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CHEMISTRY (603 journals)                  1 2 3 4 | Last

Showing 1 - 200 of 735 Journals sorted alphabetically
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African Journal of Bacteriology Research     Open Access  
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Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
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Anadolu University Journal of Science and Technology     Open Access  
Analyst     Full-text available via subscription   (Followers: 41)
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Journal Cover Biomolecular NMR Assignments
  [SJR: 0.325]   [H-I: 10]   [2 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1874-270X - ISSN (Online) 1874-2718
   Published by Springer-Verlag Homepage  [2336 journals]
  • 1 H, 15 N and 13 C backbone and side chain resonance assignments of the
           RRM domain from human RBM24
    • Authors: Santosh Kumar Upadhyay; Cameron D. Mackereth
      Pages: 237 - 240
      Abstract: Abstract Tissue development requires the expression of a regulated subset of genes, and it is becoming clear that the process of alternative splicing also plays an important role in the production of necessary tissue-specific isoforms. However, only a few of these tissue-specific splicing factors in mammals have so far been discovered. One of these factors is the RNA-binding protein RBM24 which has been recently identified as a major regulator of alternative splicing in cardiac and skeletal muscle development. The RBM24 protein contains an RNA recognition motif (RRM) domain that presumably mediates the binding to target pre-mRNA required for regulation of the splicing patterns. Here we report 1H, 15N and 13C chemical shift assignments of the backbone and sidechain atoms for the RRM domain from human RBM24. Secondary chemical shift analysis and relaxation measurement confirm the canonical architecture of the RRM domain. The data will allow for atomic level studies aimed at understanding splicing regulation of target genes in heart and muscle development and investigation into a separate role of RBM24 in modulating mRNA stability of genes involved in the p53 tumor suppressor pathway.
      PubDate: 2016-10-01
      DOI: 10.1007/s12104-016-9674-y
      Issue No: Vol. 10, No. 2 (2016)
  • Backbone and side-chain chemical shift assignments for the C-terminal
           domain of Tcb2, a cytoskeletal calcium-binding protein from Tetrahymena
    • Authors: Adina M. Kilpatrick; Theodore E. Gurrola; Robert C. Sterner; Heidi M. Sleister; Jerry E. Honts; C. Andrew Fowler
      Pages: 281 - 285
      Abstract: Abstract Tcb2 is a putative calcium-binding protein from the membrane-associated cytoskeleton of the ciliated protozoan Tetrahymena thermophila. It has been hypothesized to participate in several calcium-mediated processes in Tetrahymena, including ciliary movement, cell cortex signaling, and pronuclear exchange. Sequence analysis suggests that the protein belongs to the calmodulin family, with N- and C-terminal domains connected by a central linker, and two helix-loop-helix motifs in each domain. However, its calcium-binding properties, structure and precise biological function remain unknown. Interestingly, Tcb2 is a major component of unique contractile fibers isolated from the Tetrahymena cytoskeleton; in these fibers, addition of calcium triggers an ATP-independent type of contraction. Here we report the 1H, 13C and 15N backbone and side-chain chemical shift assignments of the C-terminal domain of the protein (Tcb2-C) in the absence and presence of calcium ions. 1H–15N HSQC spectra show that the domain is well folded both in the absence and presence of calcium, and undergoes a dramatic conformational change upon calcium addition. Secondary structure prediction from chemical shifts reveals an architecture encountered in other calcium-binding proteins, with paired EF-hand motifs connected by a flexible linker. These studies represent a starting point for the determination of the high-resolution solution structure of Tcb2-C at both low and high calcium levels, and, together with additional structural studies on the full-length protein, will help establish the molecular basis of Tcb2 function and unique contractile properties.
