, thus influencing their sub-cellular localization, activity or stability in the cell. Due to this remarkable interaction network, 14-3-3 proteins have been associated with several pathologies and the protein-protein interactions (PPIs) established with a number of partners are now considered promising drug targets. The activity of 14-3-3 proteins is often isoform specific and to our knowledge only one out of seven isoforms, 14-3-3[Formula: see text], has been assigned...
October 30, 2018: Biomolecular NMR Assignments
Faith Aguilar, Niaz Banaei, Yonghong Zhang
Clostridium difficile is a gram-positive, toxin-producing, anaerobic bacterium whose virulence factors and mechanisms of pathogenesis require further investigation. C. difficile infections (CDI) result in the severe and potentially fatal gastrointestinal diseases pseudomembranous colitis and toxic megacolon following extensive broad spectrum antibiotic treatment. The increasing C. difficile fatalities are a result of the bacteria's growing antibiotic resistance and consequential CDI recurrence, which led to the unmet need for new CDI treatment...
October 28, 2018: Biomolecular NMR Assignments
Alexandra Born, Parker J Nichols, Morkos A Henen, Celestine N Chi, Dean Strotz, Peter Bayer, Shin-Ichi Tate, Jeffrey W Peng, Beat Vögeli
Pin1 is a human peptidyl-prolyl cis-trans isomerase important for the regulation of phosphoproteins that are implicated in many diseases including cancer and Alzheimer's. Further biophysical study of Pin1 will elucidate the importance of the two-domain system to regulate its own activity. Here, we report near-complete backbone and side-chain 1 H, 13 C and 15 N NMR chemical shift assignments of full-length, apo Pin1 for the purpose of studying interdomain allostery and dynamics.
October 23, 2018: Biomolecular NMR Assignments
Liping Yu, Ravi P Yadav, Nikolai O Artemyev
Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a photoreceptor-specific chaperone of phosphodiesterase-6, a key effector enzyme in the phototransduction cascade. It contains an N-terminal FK506-binding protein (FKBP) domain and a C-terminal tetratricopeptide repeat (TPR) domain. Mutations in AIPL1, including many missense mutations in both FKBP and TPR domains, have been associated with Leber congenital amaurosis, a severe inherited retinopathy that causes blindness. TPR-domain containing proteins are known to interact with HSP90...
October 19, 2018: Biomolecular NMR Assignments
Yao Nie, Shuangli Li, Jiang Zhu, Rui Hu, Maili Liu, Ting He, Yunhuang Yang
Nanobodies (Nbs) are the variable domain of the heavy-chain antibodies produced from Camelidae, which possess comparable binding affinities and specificity to conventional antibodies. Nbs have become valuable and versatile tools for numerous biotechnology applications due to their small size (12-15 kDa), high solubility, exceptional stability, and facile genetic manipulation. The interactions between Nbs and protein antigens have been well-studied, but less work has been done to characterize their ability to bind small molecule haptens...
October 16, 2018: Biomolecular NMR Assignments
Yan Li, Wenhe Zhong, Ann Zhufang Koay, Hui Qi Ng, Xiaoying Koh-Stenta, Qianhui Nah, Siau Hoi Lim, Andreas Larsson, Julien Lescar, Jeffrey Hill, Peter C Dedon, CongBao Kang
Bacterial tRNA (guanine37 -N1 )-methyltransferase (TrmD) is an important antibacterial target due to its essential role in translation. TrmD has two domains connected with a flexible linker. The N-terminal domain (NTD) of TrmD contains the S-adenosyl-L-methionine (SAM) cofactor binding site and the C-terminal domain is critical for tRNA binding. Here we report the backbone NMR resonance assignments for NTD of Pseudomonas aeruginosa TrmD. Its secondary structure was determined based on the assigned resonances...
October 8, 2018: Biomolecular NMR Assignments
Matthew P Pond, Lydia Blachowicz, Benoît Roux
Hematopoietic cell kinase (Hck) is an important signaling enzyme and a potential drug target for HIV infections and Bcr/Abl-chronic myeloid leukemia. The protein shares the same SH4-Unique-SH3-SH2-kinase multi-domain architecture as the other eight members of the Src family of non-receptor tyrosine kinases. These enzymes are often found anchored to the intracellular side of the membrane via lipidation of the SH4 domain and are integral components of signaling cascades localized at the cell surface. Despite the detailed structural information available for the SH3, SH2, and kinase domains of Hck, the intrinsically disordered nature of the SH4 and Unique domains has resulted in a lack of information for this important region of the protein that is responsible for membrane association...
