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Journal Cover Biomolecular NMR Assignments     [SJR: 0.402]   [H-I: 7]
   [4 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  [2210 journals]
  • 1 H, 15 N, 13 C resonance assignment of human osteopontin
    • Abstract: Osteopontin (OPN) is a 33.7 kDa intrinsically disordered protein and a member of the SIBLING family of proteins. OPN is bearing a signal peptide for secretion into the extracellular space, where it exerts its main physiological function, the control of calcium biomineralization. It is often involved in tumorigenic processes influencing proliferation, migration and survival, as well as the adhesive properties of cancer cells via CD44 and integrin signaling pathways. Here we report the nearly complete NMR chemical shift assignment of recombinant human osteopontin.
      PubDate: 2015-01-24
  • NMR resonance assignments of the lantibiotic immunity protein NisI from
           Lactococcus lactis
    • Abstract: The lantibiotic nisin is a small antimicrobial peptide which acts against a wide range of Gram-positive bacteria. Nisin-producing Lactococcus lactis strains express four genes for self-protection against their own antimicrobial compound. This immunity system consists of the lipoprotein NisI and the ABC transporter NisFEG. NisI is attached to the outside of the cytoplasmic membrane via a covalently linked diacylglycerol anchor. Both the lipoprotein and the ABC transporter are needed for full immunity but the exact immunity mechanism is still unclear. To gain insights into the highly specific immunity mechanism of nisin producing strains on a structural level we present here the backbone resonance assignment of NisI (25.8 kDa) as well as the virtually complete 1H,15N,13C chemical shift assignments for the isolated 12.7 kDa N-terminal and 14.6 kDa C-terminal domains of NisI.
      PubDate: 2015-01-23
  • Chemical shift perturbations induced by residue specific mutations of CaM
           interacting with NOS peptides
    • Abstract: The regulation of nitric oxide synthase (NOS) by calmodulin (CaM) plays a major role in a number of key physiological and pathological processes. A detailed molecular level picture of how this regulation is achieved is critical for drug development and for our understanding of protein regulation in general. CaM is a small acidic calcium binding protein and is required to fully activate NOS. The exact mechanism of how CaM activates NOS is not fully understood at this time. Studies have shown CaM to act like a switch that causes a conformational change in NOS to allow for the electron transfer between the reductase and oxygenase domains through a process that is thought to be highly dynamic. The interaction of CaM with NOS is modified by a number of post-translation modifications including phosphorylation. Here we present backbone and sidechain 1H, 15N NMR assignments of modified CaM interacting with NOS peptides which provides the basis for a detailed study of CaM–NOS interaction dynamics using 15N relaxation methods.
      PubDate: 2015-01-21
  • 1 H, 13 C and 15 N assignments of EGF domains 4 to 7 of human Notch-1
    • Abstract: The Notch pathway is a core cell–cell signaling system in Metazoa which plays a key role in development and adult homeostasis. Whereas most Notch structural biology research has focused on the negative regulatory region and the intracellular domain, relatively little structural information is available for the extracellular part of human Notch-1 (hN-1) which mediates ligand recognition. This region consists of 36 epidermal growth factor-like (EGF) domains, many of which contain a calcium-binding consensus sequence. The calcium-binding site in each case is located within the N-terminal portion of the domain, and is associated with both intra- and inter-domain rigidity. The absence of calcium-binding sites in EGF6, EGF10 and EGF22, however, suggests that these domains might represent regions of flexibility in the receptor which could influence the cell-surface architecture (usually depicted as an extended rod projecting from the cell surface). To probe this, we have purified a quadruple-domain construct from hN-1, in which the non-calcium-binding EGF6 is flanked by EGF4–5 and EGF7. Here, we report 1H, 13C and 15N resonance assignments for this four-domain 157 amino acid construct. The assignments presented here are the prerequisite for a detailed study of the structure and dynamics of this region of the Notch receptor.
