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2D Materials     Hybrid Journal   (Followers: 7)
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African Journal of Chemical Education     Open Access   (Followers: 1)
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Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 4)
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Bulletin of the Chemical Society of Ethiopia     Open Access   (Followers: 3)
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C - Journal of Carbon Research     Open Access  
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Canadian Association of Radiologists Journal     Full-text available via subscription   (Followers: 4)

        1 2 3 4 5 6 | Last

Journal Cover Biomolecular NMR Assignments
  [SJR: 0.393]   [H-I: 8]   [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  [2280 journals]
  • Chemical shift assignments of the C-terminal EF-hand domain of
    • Abstract: Abstract The regulation and localization of the neuronal voltage gated Ca2+ channel CaV1.2 is important for synaptic plasticity associated with learning and memory. The cytoskeletal protein, α-actinin-1 is known to interact with CaV1.2 and stabilize its localization at the postsynaptic membrane. Here we report both backbone and sidechain NMR assignments for the C-terminal EF-hands (EF3 and EF4) of α-actinin-1 (residues 824–892, called ACTN_EF34) bound to the IQ-motif (residues 1644–1665) from CaV1.2 (BMRB accession no. 25902).
      PubDate: 2016-02-10
  • 1 H, 15 N and 13 C assignments of the N-terminal domain of the Mediator
           complex subunit MED26
    • Abstract: Abstract MED26 is a subunit of the Mediator, a very large complex involved in regulation of gene transcription by RNA Polymerase II. MED26 regulates the switch between initiation and elongation phases of the transcription. This function requires interaction of its N-terminal domain (NTD) with several protein partners implicated in transcriptional regulation. Molecular details of the structure and interaction mode of MED26 NTD would improve understanding of this complex regulation. As a first step towards structural characterization, sequence specific 1H, 13C and 15N assignments for MED26 NTD was performed based on Nuclear Magnetic Resonance spectroscopy. TALOS+ analysis of the chemical shifts data revealed a domain solely composed of helices. Assignments will be further used to solve NMR structure and dynamics of MED26 NTD and investigate the molecular details of its interaction with protein partners.
      PubDate: 2016-02-09
  • 1 H, 15 N, 13 C resonance assignment of human GAP-43
    • Abstract: Abstract GAP-43 is a 25 kDa neuronal intrinsically disordered protein, highly abundant in the neuronal growth cone during development and regeneration. The exact molecular function(s) of GAP-43 remains unclear but it appears to be involved in growth cone guidance and actin cytoskeleton organization. Therefore, GAP-43 seems to play an important role in neurotransmitter vesicle fusion and recycling, long-term potentiation, spatial memory formation and learning. Here we report the nearly complete assignment of recombinant human GAP-43.
      PubDate: 2016-01-09
  • Chemical shift assignments of calmodulin constructs with EF hand mutations
    • Abstract: Abstract Calmodulin (CaM) is a ubiquitous cytosolic Ca2+-binding protein able to bind and regulate hundreds of different proteins. It consists of two globular domains joined by a flexible central linker region. Each one of these domains contains two EF hand pairs capable of binding to Ca2+. Upon Ca2+ binding CaM undergoes a conformational change exposing hydrophobic patches that interact with its intracellular target proteins. CaM is able to bind to target proteins in the Ca2+-replete and Ca2+-deplete forms. To study the Ca2+-dependent/independent properties of binding and activation of target proteins by CaM, CaM constructs with Ca2+ binding disrupting mutations of Asp to Ala at position one of each EF hand have been used. One target protein of CaM is nitric oxide synthase, which catalyzes the production of nitric oxide. At elevated Ca2+ concentrations, CaM binds to neuronal NOS and endothelial NOS, making them the Ca2+-dependent NOS enzymes. In contrast, inducible NOS is transcriptionally regulated in vivo and binds to CaM at basal levels of Ca2+. Here we report the NMR backbone and sidechain resonance assignments of C-lobe Ca2+-replete and deplete CaM12, N-lobe Ca2+-replete and deplete CaM34, CaM1234 in the absence of Ca2+ and N-lobe Ca2+-replete CaM34 with the iNOS CaM-binding domain peptide.