      PubDate: 2016-10-01
      DOI: 10.1007/s12104-016-9684-9
      Issue No: Vol. 10, No. 2 (2016)
  • Backbone 1 H, 13 C and 15 N resonance assignments of the OB domain of the
           single stranded DNA-binding protein hSSB1 (NABP2/OBFC2B) and chemical
           shift mapping of the DNA-binding interface
    • Authors: Ruvini Kariawasam; Christine Touma; Liza Cubeddu; Roland Gamsjaeger
      Pages: 297 - 300
      Abstract: Abstract Single-stranded DNA-binding proteins (SSBs) are highly important in DNA metabolism and play an essential role in all major DNA repair pathways. SSBs are generally characterised by the presence of an oligonucleotide binding (OB) fold which is able to recognise single-stranded DNA (ssDNA) with high affinity. We discovered two news SSBs in humans (hSSB1 and hSSB2) that both contain a single OB domain followed by a divergent spacer region and a charged C-terminus. We have extensively characterised one of these, hSSB1 (NABP2/OBFC2B), in numerous important DNA processing events such as, in DNA double-stranded break repair and in the response to oxidative DNA damage. Although the structure of hSSB1 bound to ssDNA has recently been determined using X-ray crystallography, the detailed atomic level mechanism of the interaction of hSSB1 with ssDNA in solution has not been established. In this study we report the solution-state backbone chemical shift assignments of the OB domain of hSSB1. In addition, we have utilized NMR to map the DNA-binding interface of hSSB1, revealing major differences between recognition of ssDNA under physiological conditions and in the recently determined crystal structure. Our NMR data in combination with further biophysical and biochemical experiments will allow us to address these discrepancies and shed light onto the structural basis of DNA-binding by hSSB1 in solution.
      PubDate: 2016-10-01
      DOI: 10.1007/s12104-016-9687-6
      Issue No: Vol. 10, No. 2 (2016)
  • 1 H, 13 C and 15 N resonance assignments of the Cdc42-binding domain of
    • Authors: Joanna R. Watson; Daniel Nietlispach; Darerca Owen; Helen R. Mott
      Pages: 407 - 411
      Abstract: Abstract TOCA1 is a downstream effector protein of the small GTPase, Cdc42. It is a multi-domain protein that includes a membrane binding F-BAR domain, a homology region 1 (HR1) domain, which binds selectively to active Cdc42 and an SH3 domain. TOCA1 is involved in the regulation of actin dynamics in processes such as endocytosis, filopodia formation, neurite elongation, cell motility and invasion. Structural insight into the interaction between TOCA1 and Cdc42 will contribute to our understanding of the role of TOCA1 in actin dynamics. The 1H, 15N and 13C NMR backbone and sidechain resonance assignment of the HR1 domain (12 kDa) presented here provides the foundation for structural studies of the domain and its interactions.
      PubDate: 2016-10-01
      DOI: 10.1007/s12104-016-9677-8
      Issue No: Vol. 10, No. 2 (2016)
  • Backbone assignment of the binary complex of the full length Sulfolobus
           solfataricus DNA polymerase IV and DNA
    • Authors: Eunjeong Lee; Jason D. Fowler; Zucai Suo; Zhengrong Wu
      Abstract: Abstract 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.
      PubDate: 2016-10-13
      DOI: 10.1007/s12104-016-9717-4
  • NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer
           3 in complex with the ligand 5-carboxy-tetramethylrhodamine
    • Authors: Elke Duchardt-Ferner; Michael Juen; Christoph Kreutz; Jens Wöhnert
      Abstract: Abstract 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. Here, we present the NMR resonance assignment of an RNA aptamer binding to the fluorescent ligand tetramethylrhodamine (TMR) in complex with the ligand 5-carboxy-tetramethylrhodamine (5-TAMRA) as a starting point for a high-resolution structure determination using NMR spectroscopy in solution.
      PubDate: 2016-10-11
      DOI: 10.1007/s12104-016-9715-6
  • NMR assignments of the GacS histidine-kinase periplasmic detection domain
           from Pseudomonas aeruginosa PAO1
    • Authors: Ahmad Ali-Ahmad; Olivier Bornet; Firas Fadel; Yves Bourne; Florence Vincent; Christophe Bordi; Françoise Guerlesquin; Corinne Sebban-Kreuzer
      Abstract: Abstract 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. By detecting a yet unknown signal, the GacS histidine-kinase periplasmic detection domain (GacSp) is predicted to play a key role in activating the GacS/GacA pathway. Here, we present the chemical shift assignment of 96 % of backbone atoms (HN, N, C, Cα, Cβ and Hα), 88 % aliphatic hydrogen atoms and 90 % of aliphatic carbon atoms of this domain. The NMR-chemical shift data, on the basis of Talos server secondary structure predictions, reveal that GacSp consists of 3 β-strands, 3 α-helices and a major loop devoid of secondary structures.
      PubDate: 2016-10-06
      DOI: 10.1007/s12104-016-9714-7
  • 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
    • Authors: Huaqun Zhang; Cameron McGlone; Matthew M. Mannion; Richard C. Page
      Abstract: Abstract 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. In particular, the absence of a structure for CHIP-TPR in the free form presents a significant limitation upon studies seeking to rationally design inhibitors that may disrupt interactions between CHIP and heat shock proteins. Here we report the 1H, 13C, and 15N backbone and side chain chemical shift assignments for CHIP-TPR in the free form, and backbone chemical shift assignments for CHIP-TPR in the IEEVD-bound form. The NMR resonance assignments will enable further studies examining the roles of dynamics and structure in regulating interactions between CHIP and the heat shock proteins Hsp70/Hsc70 and Hsp90.