      PubDate: 2014-12-13
  • NMR assignments of actin depolymerizing factor (ADF) like UNC-60A and
           cofilin like UNC-60B proteins of Caenorhabditis elegans
    • Abstract: The actin filament dynamics in nematode, Caenorhabditis elegans, is regulated by differential activity of two proteins UNC-60A and UNC-60B. UNC-60A exhibits strong pointed end depolymerization on C. elegans actin (Ce-actin), strong inhibition of polymerization, strong monomer sequestering activity, weak severing activity, and low affinity for F-actin binding, while UNC-60B exhibits strong pointed end depolymerization on rabbit muscle actin, strong severing activity, and high affinity for F-actin binding. Structural characterization of these proteins will help to understand (1) molecular mechanism of actin dynamics regulation and (2) the differential activity of these proteins. Here, we report 1H, 13C, and 15N chemical shift assignments of these two proteins as determined by heteronuclear NMR experiments (at pH 6.5 and temperature 298 K).
      PubDate: 2014-12-11
  • Chemical shift assignments and secondary structure determination of the
           ectodomain of Bacillus subtilis morphogenic protein RodZ
    • Abstract: RodZ (also known as YfgA) is a component of the core bacterial morphogenic apparatus. RodZ is a key cell shape determinant in rod-shaped bacteria and it interacts with the actin-like cytoskeletal protein MreB. In Bacillus subtilis, this 304-residue transmembrane protein is composed of three distinct domains: a cytoplasmic domain (RodZn), a transmembrane domain, and an extra-cytoplasmic domain (RodZc). Here we report the 1H, 13C and 15N backbone and side chain resonance assignments of the RodZc domain from B. subtilis by NMR spectroscopy, and the resulting secondary structure prediction.
      PubDate: 2014-12-11
  • Chemical shift assignments of mouse HOXD13 DNA binding domain bound to
           duplex DNA
    • Abstract: The homeobox gene (Hoxd13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of proteins that control embryonic morphogenesis. We report NMR chemical shift assignments of mouse Hoxd13 DNA binding domain bound to an 11-residue DNA duplex (BMRB No. 25133).
      PubDate: 2014-12-10
  • 1 H, 15 N and 13 C resonance assignments of the RRM1 domain of the key
           post-transcriptional regulator HuR
    • Abstract: Human antigen R (HuR) is a ubiquitous protein that recognizes adenylate and uridylate-rich elements in mRNA, thereby interfering with the fate of protein translation. This protein plays a central role in the outcome of the inflammatory response as it may stabilize or silence mRNAs of key components of the immune system. HuR is able to interact with other RNA-binding proteins, reflecting a complex network that dictates mRNAs post-transcriptional control. HuR is composed of three functional domains, known as RNA-recognition motifs (RRM1, RRM2 and RRM3). It is known that RRM1 is the most important domain for mRNA-binding affinity. In this study, we completed the NMR chemical shift assignment of the RRM1 domain of HuR, as a first step to further establishing the structure, dynamics and function relationship for this protein.
      PubDate: 2014-12-09
  • Backbone resonance assignments of the 54 kDa dimeric C-terminal
           domain of murine STING in complex with DMXAA
    • Abstract: The mammalian ER protein STING (stimulators of interferon genes) is an important innate immunity protein for linking detection of novel secondary messengers c-di-GMP, c-di-AMP, cGAMP or cytosolic dsDNA to the activation of TANK kinase 1 and its downstream interferon regulator factor 3. Recently quite a few of crystal structures representing different states of the C-terminal domain (CTD) of human and murine STING (hSTING and mSTING) in complex with c-di-GMP, cGAMP or DMXAA have been reported. However, the C-terminal 42 residues of STING-CTD, which may be important in mediating the downstream reactions, is invisible or absent in all reported X-ray structures. In addition, X-ray crystal structures may be subject to crystal packing force. Hence an alternate method of determining the structure and function of STING in a near physiological condition is essential. We now report the near complete backbone resonance assignments of the 54 kDa dimeric mSTING-CTD in complex with DMXAA, which is the first step in determining its complex structure and understanding why DMXAA, which is a very efficient agent for curing mouse cancer, is totally ineffective in human.
      PubDate: 2014-12-09
  • 1 H, 13 C, and 15 N resonance assignments for the tandem PHD finger motifs
           of human CHD4
    • Abstract: The plant homeodomain (PHD) zinc finger is a structural motif of about 40–60 amino acid residues found in many eukaryotic proteins that are involved in chromatin-mediated gene regulation. The human chromodomain helicase DNA binding protein 4 (CHD4) is a multi-domain protein that harbours, at its N-terminal end, a pair of PHD finger motifs (dPHD) connected by a ~30 amino acid linker. This tandem PHD motif is thought to be involved in targeting CHD4 to chromatin via its interaction with histone tails. Here we report the 1H, 13C and 15N backbone and side-chain resonance assignment of the entire dPHD by heteronuclear multidimensional NMR spectroscopy. These assignments provide the starting point for the determination of the structure, dynamics and histone-binding properties of this tandem domain pair.
