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  Subjects -> CHEMISTRY (Total: 845 journals)
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CHEMISTRY (596 journals)                  1 2 3 | Last

Showing 1 - 200 of 735 Journals sorted alphabetically
2D Materials     Hybrid Journal   (Followers: 5)
Accreditation and Quality Assurance: Journal for Quality, Comparability and Reliability in Chemical Measurement     Hybrid Journal   (Followers: 26)
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Acta Metallurgica Sinica (English Letters)     Hybrid Journal   (Followers: 4)
adhäsion KLEBEN & DICHTEN     Hybrid Journal   (Followers: 5)
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African Journal of Chemical Education     Open Access   (Followers: 2)
African Journal of Pure and Applied Chemistry     Open Access   (Followers: 6)
Afrique Science : Revue Internationale des Sciences et Technologie     Open Access   (Followers: 2)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 3)
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American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 12)
American Journal of Chemistry     Open Access   (Followers: 23)
American Journal of Plant Physiology     Open Access   (Followers: 13)
American Mineralogist     Full-text available via subscription   (Followers: 7)
Anadolu University Journal of Science and Technology     Open Access  
Analyst     Full-text available via subscription   (Followers: 41)
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Autophagy     Hybrid Journal   (Followers: 2)
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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   (Followers: 2)
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Canadian Journal of Chemistry     Full-text available via subscription   (Followers: 6)
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Chinese Journal of Polymer Science     Hybrid Journal   (Followers: 10)
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        1 2 3 | 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  [2281 journals]
  • 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
    • 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: 2016-05-18
       
  • 1 H, 15 N, 13 C resonance assignments for Saccharomyces cerevisiae Rad23
           UBL domain
    • Abstract: Abstract Rad23 functions in nucleotide excision repair and proteasome-mediated protein degradation. It has four distinct structural domains that are connected by flexible linker regions, including an N-terminal ubiquitin-like (UBL) domain that binds proteasomes. We report in this NMR study the 1H, 15N and 13C resonance assignments for the backbone and side chain atoms of the Rad23 UBL domain (Rad23UBL) with BioMagResBank accession number 25825. We find that a Rad23 proline amino acid (P20) located in a loop undergoes isomerization. The secondary structural elements predicted from the NMR data fit well to that of the Rad23UBL when complexed with E4 ubiquitin ligase Ufd2, as reported in a crystallographic structure. These complete assignments can be used to study the protein dynamics of the Rad23UBL and its interaction of with other ubiquitin receptors or proteasome subunits.
      PubDate: 2016-05-17
       
  • NMR resonance assignments of the major apple allergen Mal d 1
    • Abstract: Abstract The major apple allergen Mal d 1 is the predominant cause of apple (Malus domestica) allergies in large parts of Europe and Northern America. Allergic reactions against this 17.5 kDa protein are the consequence of initial sensitization to the structurally homologous major allergen from birch pollen, Bet v 1. Consumption of apples can subsequently provoke immunologic cross-reactivity of Bet v 1-specific antibodies with Mal d 1 and trigger severe oral allergic syndroms, affecting more than 70 % of all individuals that are sensitized to birch pollen. While the accumulated immunological data suggest that Mal d 1 has a three-dimensional fold that is similar to Bet v 1, experimental structural data for this protein are not available to date. In a first step towards structural characterization of Mal d 1, backbone and side chain 1H, 13C and 15N chemical shifts of the isoform Mal d 1.0101 were assigned. The NMR-chemical shift data show that this protein is composed of seven β-strands and three α-helices, which is in accordance with the reported secondary structure of the major birch pollen allergen, indicating that Mal d 1 and Bet v 1 indeed have similar three-dimensional folds. The next stage in the characterization of Mal d 1 will be to utilize these resonance assignments in solving the solution structure of this protein.
      PubDate: 2016-05-11
       
  • Solid-state NMR sequential assignment of an Amyloid-β(1–42)
           fibril polymorph
    • Abstract: Abstract The formation of fibrils of the amyloid-β (Aβ) peptide is considered to be a key event in the pathology of Alzheimer’s disease (AD). The determination of a high-resolution structure of these fibrils is relevant for the understanding of the molecular basis of AD. In this work, we present the sequential resonance assignment of one of the polymorphs of Aβ(1–42) fibrils. We show that most of the protein is rigid, while a stretch of 4 residues (11–14) is not visible by solid-state NMR spectroscopy due to dynamics.
      PubDate: 2016-05-10
       