      PubDate: 2016-01-07
  • Backbone 1 H, 15 N, 13 C NMR assignment of the 518–627 fragment of
           the androgen receptor encompassing N-terminal and DNA binding domains
    • Abstract: Abstract Androgen receptor (AR) belongs to the nuclear receptor superfamily that are ligand dependent transcription factors. This protein binds to steroid hormones such as dihydrotestosterone, to specific DNA sequences as well as to a number of co-regulatory factors. A number of these interactions involve the N-terminal domain (NTD), that is predicted to be intrinsically disordered. In order to provide functional information about possible cross-talk mechanisms between the AR NTD and its DNA binding domain (DBD), we have undertaken the NMR study of a fragment of human AR encompassing the last 37 residues of the NTD and the DBD (NTD–DBD518–627). The backbone 1H, 15N, 13C NMR resonance assignments of this fragment indicate the presence of residual helical secondary structure within the AR NTD.
      PubDate: 2016-01-05
  • 1 H, 13 C and 15 N resonance assignments of human DCL-1 (CD302)
           extracellular domain
    • Abstract: Abstract DCL-1 (CD302) is a single-pass type one transmembrane protein which is predominantly expressed on myeloid cell lines. It possess the ability of endocytosis and is assumed to play a role in cell adhesion and migration. It has been also connected to several illnesses but more on the level of mRNA than on the protein expression level. More interestingly it is alternatively expressed in the form of a fusion protein with another single-pass type one transmembrane protein DEC205 (CD205) which is normally involved in antigen-uptake and endocytosis. The fusion protein has been assigned to have altered function compared to the wild type proteins. We have performed NMR structural analysis of the 16.2 kDa extracellular domain of DCL-1 to get a better insight onto this molecule. We have been able to assign nearly 97 % of resonance frequencies for the 15N and 13C labeled recombinant protein. The assignments have been deposited into Biological Magnetic Resonance Data Bank under the accession number 25802.
      PubDate: 2016-01-02
  • 1 H, 13 C and 15 N backbone resonance assignment of the intrinsically
           disordered region of the nuclear envelope protein emerin
    • Abstract: Abstract Human emerin is an inner nuclear membrane protein involved in the response of the nucleus to mechanical stress. It contributes to the physical connection between the cytoskeleton and the nucleoskeleton. It is also involved in chromatin organization. Its N-terminal region is nucleoplasmic and comprises a globular LEM domain from residue 1 to residue 43. The three-dimensional structure of this LEM domain in complex with the chromatin BAF protein was solved from NMR data. Apart from the LEM domain, the nucleoplasmic region of emerin, from residue 44 to residue 221, is predicted to be intrinsically disordered. Mutations in this region impair binding to several emerin partners as lamin A, actin or HDAC3. However the molecular details of these recognition defects are unknown. Here we report 1H, 15N, 13CO, 13Cα and 13Cβ NMR chemical shift assignments of the emerin fragment from residue 67 to residue 170, which is sufficient for nuclear localization and involved in lamin A binding. Chemical shift analysis confirms that this fragment is intrinsically disordered in 0 and 8 M urea.
      PubDate: 2016-01-02
  • NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase
           reverse transcriptase
    • Abstract: Abstract Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA fragments to the ends of chromosomes. This enzyme is the focus of substantial attention, both because its structure and mechanism of action are still poorly studied, and because of its pivotal roles in aging and cellular proliferation. The use of telomerase as a potential target for the design of new anticancer drugs is also of great interest. The catalytic protein subunit of telomerase (TERT) contains an N-terminal domain (TEN) that is essential for activity and processivity. Elucidation of the structure and dynamics of TEN in solution is important for understanding the molecular mechanism of telomerase activity and for the design of new telomerase inhibitors. To approach this problem, in this study we report the 1H, 13C, and 15N chemical shift assignments of TEN from Ogataea polymorpha. Analysis of the assigned chemical shifts allowed us to identify secondary structures and protein regions potentially involved in interaction with other participants of the telomerase catalytic cycle.
      PubDate: 2015-12-31
  • Sequence-specific 1 H, 13 C and 15 N backbone resonance assignments of the
           plakin repeat domain of human envoplakin
    • Abstract: Abstract The plakin repeat domain is a distinctive hallmark of the plakin superfamily of proteins, which are found within all epithelial tissues. Plakin repeat domains mediate the interactions of these proteins with the cell cytoskeleton and are critical for the maintenance of tissue integrity. Despite their biological importance, no solution state resonance assignments are available for any homologue. Here we report the essentially complete 1H, 13C and 15N backbone chemical shift assignments of the singular 22 kDa plakin repeat domain of human envoplakin, providing the means to investigate its interactions with ligands including intermediate filaments.