      PubDate: 2016-10-05
      DOI: 10.1007/s12104-016-9710-y
  • Backbone 1 H, 15 N, and 13 C resonance assignments of the Tom1 VHS domain
    • Abstract: Abstract 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. Here, we report the nearly complete 1H, 15N, and 13C backbone resonance assignments of the VHS domain of human Tom1.
      PubDate: 2016-10-04
      DOI: 10.1007/s12104-016-9709-4
  • Backbone and side-chain resonance assignments of Plasmodium falciparum
    • Abstract: Abstract 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. Sumoylation is the covalent attachment of SUMO protein to the substrate protein, which is mediated by an enzyme cascade involving activating (E1), conjugating (E2), and ligating enzymes (E3). Here, we report resonance assignment for 1H, 13C and 15N of Plasmodium falciparum SUMO (Pf-SUMO) protein determined by various 2D and 3D heteronuclear NMR experiments along with predicted secondary structures.
      PubDate: 2016-10-03
      DOI: 10.1007/s12104-016-9712-9
  • Backbone and methyl resonance assignments of the 42 kDa human Hsc70
           nucleotide binding domain in the ADP state
    • Abstract: Abstract 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 15N and 13C-resolved 3D NOE experiments with methyl-reprotonated samples. A combination of computer and manual data interpretation was used.
      PubDate: 2016-10-03
      DOI: 10.1007/s12104-016-9711-x
  • Backbone and side-chain 1 H, 13 C, and 15 N chemical shift assignments for
           the apo -form of the lytic polysaccharide monooxygenase Nc LPMO9C
    • Authors: Gaston Courtade; Reinhard Wimmer; Maria Dimarogona; Mats Sandgren; Vincent G. H. Eijsink; Finn L. Aachmann
      Abstract: Abstract The apo-form of the 23.3 kDa catalytic domain of the AA9 family lytic polysaccharide monooxygenase NcLPMO9C from Neurospora crassa has been isotopically labeled and recombinantly expressed in Pichia pastoris. In this paper, we report the 1H, 13C, and 15N chemical shift assignments of this LPMO.
      PubDate: 2016-10-01
      DOI: 10.1007/s12104-016-9683-x
  • Erratum to: 1 H, 13 C and 15 N resonance assignments of the Cdc42-binding
           domain of TOCA1
    • Authors: Joanna R. Watson; Daniel Nietlispach; Darerca Owen; Helen R. Mott
      PubDate: 2016-10-01
      DOI: 10.1007/s12104-016-9679-6
  • NMR study of Met-1 human Angiogenin: 1 H, 13 C, 15 N backbone and
           side-chain resonance assignment
    • Authors: Aikaterini C. Tsika; Demetra S. M. Chatzileontiadou; Demetres D. Leonidas; Georgios A. Spyroulias
      Abstract: Abstract 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 1H, 15N and 13C resonances at high percentage was obtained. Also, using TALOS+ its secondary structure elements were determined.
      PubDate: 2016-09-13
      DOI: 10.1007/s12104-016-9704-9
  • 1 H, 13 C, 15 N backbone and side-chain resonance assignment of Nostoc sp.
           C139A variant of the heme–nitric oxide/oxygen binding (H-NOX) domain
    • Authors: Ioannis I. Alexandropoulos; Aikaterini I. Argyriou; Kostas D. Marousis; Stavros Topouzis; Andreas Papapetropoulos; Georgios A. Spyroulias
      Abstract: Abstract 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 1H, 13C and 15N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.
      PubDate: 2016-09-10
      DOI: 10.1007/s12104-016-9707-6
  • 1 H, 13 C and 15 N resonance assignments for the response regulator CheY 3
           from Rhodobacter sphaeroides
    • Authors: Lorena Varela; Christian H. Bell; Judith P. Armitage; Christina Redfield
      Abstract: Abstract 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. CheY6 is the major CheY stopping the fla1 flagellar motor and associated with a cytoplasmically localised chemosensory pathway. CheY3 and CheY4 are associated with a membrane localised polar chemosensory cluster, and can bind to but not stop the motor. CheY6 and either CheY3 or CheY4 are required for chemotaxis. We are using NMR spectroscopy to characterise and compare the structure and dynamics of CheY3 and CheY6 in solution. We are interested in defining the conformational changes that occur upon activation of these two proteins and to identify differences in their properties that can explain the different functions they play in chemotaxis in R. sphaeroides. Here we present the 1H, 13C and 15N assignments for CheY3 in its active, inactive and Mg2+-free apo form. These assignments provide the starting point for detailed investigations of the structure and function of CheY3.