  • Solid-state NMR sequential assignment of the β-endorphin peptide in
           its amyloid form
    • Abstract: Abstract Insights into the three-dimensional structure of hormone fibrils are crucial for a detailed understanding of how an amyloid structure allows the storage of hormones in secretory vesicles prior to hormone secretion into the blood stream. As an example for various hormone amyloids, we have studied the endogenous opioid neuropeptide β-endorphin in one of its fibril forms. We have achieved the sequential assignment of the chemical shifts of the backbone and side-chain heavy atoms of the fibril. The secondary chemical shift analysis revealed that the β-endorphin peptide adopts three β-strands in its fibril state. This finding fosters the amyloid nature of a hormone at the atomic level.
      PubDate: 2016-05-10
       
  • Backbone and side-chain chemical shift assignments for the C-terminal
           domain of Tcb2, a cytoskeletal calcium-binding protein from Tetrahymena
           thermophila
    • 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: 2016-05-07
       
  • 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
    • 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: 2016-05-04
       
  • Erratum to: 1 H, 13 C and 15 N resonance assignments of the Cdc42-binding
           domain of TOCA1
    • PubDate: 2016-04-22
       
  • Backbone resonance assignments of the m1A22 tRNA methyltransferase TrmK
           from Bacillus subtilis
    • Abstract: Abstract RNA modification is a post-transcriptional process by which certain nucleotides are altered after their initial incorporation into an RNA chain. Transfer RNAs (tRNAs) is the most heavily modified class of RNA molecules. These modifications expand the chemical and functional diversity of tRNAs and enhance their structural stability. To date, more than 100 modifications have been identified, the majority of which are specific from one domain of life. However, few modifications are extensively present in the three domains of life. Among those, the m1A nucleotide, which consists in the methylation at position 1 of the adenine aromatic ring, is found in tRNAs and ribosomal RNAs. In tRNAs, the m1A modification occurs at position 9, 14, 22, 57 and 58. The enzyme TrmK catalyzes the m1A formation at position 22. Here we report the backbone 1H, 15N and 13C chemical shift assignments of TrmK from Bacillus subtilis obtained by heteronuclear multidimensional NMR spectroscopy as well as its secondary structure in solution as predicted by TALOS+. These assignments of TrmK pave the way for interaction studies with its tRNA substrates.
      PubDate: 2016-04-20
       
  • 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: 2016-04-01
       
  • 1 H, 15 N and 13 C assignment of the amyloidogenic protein medin using
           fast-pulsing NMR techniques
    • Abstract: Abstract Thirty-one proteins are known to form extracellular fibrillar amyloid in humans. Molecular information about many of these proteins in their monomeric, intermediate or fibrillar form and how they aggregate and interact to form the insoluble fibrils is sparse. This is because amyloid proteins are notoriously difficult to study in their soluble forms, due to their inherent propensity to aggregate. Using recent developments in fast NMR techniques, band-selective excitation short transient and band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence we have been able to assign a 5 kDa full-length amyloidogenic protein called medin. Medin is the key protein component of the most common form of localised amyloid with a proposed role in aortic aneurysm and dissection. This assignment will now enable the study of the early interactions that could influence initiation and progression of medin aggregation. The chemical shifts have been deposited in the BioMagRes-Bank accession Nos. 25399 and 26576.
      PubDate: 2016-04-01
       
  • 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: 2016-04-01
       
  • 1 H, 13 C and 15 N resonance assignments and second structure information
           of Fag s 1: Fagales allergen from Fagus sylvatica
    • Abstract: Abstract Fagales allergens belonging to the Bet v 1 family account responsible for the majority of spring pollinosis in the temperate climate zones in the Northern hemisphere. Among them, Fag s 1 from beech pollen is an important trigger of Fagales pollen associated allergic reactions. The protein shares high similarity with birch pollen Bet v 1, the best-characterized member of this allergen family. Of note, recent work on Bet v 1 and its homologues found in Fagales pollen demonstrated that not all allergenic members of this family have the capacity to induce allergic sensitization. Fag s 1 was shown to bind pre-existing IgE antibodies most likely primarily directed against other members of this multi-allergen family. Therefore, it is especially interesting to compare the structures of Bet v 1-like pollen allergens, which have the potential to induce allergic sensitization with allergens that are mainly cross-reactive. This in the end will help to identify allergy eliciting molecular pattern on Bet v 1-like allergens. In this work, we report the 1H, 15N and 13C NMR assignment of beech pollen Fag s 1 as well as the secondary structure information based on backbone chemical shifts.
      PubDate: 2016-04-01
       