October 4, 2018: Biomolecular NMR Assignments
Rachel J Coulthard, Karthik V Rajasekar, Jon P Ride, Eva I Hyde, Lorna J Smith
The SPH proteins are a large family of small, disulphide-bonded, secreted proteins, originally found to be involved in the self-incompatibility response in the field poppy (Papaver rhoeas). They are now known to be widely distributed in plants, many containing multiple members of this protein family. Apart from the PrsS proteins in Papaver the function of these proteins is unknown but they are thought to be involved in plant development and cell signalling. There has been no structural study of SPH proteins to date...
October 3, 2018: Biomolecular NMR Assignments
Brandon F Young, Braden M Roth, Christopher Davies
Gonorrhea infections are becoming more difficult to treat due to the prevalence of strains exhibiting resistance to antibiotics and new therapeutic approaches are needed. N-acetylmuramyl-L-alanine amidase (AmiC) from Neisseria gonorrhoeae is a hydrolase that functions during cell division by cleaving the bond between the N-acetylmuramyl and L-alanine moieties of peptidoglycan. Inhibiting this enzyme offers the prospect of restoring the efficacy of existing antibiotics as treatments against N. gonorrhoeae. Of its two domains, the C-terminal domain catalyses the hydrolysis reaction and the N-terminal domain (NTD) is believed to target AmiC to its peptidoglycan substrate...
October 1, 2018: Biomolecular NMR Assignments
Eva Madland, Yoshihito Kitaoku, Gerd Inger Sætrom, Maria Louise Leth, Morten Ejby, Maher Abou Hachem, Finn Lillelund Aachmann
The N-terminal domain (residues 28-165) from the glycoside hydrolase family 10 from Roseburia intestinalis (RiCBMx), has been isotopically labeled and recombinantly expressed in Escherichia coli. Here we report 1 H, 13 C and 15 N NMR chemical shift assignments for this carbohydrate binding module (CBM).
September 22, 2018: Biomolecular NMR Assignments
Naoto Iwakawa, Yutaka Mahana, Arina Ono, Izuru Ohki, Erik Walinda, Daichi Morimoto, Kenji Sugase, Masahiro Shirakawa
Epigenetic regulation is essential to various biological phenomena such as cell differentiation and cancer. DNA methylation is one of the most important epigenetic signals, as it is directly involved in gene silencing of transposable elements, genomic imprinting, and chromosome X inactivation. To mediate these processes, methyl-CpG-binding domain (MBD) proteins recognize specific signals encoded in the form of DNA methylation patterns. AtMBD6, one of the 12 MBD proteins in Arabidopsis thaliana, shares a high sequential homology in the MBD domain with mammalian MBD proteins, but a detailed characterization of its structural and functional properties remains elusive...
September 21, 2018: Biomolecular NMR Assignments
Luciana Coutinho de Oliveira, Laurent Volpon, Michael J Osborne, Katherine L B Borden
The dysregulation of translation contributes to many pathogenic conditions in humans. Discovering new translational mechanisms is important to understanding the diversity of this process and its potential mechanisms. Such mechanisms can be initially observed in viruses. With this in mind, we studied the viral protein genome-linked VPg factor from the largest genus of plant viruses. Studies in plants show that VPg binds to the eukaryotic translation initiation factor eIF4E for translation of viral RNAs. VPg contains no known eIF4E binding motifs and no sequence homology to any known proteins...
September 21, 2018: Biomolecular NMR Assignments
Jingyu Zhan, Md Alamgir Hossain, Ashish Sethi, Toyoyuki Ose, Gregory W Moseley, Paul R Gooley
The C-terminal domain of the P protein of rabies virus is a multifunctional domain that interacts with both viral and host cell proteins. Here we report the 1 H, 13 C and 15 N chemical shift assignments of this domain from P protein of the Nishigahara strain of rabies virus, a pathogenic laboratory strain well established for studies of virulence functions of rabies virus proteins, including P protein. The data and secondary structure analysis are in good agreement with the reported predominantly helical structure of the same domain from the CVS strain of rabies solved by crystallography...