      PubDate: 2015-11-21
  • 1 H, 15 N and 13 C chemical shift assignment of the Gram-positive
           conjugative transfer protein TraH pIP501
    • Abstract: Abstract Conjugative transfer of DNA represents the most important transmission pathway in terms of antibiotic resistance and virulence gene dissemination among bacteria. TraH is a putative transfer protein of the type IV secretion system (T4SS) encoded by the Gram-positive (G+) conjugative plasmid pIP501. This molecular machine involves a multi-protein core complex spanning the bacterial envelope thereby serving as a macromolecular secretion channel. Here, we report the near complete 1H, 13C and 15N resonance assignment of a soluble TraH variant comprising the C-terminal domain.
      PubDate: 2015-11-11
  • 1 H, 13 C and 15 N resonance assignments and secondary structure analysis
           of CmPI-II, a serine protease inhibitor isolated from marine snail
           Cenchritis muricatus
    • Abstract: Abstract A protease inhibitor (CmPI-II) (UNIPROT: IPK2_CENMR) from the marine mollusc Cenchritis muricatus, has been isolated and characterized. It is the first member of a new group (group 3) of non-classical Kazal-type inhibitors. CmPI-II is a tight-binding inhibitor of serine proteases: trypsin, human neutrophil elastase (HNE), subtilisin A and pancreatic elastase. This specificity is exceptional in the members of Kazal-type inhibitor family. Several models of three-dimensional structure of CmPI-II have been constructed by homology with other inhibitors of the family but its structure has not yet been solved experimentally. Here we report the 1H, 15N and 13C chemical shift assignments of CmPI-II as basis for NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data have identified three β-strands β1: residues 14–19, β2: 23–35 and β3: 43–45 and one helix α1: 28–37 arranged in the sequential order β1–β2–α1–β3. These secondary structure elements suggest that CmPI-II adopts the typical scaffold of a Kazal-type inhibitor.
      PubDate: 2015-11-07
  • Backbone and side-chain NMR assignments for the bromodomain of mouse BAZ1A
    • Abstract: Abstract BAZ1A, a non-catalytic subunit of the chromatin remodeler complexes ACF and CHRAC, is thought to modulate the ATPase’s activity of the complexes and participate in gene transcription, DNA damage checkpoint and double-strand break repair. Recently, the essential role of BAZ1A in mouse male fertility has also been reported. BAZ1A contains one C-terminal bromodomain, which specifically recognizes acetylation of lysine. Here, we report the backbone and side chain 1H, 13C and 15N resonance assignment of the mouse BAZ1A-bromodomain, as a basis for further functional studies and structure determination.
      PubDate: 2015-11-05
  • 1 H, 13 C, and 15 N chemical shift assignments of cyanobacteriochrome
           NpR6012g4 in the green-absorbing photoproduct state
    • Abstract: Abstract Cyanobacteriochromes (CBCRs) are cyanobacterial photosensory proteins with a tetrapyrrole (bilin) chromophore that belong to the phytochrome superfamily. Like phytochromes, CBCRs photoconvert between two photostates with distinct spectral properties. NpR6012g4 from Nostoc punctiforme is a model system for widespread CBCRs with conserved red/green photocycles. Atomic-level structural information for the photoproduct state in this subfamily is not known. Here, we report NMR backbone chemical shift assignments of the light-activated state of NpR6012g4 (BMRB no. 26577) as a first step toward determining its atomic resolution structure.
      PubDate: 2015-11-04
  • NMR assignments of the peptidyl-prolyl cis–trans isomerase domain of
           trigger factor from E. coli
    • Abstract: Abstract Trigger factor (TF) is a highly conserved multi-domain molecular chaperone in bacteria. It binds via its ribosome binding domain (RBD) to the ribosomal tunnel exit and facilitates co-translational folding of a broad range of protein substrates primarily through interactions with the substrate binding domain (SBD) adjacent to the RBD. Within the SBD, a peptidyl-prolyl cis–trans isomerase (PPIase) domain is inserted leading to an unusual domain insertion, which may provide stabilizing effect to the highly plastic SBD. Here we report the near complete NMR assignments of TF PPIase providing the basis for subsequent structural and folding in the context of the chaperone activity of TF.