      PubDate: 2014-10-18
  • Resonance assignment of the ligand-free cyclic nucleotide-binding domain
           from the murine ion channel HCN2
    • Abstract: Hyperpolarization activated and cyclic nucleotide-gated (HCN) ion channels as well as cyclic nucleotide-gated (CNG) ion channels are essential for the regulation of cardiac cells, neuronal excitability, and signaling in sensory cells. Both classes are composed of four subunits. Each subunit comprises a transmembrane region, intracellular N- and C-termini, and a C-terminal cyclic nucleotide-binding domain (CNBD). Binding of cyclic nucleotides to the CNBD promotes opening of both CNG and HCN channels. In case of CNG channels, binding of cyclic nucleotides to the CNBD is sufficient to open the channel. In contrast, HCN channels open upon membrane hyperpolarization and their activity is modulated by binding of cyclic nucleotides shifting the activation potential to more positive values. Although several high-resolution structures of CNBDs from HCN and CNG channels are available, the gating mechanism for murine HCN2 channel, which leads to the opening of the channel pore, is still poorly understood. As part of a structural investigation, here, we report the complete backbone and side chain resonance assignments of the murine HCN2 CNBD with part of the C-linker.
      PubDate: 2014-10-17
  • Solid-state NMR resonance assignments of the filament-forming CARD domain
           of the innate immunity signaling protein MAVS
    • Abstract: The mitochondrial antiviral signalling protein (MAVS) is a central signal transduction hub in the innate immune response against viral infections. Viral RNA present in the cytoplasm is detected by retinoic acid inducible gene I like receptors, which then activate MAVS via heterotypic interactions between their respective caspase activation and recruitment domains (CARD). This leads to the formation of active, high molecular weight MAVS complexes formed by homotypic interactions between the single N-terminal CARDs of MAVS. Filaments formed by the N-terminal MAVSCARD alone are sufficient to induce the autocatalytic conversion from a monomeric to an aggregated state in a prion-like manner. Here, we present the nearly complete spectroscopic 13C and 15N resonance assignments of human MAVSCARD filaments obtained from a single sample by magic angle spinning solid-state NMR spectroscopy. The corresponding secondary chemical shifts suggest that the filamentous form of MAVSCARD retains an exclusively alpha-helical fold that is very similar to the X-ray structure determined previously from monomeric MAVSCARD-maltose binding protein fusion constructs.
      PubDate: 2014-10-10
  • NMR study of non-structural proteins—part II: 1 H, 13 C, 15 N
           backbone and side-chain resonance assignment of macro domain from
           Venezuelan equine encephalitis virus (VEEV)
    • Abstract: Macro domains consist of 130–190 amino acid residues and appear to be highly conserved in all kingdoms of life. Intense research on this field has shown that macro domains bind ADP-ribose and other similar molecules, but their exact function still remains intangible. Macro domains are highly conserved in the Alphavirus genus and the Venezuelan equine encephalitis virus (VEEV) is a member of this genus that causes fatal encephalitis to equines and humans. In this study we report the high yield recombinant expression and preliminary solution NMR study of the macro domain of VEEV. An almost complete sequence-specific assignment of its 1H, 15N and 13C resonances was obtained and its secondary structure predicted by TALOS+. The protein shows a unique mixed α/β-fold.
      PubDate: 2014-10-08
  • Backbone 1 H, 13 C, and 15 N resonance assignments of the Fc fragment of
           human immunoglobulin G glycoprotein
    • Abstract: The Fc portion of immunoglobulin G (IgG) recruits complements and its cognate receptors, thereby promoting defensive mechanisms in the humoral immune system. These effector functions critically depend on N-glycosylation at the Fc region, which is therefore regarded as a crucial factor in the design and production of therapeutic antibodies. NMR spectroscopy plays a unique role in the characterization of conformational dynamics and intermolecular interactions of IgG-Fc in solutions. Here, we report NMR assignments of the glycosylated Fc fragment (Mr 53 kDa), cleaved from a chimeric antibody with human IgG1 constant regions, which was produced in Chinese hamster ovary cells with uniform 13C- and 15N-labeling.
