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Biomolecular NMR Assignments

Tadateru Nishikawa, Noboru Ishiyama, Feng Wang, Mitsuhiko Ikura
α-Catenin is a filamentous actin (F-actin) binding protein that links the classical cadherin-catenin complex to the actin cytoskeleton at adherens junctions (AJs). Its C-terminal F-actin binding domain is required for regulating the dynamic interaction between AJs and the actin cytoskeleton during tissue development. Thus, obtaining the molecular details of this interaction is a crucial step towards understanding how α-catenin plays critical roles in biological processes, such as morphogenesis, cell polarity, wound healing and tissue maintenance...
November 1, 2016: Biomolecular NMR Assignments
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...
October 31, 2016: Biomolecular NMR Assignments
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...
October 22, 2016: Biomolecular NMR Assignments
Eunjeong Lee, Jason D Fowler, Zucai Suo, Zhengrong Wu
Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several β-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes...
October 13, 2016: Biomolecular NMR Assignments
Elke Duchardt-Ferner, Michael Juen, Christoph Kreutz, Jens Wöhnert
RNA aptamers are used in a wide range of biotechnological or biomedical applications. In many cases the high resolution structures of these aptamers in their ligand-complexes have revealed fundamental aspects of RNA folding and RNA small molecule interactions. Fluorescent RNA-ligand complexes in particular find applications as optical sensors or as endogenous fluorescent tags for RNA tracking in vivo. Structures of RNA aptamers and aptamer ligand complexes constitute the starting point for rational function directed optimization approaches...
October 11, 2016: Biomolecular NMR Assignments
Ahmad Ali-Ahmad, Olivier Bornet, Firas Fadel, Yves Bourne, Florence Vincent, Christophe Bordi, Françoise Guerlesquin, Corinne Sebban-Kreuzer
Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen. It can infect vulnerable patients such as those with cystic fibrosis or hospitalized in intensive care units where it is responsible for both acute and chronic infection. The switch between these infections is controlled by a complex regulatory system involving the central GacS/GacA two-component system that activates the production of two small non-coding RNAs. GacS is a histidine kinase harboring one periplasmic detection domain, two inner-membrane helices and three H1/D1/H2 cytoplasmic domains...
October 6, 2016: Biomolecular NMR Assignments
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...
October 5, 2016: Biomolecular NMR Assignments
Jeffrey F Ellena, Wen Xiong, Xiaolin Zhao, Narasimhamurthy Shanaiah, Daniel G S Capelluto
Efficient trafficking of ubiquitinated receptors (cargo) to endosomes requires the recruitment of adaptor proteins that exhibit ubiquitin-binding domains for recognition and transport. Tom1 is an adaptor protein that not only associates with ubiquitinated cargo but also represents a phosphoinositide effector during specific bacterial infections. This phosphoinositide-binding property is associated with its N-terminal Vps27, Hrs, STAM (VHS) domain. Despite its biological relevance, there are no resonance assignments of Tom1 VHS available that can fully characterize its molecular interactions...
October 4, 2016: Biomolecular NMR Assignments
Jai Shankar Singh, Vaibhav Kumar Shukla, Mansi Gujrati, Ram Kumar Mishra, Ashutosh Kumar
One of the most debilitating diseases Malaria, in its different forms, is caused by protozoan of Plasmodium species. Deadliest among these forms is the "cerebral malaria" which is afflicted upon by Plasmodium falciparum. Plasmodium adopts numerous strategies including various post-translational modifications (PTMs) to infect and survive in the human host. These PTMs have proven their critical requirement in the Plasmodium biology. Recently, sumoylation has been characterized as one of the important PTMs and many of its putative substrates have been identified in Plasmodium...
October 3, 2016: Biomolecular NMR Assignments
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...
October 3, 2016: Biomolecular NMR Assignments
Robert L Evans, John A Latham, Judith P Klinman, Carrie M Wilmot, Youlin Xia
The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. RiPPs represent a rapidly expanding and diverse class of natural products-many of which have therapeutic potential-and the biosynthetic pathways for these are gaining attention. Five gene products from the pqq operon (PqqA, PqqB, PqqC, PqqD, and PqqE) are essential for PQQ biosynthesis. The substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD...
October 2016: Biomolecular NMR Assignments
Matthias Wittwer, Sonja A Dames
Mycobacterium tuberculosis protein kinase G (PknG) is a 82 kDa multidomain eukaryotic-like serine/threonine kinase mediating the survival of pathogenic mycobacteria within host macrophages. The N-terminal sequence preceding the catalytic kinase domain contains an approximately 75 residues long tail, which was predicted to show no regulatory secondary structure (1-75 = NORS) but harbors the major in vivo phosphorylation site (T63), and a rubredoxin-like metal binding motif (74-147 = RD). In the reduced rubredoxin motif, four conserved cysteine residues that are present as two C-X-X-C-G motifs coordinate a metal ion...