      PubDate: 2015-11-02
  • Backbone and side chain chemical shift assignments of apolipophorin III
           from Galleria mellonella
    • Abstract: Abstract Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain 1H, 13C and 15N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.
      PubDate: 2015-10-22
  • 1 H, 15 N, and 13 C chemical shift assignments of cyanobacteriochrome
           NpR6012g4 in the red-absorbing dark state
    • Abstract: Abstract Cyanobacteriochrome (CBCR) photosensory proteins are phytochrome homologs using bilin chromophores for light sensing across the visible spectrum. NpR6012g4 is a CBCR from Nostoc punctiforme that serves as a model for a widespread CBCR subfamily with red/green photocycles. We report NMR chemical shift assignments for both the protein backbone and side-chain resonances of the red-absorbing dark state of NpR6012g4 (BMRB no. 26582).
      PubDate: 2015-10-19
  • Sequential backbone resonance assignments of the E. coli dihydrofolate
           reductase Gly67Val mutant: folate complex
    • Abstract: Abstract Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for HN, NH, Cα and Cβ atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the HN, NH, Cα and Cβ chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38–88) and not in the distant catalytic domain.
      PubDate: 2015-10-19
  • Backbone assignment of the N-terminal 24-kDa fragment of Escherichia coli
           topoisomerase IV ParE subunit
    • Abstract: Abstract Bacterial DNA topoisomerases are important drug targets due to their importance in DNA replication and low homology to human topoisomerases. The N-terminal 24 kDa region of E. coli topoisomerase IV E subunit (eParE) contains the ATP binding pocket. Structure—based drug discovery has been proven to be an efficient way to develop potent ATP competitive inhibitors against ParEs. NMR spectroscopy is a powerful tool to understand protein and inhibitor interactions in solution. In this study, we report the backbone assignment for the N-terminal domain of E. coli ParE. The secondary structural information and the assignment will aid in structure—based antibacterial agents development targeting eParE.
      PubDate: 2015-10-19
  • Resonance assignments for the substrate binding domain of Hsp70 chaperone
           Ssa1 from Saccharomyces cerevisiae
    • Abstract: Abstract Hsp70 chaperone proteins play crucial roles in the cell. Extensive structural and functional studies have been performed for bacterial and mammalian Hsp70s. Ssa1 from Saccharomyces cerevisiae is a member of the Hsp70 family. In vivo and biochemical studies on Ssa1 have revealed that it regulates prion propagation and the cell cycle. However, no structural data has been obtained for Ssa1 up to now. Here we report the almost complete (96 %) 1H, 13C, 15N backbone and side chain NMR assignment of the 18.8 kDa Ssa1 substrate binding domain. The construct includes residues 382–554, which corresponds to the entire substrate binding domain and two following α-helices in homologous structures. The secondary structure predicted from the assigned chemical shifts is consistent with that of homologous Hsp70 substrate binding domains.
      PubDate: 2015-10-01
  • Chemical shift assignments of a new folded domain from yeast Pcf11
    • Abstract: Abstract The yeast protein Pcf11 is a component of the cleavage/polyadenylation factor IA (CF IA) complex involved in the 3′ processing of pre-mRNA. Pcf11 interacts with RNA and the C-terminal domain (CTD) of the largest subunit of RNA polymerase II via the CTD-interaction domain (CID), and other peptide regions mediate contacts with CF IA subunits Clp1 and Rna14/Rna15. We have identified a novel domain adjacent to the CID and have determined the backbone and sidechain 1H, 13C and 15N chemical shift assignments for the bacterially produced construct. Despite the reduced sequence complexity due to numerous glutamine and leucine residues, secondary chemical shift analysis indicates that the domain is composed of three well-defined helical regions with relaxation measurements consistent with a folded independent domain. The proximity of this previously uncharacterized domain close to the N-terminal CID prompts speculation for a putative role in modulating CTD and RNA binding, or possible intermolecular contacts within CF IA.
      PubDate: 2015-07-02
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