  • Sequence-specific solid-state NMR assignments of the mouse ASC PYRIN
           domain in its filament form
    • Abstract: Abstract The apoptosis-associated speck-like protein (ASC protein) plays a central role in eukaryotic innate immune response. Upon infection, multiple ASC molecules assemble into long filaments, which are fundamental for triggering the cellular defense mechanism by starting an inflammatory cascade with the activation of caspase-1. ASC is composed of two domains, the C-terminal caspase-recruitment domain, which is involved in the recruitment of the caspase, and the N-terminal PYRIN domain (PYD), which is responsible for the formation of the filament. Here we present the 13C and 15N chemical shift assignment for filaments formed by the PYD of mouse ASC, a 91-residue protein. The backbone between residues 4 and 84 is assigned without interruption. Also, 86 % of the sidechain resonances for this stretch are assigned. Residues 1–3 and 85–91 show unfavorable dynamics and are not observed. Secondary chemical-shift analysis shows the presence of six α-helices.
      PubDate: 2016-04-01
       
  • Further exploration of the conformational space of α-synuclein
           fibrils: solid-state NMR assignment of a high-pH polymorph
    • Abstract: Abstract Polymorphism is a common and important phenomenon for protein fibrils which has been linked to the appearance of strains in prion and other neurodegenerative diseases. Parkinson disease is a frequently occurring neurodegenerative pathology, tightly associated with the formation of Lewy bodies. These deposits mainly consist of α-synuclein in fibrillar, β-sheet-rich form. α-synuclein is known to form numerous different polymorphs, which show distinct structural features. Here, we describe the chemical shift assignments, and derive the secondary structure, of a polymorph that was fibrillized at higher-than-physiological pH conditions. The fibrillar core contains residues 40–95, with both the C- and N-terminus not showing any ordered, rigid parts. The chemical shifts are similar to those recorded previously for an assigned polymorph that was fibrillized at neutral pH.
      PubDate: 2016-04-01
       
  • 1 H, 13 C and 15 N resonance assignments and secondary structure of the
           human PHF6-ePHD1 domain
    • Abstract: Abstract The plant homeodomain (PHD) finger 6 (PHF6) is a multidomain protein that comprises four nuclear localization signals and two extended PHD zinc finger domains (ePHD), suggesting that the PHD domains of PHF6 may have different functions compared with other PHD domains. And the PHF6 was first identified as the gene mutated associated with Börjeson–Forssman–Lehmann syndrome, an X-linked mental retardation disorder. The mutant PHF6 is also associated with T cell acute lymphoblastic leukemia and acute myeloid leukemia. But the molecular mechanism between these diseases and PHF6 are still unclear. In addition, the first conserved ePHD (ePHD1) of PHF6 is involved in its nucleolus localization, directly interacts with upstream binding factor (UBF) and suppresses rRNA transcription. Here we show the backbone resonance and side chain assignments of the PHF6-ePHD1 domain from human by heteronuclear multidimensional NMR spectroscopy and its secondary structure as predicted by the TALOS+. These assignments of PHF6-ePHD1 domain throw a light on the further structure determination, dynamics and interaction with UBF.
      PubDate: 2016-04-01
       
  • Complete 1 H, 15 N and 13 C assignment of trappin-2 and 1 H assignment of
           its two domains, elafin and cementoin
    • Abstract: Abstract Trappin-2 is a serine protease inhibitor with a very narrow inhibitory spectrum and has significant anti-microbial activities. It is a 10 kDa cationic protein composed of two distinct domains. The N-terminal domain (38 residues) named cementoin is known to be intrinsically disordered when it is not linked to the elafin. The C-terminal domain (57 residues), corresponding to elafin, is a cysteine-rich domain stabilized by four disulfide bridges and is characterized by a flat core and a flexible N-terminal part. To our knowledge, there is no structural data available on trappin-2. We report here the complete 1H, 15N and 13C resonance assignment of the recombinant trappin-2 and the 1H assignments of cementoin and elafin, under the same experimental conditions. This is the first step towards the 3D structure determination of the trappin-2.
      PubDate: 2016-02-15
       
  • 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
       
  • 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
       
  • 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
       
 
 
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