      PubDate: 2014-10-08
  • Chemical shift assignments of DRB4 (1–153), a dsRNA binding protein
           in A. thaliana RNAi pathway
    • Abstract: RNA interference (RNAi) is a conserved biological response to dsRNA and regulates the expression of protein-coding genes to mediate resistance to both endogenous parasitic and exogenous pathogenic nucleic acids. In RNAi pathway, dsRNA binding proteins assists Dicer at various stages of RNAi. In plants, DRB4, is a multidomain protein containing two dsRNA binding domains that recognizes the long exogenous/endogenous dsRNA and presents it to Ribonuclease enzyme, Dicer like 4, resulting in the production of 21 nt small interfering RNA. Here, we report nearly complete backbone and sidechain chemical shift assignments of N-terminus of DRB4 (1–153, ~18 kDa), containing both double stranded RNA binding domains and the linker.
      PubDate: 2014-10-04
  • Backbone assignments of mini-RecA intein with short native exteins and an
           active N-terminal catalytic cysteine
    • Abstract: The backbone resonance assignments of an engineered splicing-inactive mini-RecA intein based on triple resonance experiments with [13C,15N]-labeled protein are reported. The construct contains inactivating mutations specifically designed to retain most catalytic residues, especially those that are potentially metal-coordinating. The assignments are essential for protein structure determination of a precursor with an active N-terminal catalytic cysteine and for investigation of the atomic details of splicing.
      PubDate: 2014-10-04
  • Backbone and side chain NMR assignment, along with the secondary structure
           prediction of RRM2 domain of La protein from a lower eukaryote exhibiting
           identical structural organization with its human homolog
    • Abstract: The La protein (Lupus antigen), a key mediator during biogenesis of RNA polymerase III transcripts, contains a characteristic La motif and one or two RNA recognition motif (RRM) domains, depending on the organism of origin. The RRM1 domain is conserved in higher eukaryotes and located in the N-terminal region, whereas the C-terminal RRM2 domain is absent in most lower eukaryotes and its specific role remains, so far, uncharacterized. Here, we present the backbone and side-chain assignment of the 1H, 13C and 15N resonances of RRM2 of La protein from Dictyostelium discoideum. Interestingly, the La protein in this lower eukaryote, exhibits high homology to its human counterpart. Moreover, it contains two RRM domains, instead of one, raising questions on its evolutionary origin and the putative role of RRM2 in vivo. We also provide its secondary structure as predicted by the TALOS+ online tool.
      PubDate: 2014-10-04
  • Backbone and side chain NMR assignments for the ribosome assembly factor
           Nop6 from Saccharomyces
    • Abstract: The Saccharomyces cerevisiae Nop6 protein is involved in the maturation of the small ribosomal subunit. It contains a central RNA binding domain and a predicted C-terminal coiled-coil domain. Here we report the almost complete (>90 %) 1H,13C,15N backbone and side chain NMR assignment of a 15 kDa Nop6 construct comprising the RNA binding and coiled-coil domains.
      PubDate: 2014-10-01
  • Erratum to: Backbone 1H, 13C and 15N assignments of YibK and a variant
           containing a unique cysteine residue at C-terminus in 8 M urea-denatured
    • PubDate: 2014-10-01
  • Resonance assignments of the microtubule-binding domain of the        class="a-plus-plus">C. elegans spindle and
           kinetochore-associated protein 1
    • Abstract: During mitosis, kinetochores coordinate the attachment of centromeric DNA to the dynamic plus ends of microtubules, which is hypothesized to pull sister chromatids toward opposing poles of the mitotic spindle. The outer kinetochore Ndc80 complex acts synergistically with the Ska (spindle and kinetochore-associated) complex to harness the energy of depolymerizing microtubules and power chromosome movement. The Ska complex is a hexamer consisting of two copies of the proteins Ska1, Ska2 and Ska3, respectively. The C-terminal domain of the spindle and kinetochore-associated protein 1 (Ska1) is the microtubule-binding domain of the Ska complex. We solved the solution structure of the C. elegans microtubule-binding domain (MTBD) of the protein Ska1 using NMR spectroscopy. Here, we report the resonance assignments of the MTBD of C. elegans Ska1.
      PubDate: 2014-10-01
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