      PubDate: 2016-07-29
      DOI: 10.1007/s12104-016-9703-x
  • 1 H, 15 N and 13 C resonance assignments of the C-terminal domain of
           Vibrio cholerae TolA protein
    • Authors: Romain Navarro; Olivier Bornet; Laetitia Houot; Roland Lloubes; Françoise Guerlesquin; Matthieu Nouailler
      Abstract: Abstract 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 (pIIICTX) 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. cholerae TolAIII domain by 2D and 3D heteronuclear NMR. With the exception of the His-tag (H123–H128), 97 % of backbone 1H, 15N and 13C resonances were assigned and the side chain assignments for 92 % of the protein were obtained (BMRB deposit with accession number 25689).
      PubDate: 2016-07-19
      DOI: 10.1007/s12104-016-9690-y
  • Backbone and side chain assignments of human cell cycle regulatory protein
           S-phase kinase-associated protein 1
    • Authors: Nitin Nathubhai Kachariya; Sarath Chandra Dantu; Ashutosh Kumar
      Abstract: Abstract Ubiquitination of proteins is required to regulate several cellular mechanisms in cells. Skp1-Cullin-1-F-box (SCF), the largest family of the RING E3 ligases, recognizes and carries out the poly-ubiquitination of many substrate proteins. SCF E3 ligase is a multi-component protein complex, and the human S-phase kinase-associated protein 1 (Skp1) is the adapter protein, which binds and presents the substrate binding protein F-box (FBP) to the rest of the E3 ligase. Several crystallographic studies have solved the partial structure of Skp1 in complex with various FBPs, but there is no structure of standalone Skp1. Understanding the conformational and structural properties of Skp1 with and without FBPs is required to understand the complete mechanism of poly-ubiquitination. Here, we report ~90 % backbone and 64 % side chain 1H, 13C, 15N assignments of Skp1 protein using various double and triple resonance NMR experiments.
      PubDate: 2016-07-09
      DOI: 10.1007/s12104-016-9699-2
  • Backbone resonance assignments for the SET domain of the human
           methyltransferase NSD2
    • Authors: Romel Bobby; Karolina Peciak; Alexander G. Milbradt
      Abstract: Abstract Aberrant NSD2 methyltransferase activity is implicated as the oncogenic driver in multiple myeloma, suggesting opportunities for novel therapeutic intervention. The methyltransferase activity of NSD2 resides in its catalytic SET domain, which is conserved among most lysine methyltransferases. Here we report the backbone \(\hbox {H}^{\mathrm{N}}\) , N, C \(^{\prime }\) , \(\hbox {C}^\alpha\) and side-chain \(\hbox {C}^\beta\) assignments of a 25 kDa NSD2 SET domain construct, spanning residues 991–1203. A chemical shift analysis of C \(^{\prime }\) , \(\hbox {C}^\alpha\) and \(\hbox {C}^\beta\) resonances predicts a secondary structural pattern that is in agreement with homology models.
      PubDate: 2016-07-01
      DOI: 10.1007/s12104-016-9689-4
  • Chemical shift assignments and secondary structure prediction for Q4DY78,
           a conserved kinetoplastid-specific protein from Trypanosoma cruzi
    • Authors: Éverton Dias D’Andréa; Anne Diehl; Peter Schmieder; Hartmut Oschkinat; José Ricardo Pires
      Abstract: Abstract Trypanosoma cruzi, Trypanosma brucei and Leishmania spp. are kinetoplastid protozoa causative agents of Chagas disease, sleeping sickness and leishmaniasis, respectively, neglected tropical diseases estimated to infect millions of people worldwide. Their genome sequencing has revealed approximately 50 % of genes encoding hypothetical proteins of unknown function, opening possibilities for novel target identification and drug discovery. Q4DY78 is a putative essential protein from T. cruzi conserved in the related kinetoplastids and divergent from mammalian host proteins. Here we report the 1H, 15N, and 13C chemical shift assignments and secondary structure analysis of the Q4DY78 protein as basis for NMR structure determination, functional analysis and drug screening.
      PubDate: 2016-06-29
      DOI: 10.1007/s12104-016-9693-8
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