October 2016: Biomolecular NMR Assignments
Aikaterini C Tsika, Demetra S M Chatzileontiadou, Demetres D Leonidas, Georgios A Spyroulias
Here, we report the high yield expression and preliminary structural analysis via solution hetero-nuclear NMR spectroscopy of the recombinant Met-1 human Angiogenin. The analysis reveals a well folded as well as, a monomeric polypeptide. Τhe sequence-specific assignment of its (1)H, (15)N and (13)C resonances at high percentage was obtained. Also, using TALOS+ its secondary structure elements were determined.
October 2016: Biomolecular NMR Assignments
Ioannis I Alexandropoulos, Aikaterini I Argyriou, Kostas D Marousis, Stavros Topouzis, Andreas Papapetropoulos, Georgios A Spyroulias
The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp...
October 2016: Biomolecular NMR Assignments
Jiaping Chen, Xiaodong Xu, Hu Tao, Yuanyuan Wang, Hongying Chen
Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of porcine reproductive and respiratory syndrome, a destructive disease of swine. PRRSV has a single strand positive-sense RNA genome which contains at least ten open reading frames, of these, ORF1a and ORF1b encode polyproteins pp1a and pp1ab. Subsequently, pp1a is cleaved into ten nonstructural proteins, including nonstructural protein 7α and 7β (nsp7α and 7β), the internal cleavage products of a conserved nonstructural protein nsp7...
October 2016: Biomolecular NMR Assignments
M Salim, C R Willcox, F Mohammed, A C Hayday, M Overduin, B E Willcox, T J Knowles
A study describing the (1)H, (13)C and (15)N backbone and side chain chemical shift assignments and secondary structure of Skint-1 a prototypic member of a family of mouse genes, of which Skint-1 is involved in the development of the dendritic epidermal T cell (DETC) subset of γδ T cells.
October 2016: Biomolecular NMR Assignments
Lorena Varela, Christian H Bell, Judith P Armitage, Christina Redfield
Rhodobacter sphaeroides has emerged as a model system for studies of the complex chemotaxis pathways that are a hallmark of many non-enteric bacteria. The genome of R. sphaeroides encodes two sets of flagellar genes, fla1 and fla2, that are controlled by three different operons. Each operon encodes homologues of most of the proteins required for the well-studied E. coli chemotaxis pathway. R. sphaeroides has six homologues of the response regulator CheY that are localized to and are regulated by different clusters of chemosensory proteins in the cell and have different effects on chemotaxis...
October 2016: Biomolecular NMR Assignments
Romain Navarro, Olivier Bornet, Laetitia Houot, Roland Lloubes, Françoise Guerlesquin, Matthieu Nouailler
Vibrio cholerae is the bacterial causative agent of the human disease cholera. Non-pathogenic bacterium can be converted to pathogenic following infection by a filamentous phage, CTXΦ, that carries the cholera toxin encoding genes. A crucial step during phage infection requires a direct interaction between the CTXΦ minor coat protein (pIII(CTX)) and the C-terminal domain of V. cholerae TolA protein (TolAIIIvc). In order to get a better understanding of TolA function during the infection process, we have initiated a study of the V...
October 2016: Biomolecular NMR Assignments
Biling Huang, Jinglin Fu, Chenyun Guo, Xueji Wu, Donghai Lin, Xinli Liao
Ribosomal protein S1 of Mycobacterium tuberculosis (MtRpsA) binds to ribosome and mRNA, and plays significant role in the regulation of translation initiation, conventional protein synthesis and transfer-messenger RNA (tmRNA) mediated trans-translation. It has been identified as the target of pyrazinoic acid (POA), a bactericidal moiety from hydrolysis of pyrazinamide, which is a mainstay of combination therapy for tuberculosis. POA prevented the interactions between the C-terminal S1 domain of MtRpsA (residues 280-368, MtRpsA(CTD)_S1) and tmRNA; so that POA can inhibit the trans-translation, which is a key component of multiple quality control pathways in bacteria...
October 2016: Biomolecular NMR Assignments
Florent Delhommel, Nicolas Wolff, Florence Cordier
Mammals perceive sounds thanks to mechanosensory hair cells located in the inner ear. The stereocilia of these cells are tightly bound together in bundles by a network of cadherins and scaffolding proteins. Stereocilia deflection induces stretching of this network and is responsible for hair cell depolarization that triggers the neuronal message, transducing the mechanical signal into an electric signal transmissible to the brain. Nearly all proteins involved in this mechano-electrical transduction network contain short C-terminal motifs of interaction with PDZ domains (PSD-95, Discs Large, ZO-1)...
October 2016: Biomolecular NMR Assignments
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