September 20, 2018: Biomolecular NMR Assignments
Ashish Kabra, Catherine A Benson, Ying Li
Ubiquitination is one of the most prevalent forms of post-translational modifications that are important for regulating many cellular processes in eukaryotes. Deubiquitinases are proteases that hydrolyze the isopeptide or peptide bonds formed between ubiquitin and the target proteins or within a polyubiquitin chain. Deubiquitinase A (DUBA) is a deubiquitinase known to be a negative regulator of innate immune responses in humans by suppressing production of type I interferons (INF-I). Excess INF-I production has been associated with autoimmune diseases...
September 19, 2018: Biomolecular NMR Assignments
Khandekar Jishan Bari, Shrikant Sharma, Kandala V R Chary
The high solubility and stability of crystallins present in the human eye lens maintains its transparency and refractive index with negligible protein turnover. Monomeric γ-crystallins and oligomeric β-crystallins are made up of highly homologous double Greek key domains. These domains are symmetric and possess higher stability as a result of the complex topology of individual Greek key motifs. γS-crystallin is one of the most abundant structural βγ-crystallins present in the human eye lens. In order to understand the structural stability of individual domains of human γS-crystallin in isolation vis-à-vis full length protein, we set out to structurally characterize its C-terminal domain (abbreviated hereafter as γS-CTD) by solution NMR...
September 19, 2018: Biomolecular NMR Assignments
Janeka Gartia, Ravi Pratap Barnwal, Raveendra Anangi, Ashok R Giri, Glenn King, Kandala V R Chary
Helicoverpa species are polyphagous pests, with the larval stages causing major damage to economically valuable crops such as cotton, tomato, corn, sorghum, peas, sunflower, wheat and other pulses. Over the years, Helicoverpa armigera has developed resistance to most classes of chemical insecticides, and consequently it is now largely controlled on cotton plants via the use of Bt transgenic crops that express insecticidal Cry toxins which in-turn expedited resistance development in a number of pest species including H...
September 18, 2018: Biomolecular NMR Assignments
Steven A Beasley, Roela Bardhi, Donald E Spratt
ITCH (aka Atrophin-1-interacting protein 4) is a prominent member of the NEDD4 HECT (Homologous to E6AP C-Terminus) E3 ubiquitin ligase family that regulates numerous cellular functions including inflammatory responses through T-cell activation, cell differentiation, and apoptosis. Known intracellular targets of ITCH-dependent ubiquitylation include receptor proteins, signaling molecules, and transcription factors. The HECT C-terminal lobe of ITCH contains the conserved catalytic cysteine required for the covalent attachment of ubiquitin onto a substrate and polyubiquitin chain assembly...
September 18, 2018: Biomolecular NMR Assignments
Juan M Lopez, Ricardo Antiparra, Guy Lippens, Mirko Zimic, Patricia Sheen, Helena Maruenda
Chagas disease is a trypanosomiasis disease inflicted by Trypanosoma cruzi parasite. In Latin America, at least 10 million people are infected and annually, 10,000 casualties are deplored. Macrophage infectivity potentiator protein is one of the major virulence factors secreted by T. cruzi (TcMIP) in order to infect its host but little is known about its mechanism of action. Studies confer TcMIP an important role in the extracellular matrix transmigration and basal lamina penetration. Here, we report the backbone 1 H, 13 C, and 15 N resonance assignment of TcMIP and the comparison of the secondary structure obtained against reported X-ray crystallography data...
September 18, 2018: Biomolecular NMR Assignments
Wenbo Zhang, Cong Zhao, Yunfei Hu, Changwen Jin
The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated proteins in eukaryotic cells. It consists of a 20S barrel-shaped core particle capped by two 19S regulatory particle at both ends. The Rpn5 subunit is a non-ATPase subunit located in the lid subcomplex of the 19S regulatory particle and is identified to inhibit the Rpn11 deubiquitinase activity in the isolated lid. The protein contains a C-terminal proteasome-CSN-eIF3 (PCI) domain and an N-terminal α-solenoid domain, the latter has been shown to be highly flexible in the isolated lid and may participate in interactions with different subunits of the proteasome...
September 18, 2018: Biomolecular NMR Assignments
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